Starting phenix.real_space_refine on Tue Feb 13 22:31:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flj_29280/02_2024/8flj_29280.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flj_29280/02_2024/8flj_29280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flj_29280/02_2024/8flj_29280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flj_29280/02_2024/8flj_29280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flj_29280/02_2024/8flj_29280.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flj_29280/02_2024/8flj_29280.pdb" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 350 5.49 5 S 66 5.16 5 C 18737 2.51 5 N 6003 2.21 5 O 6638 1.98 5 H 25297 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 96": "OE1" <-> "OE2" Residue "M ASP 68": "OD1" <-> "OD2" Residue "M GLU 103": "OE1" <-> "OE2" Residue "M GLU 577": "OE1" <-> "OE2" Residue "M ASP 579": "OD1" <-> "OD2" Residue "N GLU 10": "OE1" <-> "OE2" Residue "N GLU 30": "OE1" <-> "OE2" Residue "N GLU 665": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 57091 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 4834 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 8, 'TRANS': 301} Chain: "B" Number of atoms: 4940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4940 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "C" Number of atoms: 4162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 4162 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 8, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 126 Chain: "D" Number of atoms: 4920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 4920 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 8, 'TRANS': 306} Chain: "E" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 680 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 398 Unresolved non-hydrogen dihedrals: 260 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 14, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 194 Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 670 Classifications: {'peptide': 94} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 157 Chain: "G" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 708 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 406 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 14, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 194 Chain: "H" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 670 Classifications: {'peptide': 94} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 157 Chain: "I" Number of atoms: 4419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 4419 Classifications: {'DNA': 139} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 138} Chain: "J" Number of atoms: 4709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 4709 Classifications: {'DNA': 148} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 147} Chain: "K" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 1145 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "L" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 854 Classifications: {'DNA': 27} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 26} Chain: "M" Number of atoms: 12232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 970, 12232 Classifications: {'peptide': 970} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 51, 'TRANS': 918} Chain breaks: 11 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1134 Unresolved non-hydrogen angles: 1440 Unresolved non-hydrogen dihedrals: 937 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 23, 'TYR:plan': 7, 'ASN:plan1': 14, 'TRP:plan': 3, 'HIS:plan': 15, 'PHE:plan': 8, 'GLU:plan': 28, 'ARG:plan': 42} Unresolved non-hydrogen planarities: 696 Chain: "N" Number of atoms: 12148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 12148 Classifications: {'peptide': 954} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 51, 'TRANS': 902} Chain breaks: 11 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1054 Unresolved non-hydrogen angles: 1335 Unresolved non-hydrogen dihedrals: 864 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 20, 'TYR:plan': 6, 'ASN:plan1': 14, 'TRP:plan': 2, 'HIS:plan': 13, 'PHE:plan': 6, 'GLU:plan': 27, 'ARG:plan': 42} Unresolved non-hydrogen planarities: 645 Time building chain proxies: 19.29, per 1000 atoms: 0.34 Number of scatterers: 57091 At special positions: 0 Unit cell: (171.787, 176.055, 205.931, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 350 15.00 O 6638 8.00 N 6003 7.00 C 18737 6.00 H 25297 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 37.52 Conformation dependent library (CDL) restraints added in 4.2 seconds 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6592 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 23 sheets defined 57.7% alpha, 9.8% beta 162 base pairs and 286 stacking pairs defined. Time for finding SS restraints: 21.46 Creating SS restraints... Processing helix chain 'A' and resid 41 through 50 removed outlier: 6.112A pdb=" N HIS A 46 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N TYR A 47 " --> pdb=" O HIS A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 78 Processing helix chain 'A' and resid 86 through 89 removed outlier: 3.693A pdb=" N THR A 89 " --> pdb=" O GLY A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 89' Processing helix chain 'A' and resid 114 through 124 removed outlier: 3.539A pdb=" N ARG A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 150 Processing helix chain 'A' and resid 152 through 158 Processing helix chain 'A' and resid 163 through 178 removed outlier: 3.580A pdb=" N GLU A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 206 removed outlier: 3.664A pdb=" N THR A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 245 Processing helix chain 'A' and resid 260 through 286 removed outlier: 3.815A pdb=" N PHE A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE A 270 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASP A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N SER A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LEU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 288 through 304 Processing helix chain 'A' and resid 304 through 321 removed outlier: 3.875A pdb=" N THR A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 17 removed outlier: 3.629A pdb=" N ARG B 17 " --> pdb=" O HIS B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 55 Processing helix chain 'B' and resid 68 through 78 Processing helix chain 'B' and resid 114 through 123 Processing helix chain 'B' and resid 125 through 151 removed outlier: 3.563A pdb=" N ASP B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 removed outlier: 3.576A pdb=" N ARG B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 180 Processing helix chain 'B' and resid 182 through 205 Processing helix chain 'B' and resid 220 through 244 removed outlier: 3.916A pdb=" N TYR B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 232 " --> pdb=" O HIS B 228 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'B' and resid 260 through 272 removed outlier: 4.248A pdb=" N PHE B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B 269 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP B 272 " --> pdb=" O ASP B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 286 removed outlier: 3.542A pdb=" N PHE B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 303 Processing helix chain 'B' and resid 304 through 320 Processing helix chain 'C' and resid 41 through 50 removed outlier: 6.296A pdb=" N HIS C 46 " --> pdb=" O ARG C 43 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR C 47 " --> pdb=" O HIS C 44 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP C 48 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 78 Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.736A pdb=" N THR C 89 " --> pdb=" O GLY C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 124 removed outlier: 3.535A pdb=" N ARG C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE C 124 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 151 removed outlier: 3.914A pdb=" N LEU C 149 " --> pdb=" O ARG C 145 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 157 Processing helix chain 'C' and resid 162 through 176 removed outlier: 4.115A pdb=" N LEU C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 180 removed outlier: 3.699A pdb=" N ALA C 180 " --> pdb=" O LEU C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 180' Processing helix chain 'C' and resid 182 through 206 removed outlier: 3.693A pdb=" N LYS C 199 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 245 Processing helix chain 'C' and resid 260 through 286 removed outlier: 3.652A pdb=" N LEU C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP C 272 " --> pdb=" O ASP C 268 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N SER C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Proline residue: C 277 - end of helix Processing helix chain 'C' and resid 288 through 304 Processing helix chain 'C' and resid 304 through 321 removed outlier: 4.038A pdb=" N THR C 321 " --> pdb=" O ALA C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 12 removed outlier: 3.662A pdb=" N THR D 11 " --> pdb=" O GLU D 8 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE D 12 " --> pdb=" O LEU D 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 8 through 12' Processing helix chain 'D' and resid 13 through 17 Processing helix chain 'D' and resid 51 through 53 No H-bonds generated for 'chain 'D' and resid 51 through 53' Processing helix chain 'D' and resid 68 through 77 Processing helix chain 'D' and resid 86 through 89 Processing helix chain 'D' and resid 113 through 124 removed outlier: 4.318A pdb=" N PHE D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 151 removed outlier: 3.851A pdb=" N ASP D 151 " --> pdb=" O SER D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 158 removed outlier: 3.855A pdb=" N ARG D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 178 removed outlier: 3.558A pdb=" N GLU D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 204 Processing helix chain 'D' and resid 220 through 245 removed outlier: 3.989A pdb=" N TYR D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 257 removed outlier: 4.184A pdb=" N LYS D 256 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 286 removed outlier: 4.542A pdb=" N LEU D 269 " --> pdb=" O ASP D 265 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE D 270 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N SER D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) Proline residue: D 277 - end of helix Processing helix chain 'D' and resid 288 through 303 Processing helix chain 'D' and resid 304 through 322 removed outlier: 3.942A pdb=" N VAL D 322 " --> pdb=" O GLN D 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 20 Processing helix chain 'E' and resid 22 through 43 removed outlier: 3.616A pdb=" N PHE E 34 " --> pdb=" O VAL E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 95 removed outlier: 3.630A pdb=" N ARG E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 14 Processing helix chain 'F' and resid 20 through 42 removed outlier: 3.781A pdb=" N MET F 35 " --> pdb=" O MET F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 93 Processing helix chain 'G' and resid 7 through 20 Processing helix chain 'G' and resid 22 through 43 removed outlier: 3.643A pdb=" N GLU G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG G 38 " --> pdb=" O PHE G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 95 Processing helix chain 'H' and resid 5 through 16 removed outlier: 3.769A pdb=" N GLU H 10 " --> pdb=" O SER H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 41 Processing helix chain 'H' and resid 85 through 93 Processing helix chain 'M' and resid 10 through 22 removed outlier: 3.572A pdb=" N LEU M 14 " --> pdb=" O GLU M 10 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER M 15 " --> pdb=" O LYS M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 52 removed outlier: 3.739A pdb=" N SER M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 82 Processing helix chain 'M' and resid 108 through 121 Processing helix chain 'M' and resid 122 through 123 No H-bonds generated for 'chain 'M' and resid 122 through 123' Processing helix chain 'M' and resid 124 through 128 Processing helix chain 'M' and resid 129 through 138 Processing helix chain 'M' and resid 148 through 161 removed outlier: 4.170A pdb=" N VAL M 152 " --> pdb=" O ARG M 148 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER M 153 " --> pdb=" O HIS M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 176 removed outlier: 3.588A pdb=" N TRP M 170 " --> pdb=" O SER M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 188 Processing helix chain 'M' and resid 207 through 219 Processing helix chain 'M' and resid 230 through 236 removed outlier: 3.821A pdb=" N ARG M 236 " --> pdb=" O ALA M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 246 Processing helix chain 'M' and resid 252 through 259 removed outlier: 3.749A pdb=" N ALA M 258 " --> pdb=" O LYS M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 266 through 269 removed outlier: 3.573A pdb=" N ALA M 269 " --> pdb=" O LEU M 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 266 through 269' Processing helix chain 'M' and resid 270 through 287 Processing helix chain 'M' and resid 289 through 299 Proline residue: M 295 - end of helix removed outlier: 3.627A pdb=" N HIS M 299 " --> pdb=" O PRO M 295 " (cutoff:3.500A) Processing helix chain 'M' and resid 301 through 320 removed outlier: 3.502A pdb=" N SER M 320 " --> pdb=" O HIS M 316 " (cutoff:3.500A) Processing helix chain 'M' and resid 349 through 374 Proline residue: M 368 - end of helix removed outlier: 4.304A pdb=" N GLU M 371 " --> pdb=" O LEU M 367 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG M 372 " --> pdb=" O PRO M 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 380 through 385 removed outlier: 3.631A pdb=" N THR M 384 " --> pdb=" O HIS M 380 " (cutoff:3.500A) Processing helix chain 'M' and resid 389 through 391 No H-bonds generated for 'chain 'M' and resid 389 through 391' Processing helix chain 'M' and resid 392 through 412 removed outlier: 4.155A pdb=" N ASP M 396 " --> pdb=" O PHE M 392 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS M 405 " --> pdb=" O CYS M 401 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLU M 407 " --> pdb=" O MET M 403 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLN M 408 " --> pdb=" O ALA M 404 " (cutoff:3.500A) Processing helix chain 'M' and resid 425 through 438 removed outlier: 3.649A pdb=" N ALA M 429 " --> pdb=" O GLY M 425 " (cutoff:3.500A) Processing helix chain 'M' and resid 456 through 468 removed outlier: 3.913A pdb=" N GLY M 460 " --> pdb=" O THR M 456 " (cutoff:3.500A) Processing helix chain 'M' and resid 483 through 497 removed outlier: 3.857A pdb=" N PHE M 487 " --> pdb=" O ALA M 483 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER M 497 " --> pdb=" O ARG M 493 " (cutoff:3.500A) Processing helix chain 'M' and resid 499 through 503 Processing helix chain 'M' and resid 517 through 522 removed outlier: 3.576A pdb=" N GLY M 521 " --> pdb=" O LEU M 518 " (cutoff:3.500A) Proline residue: M 522 - end of helix Processing helix chain 'M' and resid 523 through 528 Processing helix chain 'M' and resid 530 through 539 Processing helix chain 'M' and resid 546 through 550 Processing helix chain 'M' and resid 550 through 555 Processing helix chain 'M' and resid 561 through 570 Processing helix chain 'M' and resid 578 through 581 Processing helix chain 'M' and resid 582 through 584 No H-bonds generated for 'chain 'M' and resid 582 through 584' Processing helix chain 'M' and resid 585 through 599 Processing helix chain 'M' and resid 611 through 631 removed outlier: 3.884A pdb=" N ARG M 631 " --> pdb=" O GLU M 627 " (cutoff:3.500A) Processing helix chain 'M' and resid 659 through 681 Processing helix chain 'M' and resid 698 through 704 removed outlier: 3.515A pdb=" N LEU M 702 " --> pdb=" O ALA M 698 " (cutoff:3.500A) Processing helix chain 'M' and resid 715 through 721 Processing helix chain 'M' and resid 739 through 753 removed outlier: 3.530A pdb=" N LEU M 743 " --> pdb=" O ASN M 739 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN M 753 " --> pdb=" O ALA M 749 " (cutoff:3.500A) Processing helix chain 'M' and resid 771 through 786 Processing helix chain 'M' and resid 795 through 799 Processing helix chain 'M' and resid 799 through 805 Processing helix chain 'M' and resid 821 through 826 removed outlier: 3.647A pdb=" N VAL M 826 " --> pdb=" O VAL M 823 " (cutoff:3.500A) Processing helix chain 'M' and resid 841 through 852 removed outlier: 3.564A pdb=" N ILE M 852 " --> pdb=" O LEU M 848 " (cutoff:3.500A) Processing helix chain 'M' and resid 871 through 876 Processing helix chain 'M' and resid 913 through 918 Processing helix chain 'M' and resid 928 through 942 Processing helix chain 'M' and resid 954 through 959 Processing helix chain 'M' and resid 960 through 964 Processing helix chain 'M' and resid 965 through 971 Processing helix chain 'M' and resid 1008 through 1011 Processing helix chain 'M' and resid 1029 through 1042 Processing helix chain 'M' and resid 1044 through 1053 Processing helix chain 'N' and resid 10 through 22 removed outlier: 3.758A pdb=" N SER N 15 " --> pdb=" O LYS N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 52 removed outlier: 3.920A pdb=" N SER N 52 " --> pdb=" O LEU N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 82 Processing helix chain 'N' and resid 108 through 124 removed outlier: 4.801A pdb=" N ASP N 124 " --> pdb=" O ALA N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 128 Processing helix chain 'N' and resid 129 through 138 Processing helix chain 'N' and resid 148 through 162 removed outlier: 3.538A pdb=" N VAL N 152 " --> pdb=" O ARG N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 176 removed outlier: 3.633A pdb=" N TRP N 170 " --> pdb=" O SER N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 188 removed outlier: 4.064A pdb=" N GLN N 187 " --> pdb=" O ALA N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 207 through 219 Processing helix chain 'N' and resid 230 through 235 Processing helix chain 'N' and resid 242 through 247 removed outlier: 3.921A pdb=" N GLY N 247 " --> pdb=" O GLN N 244 " (cutoff:3.500A) Processing helix chain 'N' and resid 252 through 260 removed outlier: 3.501A pdb=" N LYS N 256 " --> pdb=" O ASP N 252 " (cutoff:3.500A) Processing helix chain 'N' and resid 266 through 269 removed outlier: 3.736A pdb=" N ALA N 269 " --> pdb=" O LEU N 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 266 through 269' Processing helix chain 'N' and resid 270 through 287 Processing helix chain 'N' and resid 289 through 300 Proline residue: N 295 - end of helix removed outlier: 3.943A pdb=" N HIS N 299 " --> pdb=" O PRO N 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 300 through 320 Processing helix chain 'N' and resid 349 through 367 Processing helix chain 'N' and resid 369 through 374 Processing helix chain 'N' and resid 380 through 385 removed outlier: 3.676A pdb=" N THR N 384 " --> pdb=" O HIS N 380 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG N 385 " --> pdb=" O LYS N 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 380 through 385' Processing helix chain 'N' and resid 389 through 391 No H-bonds generated for 'chain 'N' and resid 389 through 391' Processing helix chain 'N' and resid 392 through 404 removed outlier: 4.032A pdb=" N ASP N 396 " --> pdb=" O PHE N 392 " (cutoff:3.500A) Processing helix chain 'N' and resid 405 through 413 Processing helix chain 'N' and resid 425 through 438 removed outlier: 3.566A pdb=" N ALA N 429 " --> pdb=" O GLY N 425 " (cutoff:3.500A) Processing helix chain 'N' and resid 456 through 468 removed outlier: 3.705A pdb=" N GLY N 460 " --> pdb=" O THR N 456 " (cutoff:3.500A) Processing helix chain 'N' and resid 483 through 495 removed outlier: 3.723A pdb=" N PHE N 487 " --> pdb=" O ALA N 483 " (cutoff:3.500A) Processing helix chain 'N' and resid 499 through 503 Processing helix chain 'N' and resid 523 through 528 Processing helix chain 'N' and resid 530 through 539 Processing helix chain 'N' and resid 547 through 549 No H-bonds generated for 'chain 'N' and resid 547 through 549' Processing helix chain 'N' and resid 550 through 555 Processing helix chain 'N' and resid 558 through 560 No H-bonds generated for 'chain 'N' and resid 558 through 560' Processing helix chain 'N' and resid 561 through 571 Processing helix chain 'N' and resid 578 through 581 removed outlier: 3.616A pdb=" N PHE N 581 " --> pdb=" O VAL N 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 578 through 581' Processing helix chain 'N' and resid 582 through 584 No H-bonds generated for 'chain 'N' and resid 582 through 584' Processing helix chain 'N' and resid 585 through 599 Processing helix chain 'N' and resid 611 through 630 Processing helix chain 'N' and resid 659 through 679 Processing helix chain 'N' and resid 698 through 704 Processing helix chain 'N' and resid 715 through 721 Processing helix chain 'N' and resid 739 through 754 removed outlier: 3.583A pdb=" N LEU N 743 " --> pdb=" O ASN N 739 " (cutoff:3.500A) Processing helix chain 'N' and resid 771 through 786 Processing helix chain 'N' and resid 795 through 798 Processing helix chain 'N' and resid 799 through 805 Processing helix chain 'N' and resid 822 through 826 removed outlier: 3.836A pdb=" N VAL N 826 " --> pdb=" O VAL N 823 " (cutoff:3.500A) Processing helix chain 'N' and resid 841 through 851 Processing helix chain 'N' and resid 871 through 876 Processing helix chain 'N' and resid 913 through 918 Processing helix chain 'N' and resid 928 through 942 Processing helix chain 'N' and resid 954 through 959 removed outlier: 3.567A pdb=" N THR N 959 " --> pdb=" O LEU N 955 " (cutoff:3.500A) Processing helix chain 'N' and resid 960 through 964 Processing helix chain 'N' and resid 965 through 971 Processing helix chain 'N' and resid 1029 through 1042 Processing helix chain 'N' and resid 1044 through 1053 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 39 removed outlier: 3.615A pdb=" N SER A 65 " --> pdb=" O CYS A 26 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A 30 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL B 30 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN N 91 " --> pdb=" O TYR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 84 removed outlier: 3.577A pdb=" N VAL B 81 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 20 through 22 removed outlier: 6.361A pdb=" N TYR C 21 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 93 " --> pdb=" O PHE C 83 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR D 56 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N GLY D 82 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU D 58 " --> pdb=" O GLY D 82 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N CYS D 84 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU D 60 " --> pdb=" O CYS D 84 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASN D 19 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N SER D 57 " --> pdb=" O ASN D 19 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.513A pdb=" N SER C 65 " --> pdb=" O CYS C 26 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 30 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL D 30 " --> pdb=" O THR D 67 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN M 91 " --> pdb=" O TYR D 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 47 through 49 removed outlier: 3.552A pdb=" N ASN E 54 " --> pdb=" O ARG E 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AA9, first strand: chain 'F' and resid 61 through 64 Processing sheet with id=AB1, first strand: chain 'G' and resid 47 through 48 Processing sheet with id=AB2, first strand: chain 'G' and resid 54 through 60 Processing sheet with id=AB3, first strand: chain 'G' and resid 63 through 66 Processing sheet with id=AB4, first strand: chain 'H' and resid 51 through 58 Processing sheet with id=AB5, first strand: chain 'H' and resid 61 through 64 Processing sheet with id=AB6, first strand: chain 'M' and resid 32 through 36 removed outlier: 4.687A pdb=" N ASN M 2 " --> pdb=" O ILE M 64 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL M 59 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE M 75 " --> pdb=" O VAL M 59 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N CYS M 61 " --> pdb=" O LEU M 73 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 335 through 338 removed outlier: 6.354A pdb=" N HIS M 335 " --> pdb=" O ARG M 348 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG M 348 " --> pdb=" O HIS M 335 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASN M 337 " --> pdb=" O LYS M 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 512 through 513 removed outlier: 5.094A pdb=" N THR M 545 " --> pdb=" O LEU M 477 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU M 573 " --> pdb=" O LEU M 604 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N SER M 606 " --> pdb=" O LEU M 573 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU M 575 " --> pdb=" O SER M 606 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 687 through 690 removed outlier: 6.582A pdb=" N GLN M 688 " --> pdb=" O LEU M 867 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA M 835 " --> pdb=" O TYR M 866 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU M 868 " --> pdb=" O ALA M 835 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL M 837 " --> pdb=" O LEU M 868 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'M' and resid 1005 through 1006 Processing sheet with id=AC2, first strand: chain 'N' and resid 32 through 36 removed outlier: 5.284A pdb=" N ASN N 2 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL N 59 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE N 75 " --> pdb=" O VAL N 59 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N CYS N 61 " --> pdb=" O LEU N 73 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG N 65 " --> pdb=" O HIS N 69 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS N 69 " --> pdb=" O ARG N 65 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 335 through 338 removed outlier: 6.795A pdb=" N GLN N 347 " --> pdb=" O ALA N 336 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR N 338 " --> pdb=" O LEU N 345 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU N 345 " --> pdb=" O THR N 338 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 512 through 513 removed outlier: 6.310A pdb=" N ALA N 475 " --> pdb=" O ALA N 543 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N THR N 545 " --> pdb=" O ALA N 475 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N LEU N 477 " --> pdb=" O THR N 545 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU N 542 " --> pdb=" O PHE N 446 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU N 573 " --> pdb=" O LEU N 604 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N SER N 606 " --> pdb=" O LEU N 573 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU N 575 " --> pdb=" O SER N 606 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 687 through 688 removed outlier: 6.645A pdb=" N GLN N 688 " --> pdb=" O LEU N 867 " (cutoff:3.500A) 1482 hydrogen bonds defined for protein. 4230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 394 hydrogen bonds 782 hydrogen bond angles 0 basepair planarities 162 basepair parallelities 286 stacking parallelities Total time for adding SS restraints: 24.69 Time building geometry restraints manager: 39.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 25263 1.02 - 1.22: 148 1.22 - 1.42: 14581 1.42 - 1.62: 18284 1.62 - 1.82: 98 Bond restraints: 58374 Sorted by residual: bond pdb=" CG LEU C 130 " pdb=" CD2 LEU C 130 " ideal model delta sigma weight residual 1.521 1.233 0.288 3.30e-02 9.18e+02 7.60e+01 bond pdb=" CG GLU B 96 " pdb=" CD GLU B 96 " ideal model delta sigma weight residual 1.516 1.364 0.152 2.50e-02 1.60e+03 3.68e+01 bond pdb=" CG GLN N 458 " pdb=" CD GLN N 458 " ideal model delta sigma weight residual 1.516 1.391 0.125 2.50e-02 1.60e+03 2.48e+01 bond pdb=" CG LEU N 967 " pdb=" CD1 LEU N 967 " ideal model delta sigma weight residual 1.521 1.360 0.161 3.30e-02 9.18e+02 2.38e+01 bond pdb=" CB ARG M 148 " pdb=" CG ARG M 148 " ideal model delta sigma weight residual 1.520 1.385 0.135 3.00e-02 1.11e+03 2.01e+01 ... (remaining 58369 not shown) Histogram of bond angle deviations from ideal: 85.66 - 96.50: 9 96.50 - 107.34: 4229 107.34 - 118.18: 71064 118.18 - 129.02: 28801 129.02 - 139.86: 463 Bond angle restraints: 104566 Sorted by residual: angle pdb=" CG ARG N 67 " pdb=" CD ARG N 67 " pdb=" NE ARG N 67 " ideal model delta sigma weight residual 112.00 139.86 -27.86 2.20e+00 2.07e-01 1.60e+02 angle pdb=" CG ARG M 148 " pdb=" CD ARG M 148 " pdb=" NE ARG M 148 " ideal model delta sigma weight residual 112.00 85.66 26.34 2.20e+00 2.07e-01 1.43e+02 angle pdb=" CG LYS C 271 " pdb=" CD LYS C 271 " pdb=" CE LYS C 271 " ideal model delta sigma weight residual 111.30 135.55 -24.25 2.30e+00 1.89e-01 1.11e+02 angle pdb=" CA ARG M 385 " pdb=" CB ARG M 385 " pdb=" CG ARG M 385 " ideal model delta sigma weight residual 114.10 133.47 -19.37 2.00e+00 2.50e-01 9.38e+01 angle pdb=" CB GLN N 458 " pdb=" CG GLN N 458 " pdb=" CD GLN N 458 " ideal model delta sigma weight residual 112.60 126.73 -14.13 1.70e+00 3.46e-01 6.91e+01 ... (remaining 104561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 24383 34.85 - 69.70: 2238 69.70 - 104.55: 34 104.55 - 139.40: 1 139.40 - 174.25: 9 Dihedral angle restraints: 26665 sinusoidal: 15209 harmonic: 11456 Sorted by residual: dihedral pdb=" C HIS N 897 " pdb=" N HIS N 897 " pdb=" CA HIS N 897 " pdb=" CB HIS N 897 " ideal model delta harmonic sigma weight residual -122.60 -146.41 23.81 0 2.50e+00 1.60e-01 9.07e+01 dihedral pdb=" CD ARG N 65 " pdb=" NE ARG N 65 " pdb=" CZ ARG N 65 " pdb=" NH1 ARG N 65 " ideal model delta sinusoidal sigma weight residual 0.00 -81.21 81.21 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" N HIS N 897 " pdb=" C HIS N 897 " pdb=" CA HIS N 897 " pdb=" CB HIS N 897 " ideal model delta harmonic sigma weight residual 122.80 142.06 -19.26 0 2.50e+00 1.60e-01 5.93e+01 ... (remaining 26662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.381: 5319 0.381 - 0.762: 8 0.762 - 1.143: 1 1.143 - 1.525: 0 1.525 - 1.906: 1 Chirality restraints: 5329 Sorted by residual: chirality pdb=" CG LEU N 967 " pdb=" CB LEU N 967 " pdb=" CD1 LEU N 967 " pdb=" CD2 LEU N 967 " both_signs ideal model delta sigma weight residual False -2.59 -0.68 -1.91 2.00e-01 2.50e+01 9.08e+01 chirality pdb=" CA HIS N 897 " pdb=" N HIS N 897 " pdb=" C HIS N 897 " pdb=" CB HIS N 897 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.15e+01 chirality pdb=" CG LEU M 354 " pdb=" CB LEU M 354 " pdb=" CD1 LEU M 354 " pdb=" CD2 LEU M 354 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.34e+00 ... (remaining 5326 not shown) Planarity restraints: 8521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 65 " 0.989 9.50e-02 1.11e+02 3.31e-01 1.21e+02 pdb=" NE ARG N 65 " -0.053 2.00e-02 2.50e+03 pdb=" CZ ARG N 65 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG N 65 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG N 65 " -0.017 2.00e-02 2.50e+03 pdb="HH11 ARG N 65 " -0.006 2.00e-02 2.50e+03 pdb="HH12 ARG N 65 " 0.019 2.00e-02 2.50e+03 pdb="HH21 ARG N 65 " -0.006 2.00e-02 2.50e+03 pdb="HH22 ARG N 65 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 892 " -0.002 2.00e-02 2.50e+03 5.96e-02 1.07e+02 pdb=" CG PHE N 892 " -0.146 2.00e-02 2.50e+03 pdb=" CD1 PHE N 892 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE N 892 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE N 892 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE N 892 " 0.059 2.00e-02 2.50e+03 pdb=" CZ PHE N 892 " -0.012 2.00e-02 2.50e+03 pdb=" HD1 PHE N 892 " 0.079 2.00e-02 2.50e+03 pdb=" HD2 PHE N 892 " 0.094 2.00e-02 2.50e+03 pdb=" HE1 PHE N 892 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE N 892 " -0.046 2.00e-02 2.50e+03 pdb=" HZ PHE N 892 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 372 " 0.719 9.50e-02 1.11e+02 2.40e-01 6.68e+01 pdb=" NE ARG N 372 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG N 372 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG N 372 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG N 372 " -0.016 2.00e-02 2.50e+03 pdb="HH11 ARG N 372 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG N 372 " 0.013 2.00e-02 2.50e+03 pdb="HH21 ARG N 372 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG N 372 " 0.018 2.00e-02 2.50e+03 ... (remaining 8518 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 1248 2.10 - 2.72: 85320 2.72 - 3.35: 153371 3.35 - 3.97: 198151 3.97 - 4.60: 301534 Nonbonded interactions: 739624 Sorted by model distance: nonbonded pdb=" OE1 GLU A 114 " pdb=" H GLU A 114 " model vdw 1.469 1.850 nonbonded pdb=" HD1 HIS D 254 " pdb=" OD1 ASP D 265 " model vdw 1.486 1.850 nonbonded pdb=" O MET M 304 " pdb=" HG SER M 307 " model vdw 1.496 1.850 nonbonded pdb=" HG SER B 5 " pdb=" O SER B 7 " model vdw 1.499 1.850 nonbonded pdb=" OE1 GLU M 150 " pdb=" H GLU M 150 " model vdw 1.512 1.850 ... (remaining 739619 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2 or name HA or name HB2 or name HB3 or name HD \ 21 or name HD22)) or resid 20 through 148 or (resid 149 through 156 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 157 t \ hrough 158 or (resid 159 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 160 or (resid 161 through 162 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 163 or (res \ id 164 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 165 or (resid 166 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 167 or (resid 168 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 169 or (resid 17 \ 0 through 173 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 174 or (resid 175 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 176 or (resid 177 through 179 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 180 or (resid 181 and (name N or name CA or name C or name O or name CB or na \ me HA )) or (resid 182 through 190 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 191 or (resid 192 through 200 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 2 \ 01 through 202 or (resid 203 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 204 or (resid 205 through 207 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 208 or \ (resid 209 through 212 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 213 or (resid 214 through 215 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 216 or (resid \ 217 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 218 through 321)) selection = (chain 'B' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2 or name HA or name HB2 or name HB3 or name HD \ 21 or name HD22)) or resid 20 through 148 or (resid 149 through 156 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 157 t \ hrough 158 or (resid 159 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 160 or (resid 161 through 162 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 163 or (res \ id 164 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 165 or (resid 166 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 167 or (resid 168 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 169 or (resid 17 \ 0 through 173 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 174 or (resid 175 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 176 or (resid 177 through 179 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 180 or (resid 181 and (name N or name CA or name C or name O or name CB or na \ me HA )) or (resid 182 through 190 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 191 or (resid 192 through 200 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 2 \ 01 through 202 or (resid 203 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 204 or (resid 205 through 207 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 208 or \ (resid 209 through 212 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 213 or (resid 214 through 215 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 216 or (resid \ 217 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 218 through 321)) selection = (chain 'C' and (resid 19 through 253 or (resid 254 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 255 through 321)) selection = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2 or name HA or name HB2 or name HB3 or name HD \ 21 or name HD22)) or resid 20 through 148 or (resid 149 through 156 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 157 t \ hrough 158 or (resid 159 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 160 or (resid 161 through 162 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 163 or (res \ id 164 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 165 or (resid 166 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 167 or (resid 168 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 169 or (resid 17 \ 0 through 173 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 174 or (resid 175 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 176 or (resid 177 through 179 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 180 or (resid 181 and (name N or name CA or name C or name O or name CB or na \ me HA )) or (resid 182 through 190 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 191 or (resid 192 through 200 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 2 \ 01 through 202 or (resid 203 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 204 or (resid 205 through 207 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 208 or \ (resid 209 through 212 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 213 or (resid 214 through 215 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 216 or (resid \ 217 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 218 through 321)) } ncs_group { reference = chain 'E' selection = (chain 'G' and resid 5 through 98) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = (chain 'M' and (resid 1 through 177 or (resid 178 through 180 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 181 or (res \ id 182 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 183 through 187 or (resid 188 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 189 or (resid 190 through 195 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 196 through 224 or (resid 225 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 226 through 237 or (resid 238 and ( \ name N or name CA or name C or name O or name CB or name HA )) or resid 239 or ( \ resid 240 and (name N or name CA or name C or name O or name CB or name HA )) or \ resid 241 through 346 or (resid 347 through 349 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 350 through 379 or (resi \ d 380 and (name N or name CA or name C or name O or name CB or name CG or name N \ D1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name \ HB3 or name HD1 or name HD2 or name HE1)) or resid 381 through 480 or (resid 481 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 482 through 631 or (resid 632 and (name N or name CA or name C or name O \ or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H \ or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or res \ id 633 through 689 or (resid 692 and (name N or name CA or name C or name O or n \ ame CB or name HA )) or resid 693 through 805 or resid 822 through 826 or (resid \ 832 and (name N or name CA or name C or name O or name CB or name HA )) or resi \ d 833 through 982 or (resid 1005 and (name N or name CA or name C or name O or n \ ame CB or name HA )) or resid 1006 through 1059)) selection = (chain 'N' and (resid 1 through 122 or (resid 123 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 124 through 533 or (resid 534 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 535 through 672 or (resid 67 \ 3 through 675 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 676 or (resid 677 through 681 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 682 through 889 or (re \ sid 890 and (name N or name CA or name C or name O or name CB or name HA )) or ( \ resid 891 through 892 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or (resid 893 and (name N or name CA or name C or name O or \ name CB or name HA )) or (resid 894 through 899 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 906 through 1059)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.650 Extract box with map and model: 13.450 Check model and map are aligned: 0.650 Set scattering table: 0.420 Process input model: 161.370 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.288 33077 Z= 0.323 Angle : 0.836 27.860 46500 Z= 0.459 Chirality : 0.056 1.906 5329 Planarity : 0.011 0.426 4905 Dihedral : 22.118 174.246 12090 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.21 % Allowed : 14.45 % Favored : 85.35 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3485 helix: 0.46 (0.12), residues: 1699 sheet: -0.36 (0.29), residues: 326 loop : -0.82 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 595 HIS 0.074 0.002 HIS N 272 PHE 0.112 0.002 PHE N 892 TYR 0.015 0.001 TYR C 115 ARG 0.071 0.002 ARG M 442 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue VAL 211 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 675 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 821 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue SER 896 is missing expected H atoms. Skipping. Residue LEU 899 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue LEU 984 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LEU 994 is missing expected H atoms. Skipping. Residue SER 997 is missing expected H atoms. Skipping. Residue TYR 999 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Evaluate side-chains 606 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 602 time to evaluate : 3.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8946 (tp) cc_final: 0.8741 (tt) REVERT: A 203 GLN cc_start: 0.8985 (mt0) cc_final: 0.8635 (tm-30) REVERT: B 41 GLU cc_start: 0.8162 (tp30) cc_final: 0.7933 (tm-30) REVERT: B 54 ASN cc_start: 0.7948 (m-40) cc_final: 0.7413 (m-40) REVERT: B 97 VAL cc_start: 0.8779 (t) cc_final: 0.8200 (t) REVERT: B 105 THR cc_start: 0.9000 (p) cc_final: 0.8425 (p) REVERT: B 107 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7522 (mm110) REVERT: B 189 GLU cc_start: 0.8552 (mm-30) cc_final: 0.7969 (mt-10) REVERT: B 199 LYS cc_start: 0.8943 (tptp) cc_final: 0.8695 (tppp) REVERT: C 271 LYS cc_start: 0.8415 (mtpp) cc_final: 0.8164 (tttt) REVERT: C 292 PHE cc_start: 0.8989 (t80) cc_final: 0.8526 (t80) REVERT: D 10 LYS cc_start: 0.7973 (pttm) cc_final: 0.7462 (ptmm) REVERT: D 244 LEU cc_start: 0.8380 (mp) cc_final: 0.8147 (mp) REVERT: M 100 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8485 (mtpp) REVERT: M 179 GLU cc_start: 0.7729 (mp0) cc_final: 0.7300 (mp0) REVERT: M 205 ARG cc_start: 0.9118 (mmm160) cc_final: 0.8753 (tpt-90) REVERT: M 218 VAL cc_start: 0.9214 (p) cc_final: 0.9003 (p) REVERT: M 371 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7901 (tm-30) REVERT: M 421 SER cc_start: 0.8917 (m) cc_final: 0.8668 (p) REVERT: M 458 GLN cc_start: 0.8893 (mm110) cc_final: 0.8512 (mp10) REVERT: M 553 SER cc_start: 0.8555 (p) cc_final: 0.8332 (p) REVERT: M 620 GLU cc_start: 0.8452 (tp30) cc_final: 0.8242 (tp30) REVERT: N 34 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7762 (tm-30) REVERT: N 43 ASP cc_start: 0.8851 (t70) cc_final: 0.8454 (m-30) REVERT: N 103 GLU cc_start: 0.7554 (pm20) cc_final: 0.7323 (pm20) REVERT: N 114 LEU cc_start: 0.8859 (mt) cc_final: 0.8526 (mt) REVERT: N 167 ASP cc_start: 0.8832 (m-30) cc_final: 0.8604 (m-30) REVERT: N 168 GLU cc_start: 0.9155 (tt0) cc_final: 0.8921 (tt0) REVERT: N 205 ARG cc_start: 0.9026 (mmm160) cc_final: 0.8753 (mmm-85) REVERT: N 256 LYS cc_start: 0.8237 (mtpt) cc_final: 0.8019 (mtpt) REVERT: N 408 GLN cc_start: 0.8755 (mm110) cc_final: 0.8480 (tp40) REVERT: N 435 TYR cc_start: 0.9254 (t80) cc_final: 0.8944 (t80) REVERT: N 466 ARG cc_start: 0.8673 (mtt180) cc_final: 0.8396 (mtt180) REVERT: N 546 ILE cc_start: 0.9441 (mt) cc_final: 0.9158 (mt) REVERT: N 671 VAL cc_start: 0.9350 (t) cc_final: 0.9100 (p) REVERT: N 967 LEU cc_start: 0.8995 (mm) cc_final: 0.8417 (tt) outliers start: 4 outliers final: 2 residues processed: 603 average time/residue: 0.8050 time to fit residues: 751.2024 Evaluate side-chains 398 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 396 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain D residue 95 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 323 optimal weight: 3.9990 chunk 290 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 155 optimal weight: 40.0000 chunk 300 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 347 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN D 299 ASN M 616 GLN N 458 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 33077 Z= 0.306 Angle : 0.681 8.405 46500 Z= 0.393 Chirality : 0.043 0.178 5329 Planarity : 0.006 0.193 4905 Dihedral : 23.791 173.252 7700 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 3.10 % Allowed : 17.03 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3485 helix: 1.13 (0.12), residues: 1731 sheet: -0.34 (0.28), residues: 332 loop : -0.85 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 170 HIS 0.012 0.002 HIS M 548 PHE 0.019 0.002 PHE N 650 TYR 0.017 0.002 TYR B 110 ARG 0.020 0.001 ARG M 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue VAL 211 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 675 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 821 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue SER 896 is missing expected H atoms. Skipping. Residue LEU 899 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue LEU 984 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LEU 994 is missing expected H atoms. Skipping. Residue SER 997 is missing expected H atoms. Skipping. Residue TYR 999 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Evaluate side-chains 440 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 380 time to evaluate : 3.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7790 (mm-30) REVERT: A 130 LEU cc_start: 0.9132 (tp) cc_final: 0.8907 (tt) REVERT: A 168 VAL cc_start: 0.8870 (t) cc_final: 0.8669 (p) REVERT: A 268 ASP cc_start: 0.8138 (t0) cc_final: 0.7870 (t0) REVERT: B 41 GLU cc_start: 0.8378 (tp30) cc_final: 0.8062 (tm-30) REVERT: B 43 ARG cc_start: 0.7899 (mmm160) cc_final: 0.7488 (mmm160) REVERT: B 91 LEU cc_start: 0.8893 (tp) cc_final: 0.8639 (tt) REVERT: B 189 GLU cc_start: 0.8660 (mm-30) cc_final: 0.7973 (mt-10) REVERT: B 199 LYS cc_start: 0.9188 (tptp) cc_final: 0.8893 (tppp) REVERT: B 284 MET cc_start: 0.7787 (mmp) cc_final: 0.7498 (mmp) REVERT: C 270 ILE cc_start: 0.8756 (mm) cc_final: 0.8500 (mm) REVERT: C 318 GLN cc_start: 0.9127 (tt0) cc_final: 0.8770 (tp-100) REVERT: D 10 LYS cc_start: 0.8089 (pttm) cc_final: 0.7491 (ptmm) REVERT: D 41 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7187 (mm-30) REVERT: D 256 LYS cc_start: 0.9326 (pptt) cc_final: 0.9075 (ptmm) REVERT: D 268 ASP cc_start: 0.8661 (m-30) cc_final: 0.7747 (t0) REVERT: M 179 GLU cc_start: 0.7790 (mp0) cc_final: 0.7289 (mp0) REVERT: M 205 ARG cc_start: 0.9146 (mmm160) cc_final: 0.8804 (mmt90) REVERT: M 371 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8065 (tm-30) REVERT: M 393 ARG cc_start: 0.9178 (ttm170) cc_final: 0.8869 (mmm-85) REVERT: M 421 SER cc_start: 0.9131 (m) cc_final: 0.8841 (p) REVERT: M 550 MET cc_start: 0.9454 (tpt) cc_final: 0.9008 (mmm) REVERT: M 627 GLU cc_start: 0.8326 (tt0) cc_final: 0.7683 (tm-30) REVERT: M 657 HIS cc_start: 0.8815 (m-70) cc_final: 0.8456 (m90) REVERT: N 103 GLU cc_start: 0.8081 (pm20) cc_final: 0.7788 (pm20) REVERT: N 167 ASP cc_start: 0.8899 (m-30) cc_final: 0.8666 (m-30) REVERT: N 408 GLN cc_start: 0.8794 (mm110) cc_final: 0.8483 (tp40) REVERT: N 458 GLN cc_start: 0.8897 (mm110) cc_final: 0.8451 (mm-40) REVERT: N 893 PRO cc_start: 0.8122 (Cg_endo) cc_final: 0.7744 (Cg_exo) outliers start: 60 outliers final: 35 residues processed: 412 average time/residue: 0.7147 time to fit residues: 468.8628 Evaluate side-chains 365 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 330 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 61 CYS Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 439 ASP Chi-restraints excluded: chain M residue 447 SER Chi-restraints excluded: chain M residue 450 LEU Chi-restraints excluded: chain M residue 478 VAL Chi-restraints excluded: chain M residue 571 SER Chi-restraints excluded: chain N residue 298 LEU Chi-restraints excluded: chain N residue 469 LEU Chi-restraints excluded: chain N residue 609 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 193 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 289 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 348 optimal weight: 2.9990 chunk 376 optimal weight: 1.9990 chunk 310 optimal weight: 5.9990 chunk 345 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 279 optimal weight: 0.0070 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 HIS M 616 GLN N 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33077 Z= 0.213 Angle : 0.579 7.387 46500 Z= 0.339 Chirality : 0.039 0.147 5329 Planarity : 0.004 0.057 4905 Dihedral : 23.661 171.803 7697 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.06 % Allowed : 18.78 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.14), residues: 3485 helix: 1.96 (0.12), residues: 1726 sheet: -0.37 (0.28), residues: 331 loop : -0.64 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 103 HIS 0.017 0.001 HIS M 380 PHE 0.020 0.001 PHE M 383 TYR 0.016 0.001 TYR M 147 ARG 0.006 0.000 ARG N 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue VAL 211 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 675 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 821 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue SER 896 is missing expected H atoms. Skipping. Residue LEU 899 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue LEU 984 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LEU 994 is missing expected H atoms. Skipping. Residue SER 997 is missing expected H atoms. Skipping. Residue TYR 999 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Evaluate side-chains 379 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 339 time to evaluate : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.9134 (tp) cc_final: 0.8876 (tt) REVERT: A 268 ASP cc_start: 0.8251 (t0) cc_final: 0.7947 (t0) REVERT: B 41 GLU cc_start: 0.8530 (tp30) cc_final: 0.8184 (tm-30) REVERT: B 43 ARG cc_start: 0.7993 (mmm160) cc_final: 0.7602 (mmm160) REVERT: B 189 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8026 (mt-10) REVERT: C 318 GLN cc_start: 0.9173 (tt0) cc_final: 0.8849 (tp-100) REVERT: D 10 LYS cc_start: 0.8139 (pttm) cc_final: 0.7526 (ptmm) REVERT: D 41 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7354 (mm-30) REVERT: D 256 LYS cc_start: 0.9343 (pptt) cc_final: 0.9038 (ptmm) REVERT: D 268 ASP cc_start: 0.8673 (m-30) cc_final: 0.7892 (t0) REVERT: M 179 GLU cc_start: 0.7778 (mp0) cc_final: 0.7300 (mp0) REVERT: M 205 ARG cc_start: 0.9126 (mmm160) cc_final: 0.8691 (tpt-90) REVERT: M 280 CYS cc_start: 0.9269 (m) cc_final: 0.9053 (m) REVERT: M 421 SER cc_start: 0.9171 (m) cc_final: 0.8871 (p) REVERT: M 550 MET cc_start: 0.9413 (OUTLIER) cc_final: 0.9023 (mmm) REVERT: N 103 GLU cc_start: 0.8130 (pm20) cc_final: 0.7895 (pm20) REVERT: N 167 ASP cc_start: 0.8983 (m-30) cc_final: 0.8741 (m-30) REVERT: N 284 MET cc_start: 0.9359 (mtt) cc_final: 0.9146 (mmm) REVERT: N 408 GLN cc_start: 0.8849 (mm110) cc_final: 0.8553 (tp40) REVERT: N 458 GLN cc_start: 0.9006 (mm110) cc_final: 0.8789 (mm110) REVERT: N 572 ASP cc_start: 0.8341 (m-30) cc_final: 0.8089 (m-30) REVERT: N 893 PRO cc_start: 0.7896 (Cg_endo) cc_final: 0.7480 (Cg_exo) outliers start: 40 outliers final: 28 residues processed: 364 average time/residue: 0.7507 time to fit residues: 443.7105 Evaluate side-chains 344 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 315 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 260 TRP Chi-restraints excluded: chain M residue 309 LEU Chi-restraints excluded: chain M residue 356 VAL Chi-restraints excluded: chain M residue 439 ASP Chi-restraints excluded: chain M residue 478 VAL Chi-restraints excluded: chain M residue 550 MET Chi-restraints excluded: chain M residue 571 SER Chi-restraints excluded: chain N residue 609 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 344 optimal weight: 0.9990 chunk 261 optimal weight: 20.0000 chunk 180 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 349 optimal weight: 2.9990 chunk 370 optimal weight: 0.0070 chunk 182 optimal weight: 10.0000 chunk 331 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 33077 Z= 0.272 Angle : 0.593 7.146 46500 Z= 0.346 Chirality : 0.040 0.176 5329 Planarity : 0.004 0.056 4905 Dihedral : 23.615 172.305 7697 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 2.73 % Allowed : 18.73 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.15), residues: 3485 helix: 2.01 (0.13), residues: 1734 sheet: -0.44 (0.30), residues: 300 loop : -0.65 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 170 HIS 0.007 0.001 HIS M 149 PHE 0.021 0.002 PHE N 383 TYR 0.028 0.002 TYR N 435 ARG 0.008 0.001 ARG M 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue VAL 211 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 675 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 821 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue SER 896 is missing expected H atoms. Skipping. Residue LEU 899 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue LEU 984 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LEU 994 is missing expected H atoms. Skipping. Residue SER 997 is missing expected H atoms. Skipping. Residue TYR 999 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Evaluate side-chains 347 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 294 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 ASP cc_start: 0.8327 (t0) cc_final: 0.8017 (t0) REVERT: B 41 GLU cc_start: 0.8702 (tp30) cc_final: 0.8212 (tm-30) REVERT: B 195 LYS cc_start: 0.9636 (ttpt) cc_final: 0.9379 (ttmm) REVERT: B 284 MET cc_start: 0.8765 (mmp) cc_final: 0.8326 (mmm) REVERT: C 259 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7281 (pmt-80) REVERT: C 276 LEU cc_start: 0.9394 (mt) cc_final: 0.9165 (mt) REVERT: C 318 GLN cc_start: 0.9213 (tt0) cc_final: 0.8969 (tp-100) REVERT: D 10 LYS cc_start: 0.8085 (pttm) cc_final: 0.7502 (ptmm) REVERT: D 41 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7481 (mm-30) REVERT: D 256 LYS cc_start: 0.9379 (pptt) cc_final: 0.9174 (ptmm) REVERT: M 100 LYS cc_start: 0.9238 (mtpt) cc_final: 0.9002 (mtpp) REVERT: M 179 GLU cc_start: 0.7781 (mp0) cc_final: 0.7311 (mp0) REVERT: M 205 ARG cc_start: 0.9112 (mmm160) cc_final: 0.8667 (tpt-90) REVERT: M 421 SER cc_start: 0.9144 (m) cc_final: 0.8845 (p) REVERT: M 582 ASP cc_start: 0.8186 (p0) cc_final: 0.7859 (p0) REVERT: N 458 GLN cc_start: 0.9097 (mm110) cc_final: 0.8822 (mm110) REVERT: N 893 PRO cc_start: 0.7809 (Cg_endo) cc_final: 0.7355 (Cg_exo) outliers start: 53 outliers final: 42 residues processed: 329 average time/residue: 0.7766 time to fit residues: 409.7510 Evaluate side-chains 310 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 267 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 259 ARG Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 309 LEU Chi-restraints excluded: chain M residue 356 VAL Chi-restraints excluded: chain M residue 439 ASP Chi-restraints excluded: chain M residue 459 THR Chi-restraints excluded: chain M residue 465 GLU Chi-restraints excluded: chain M residue 478 VAL Chi-restraints excluded: chain M residue 571 SER Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 219 SER Chi-restraints excluded: chain N residue 279 LEU Chi-restraints excluded: chain N residue 298 LEU Chi-restraints excluded: chain N residue 609 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 308 optimal weight: 1.9990 chunk 210 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 275 optimal weight: 0.6980 chunk 152 optimal weight: 5.9990 chunk 315 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 332 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33077 Z= 0.281 Angle : 0.583 7.840 46500 Z= 0.342 Chirality : 0.040 0.182 5329 Planarity : 0.004 0.093 4905 Dihedral : 23.590 171.162 7697 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.76 % Rotamer: Outliers : 2.58 % Allowed : 18.89 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.15), residues: 3485 helix: 2.14 (0.13), residues: 1727 sheet: -0.47 (0.31), residues: 284 loop : -0.58 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 103 HIS 0.005 0.001 HIS A 228 PHE 0.012 0.001 PHE D 308 TYR 0.026 0.002 TYR N 399 ARG 0.015 0.001 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue VAL 211 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 675 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 821 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue SER 896 is missing expected H atoms. Skipping. Residue LEU 899 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue LEU 984 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LEU 994 is missing expected H atoms. Skipping. Residue SER 997 is missing expected H atoms. Skipping. Residue TYR 999 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Evaluate side-chains 318 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 268 time to evaluate : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 ASP cc_start: 0.8381 (t0) cc_final: 0.8091 (t0) REVERT: B 41 GLU cc_start: 0.8793 (tp30) cc_final: 0.8192 (tm-30) REVERT: B 195 LYS cc_start: 0.9645 (ttpt) cc_final: 0.9400 (ttmm) REVERT: B 284 MET cc_start: 0.8939 (mmp) cc_final: 0.8448 (mmm) REVERT: C 276 LEU cc_start: 0.9389 (mt) cc_final: 0.9126 (mt) REVERT: D 111 ARG cc_start: 0.8239 (mmm160) cc_final: 0.7983 (mmm160) REVERT: D 256 LYS cc_start: 0.9391 (pptt) cc_final: 0.9145 (ptmm) REVERT: M 100 LYS cc_start: 0.9285 (mtpt) cc_final: 0.9046 (mtpp) REVERT: M 179 GLU cc_start: 0.7805 (mp0) cc_final: 0.7368 (mp0) REVERT: M 205 ARG cc_start: 0.9120 (mmm160) cc_final: 0.8621 (tpt-90) REVERT: M 284 MET cc_start: 0.9249 (mtp) cc_final: 0.9019 (mtt) REVERT: N 403 MET cc_start: 0.9016 (tpp) cc_final: 0.8816 (tpp) REVERT: N 458 GLN cc_start: 0.9087 (mm110) cc_final: 0.8768 (mm110) outliers start: 50 outliers final: 45 residues processed: 306 average time/residue: 0.7448 time to fit residues: 367.5036 Evaluate side-chains 300 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 255 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 225 ASN Chi-restraints excluded: chain M residue 252 ASP Chi-restraints excluded: chain M residue 309 LEU Chi-restraints excluded: chain M residue 356 VAL Chi-restraints excluded: chain M residue 459 THR Chi-restraints excluded: chain M residue 465 GLU Chi-restraints excluded: chain M residue 478 VAL Chi-restraints excluded: chain M residue 571 SER Chi-restraints excluded: chain M residue 605 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 114 LEU Chi-restraints excluded: chain N residue 279 LEU Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 437 LEU Chi-restraints excluded: chain N residue 609 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 124 optimal weight: 30.0000 chunk 333 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 370 optimal weight: 0.5980 chunk 307 optimal weight: 0.0970 chunk 171 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 33077 Z= 0.185 Angle : 0.543 7.218 46500 Z= 0.320 Chirality : 0.038 0.164 5329 Planarity : 0.003 0.046 4905 Dihedral : 23.514 171.038 7697 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 2.32 % Allowed : 19.81 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.15), residues: 3485 helix: 2.51 (0.13), residues: 1722 sheet: -0.46 (0.31), residues: 286 loop : -0.42 (0.17), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 595 HIS 0.004 0.001 HIS N 123 PHE 0.015 0.001 PHE D 308 TYR 0.013 0.001 TYR M 147 ARG 0.005 0.000 ARG N 308 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue VAL 211 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 675 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 821 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue SER 896 is missing expected H atoms. Skipping. Residue LEU 899 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue LEU 984 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LEU 994 is missing expected H atoms. Skipping. Residue SER 997 is missing expected H atoms. Skipping. Residue TYR 999 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Evaluate side-chains 308 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 263 time to evaluate : 3.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 ASP cc_start: 0.8332 (t0) cc_final: 0.7970 (t0) REVERT: B 41 GLU cc_start: 0.8808 (tp30) cc_final: 0.8252 (tm-30) REVERT: B 195 LYS cc_start: 0.9635 (ttpt) cc_final: 0.9373 (ttmm) REVERT: B 284 MET cc_start: 0.8909 (mmp) cc_final: 0.8410 (mmm) REVERT: C 276 LEU cc_start: 0.9387 (mt) cc_final: 0.9141 (mt) REVERT: D 256 LYS cc_start: 0.9377 (pptt) cc_final: 0.9137 (ptmm) REVERT: M 205 ARG cc_start: 0.9075 (mmm160) cc_final: 0.8559 (tpt-90) REVERT: N 458 GLN cc_start: 0.9107 (mm110) cc_final: 0.8790 (mm110) outliers start: 45 outliers final: 37 residues processed: 294 average time/residue: 0.7188 time to fit residues: 339.7024 Evaluate side-chains 287 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 250 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 309 LEU Chi-restraints excluded: chain M residue 356 VAL Chi-restraints excluded: chain M residue 439 ASP Chi-restraints excluded: chain M residue 459 THR Chi-restraints excluded: chain M residue 465 GLU Chi-restraints excluded: chain M residue 478 VAL Chi-restraints excluded: chain M residue 545 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 114 LEU Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 609 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 357 optimal weight: 0.9990 chunk 41 optimal weight: 0.0770 chunk 211 optimal weight: 2.9990 chunk 270 optimal weight: 6.9990 chunk 209 optimal weight: 4.9990 chunk 311 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 chunk 369 optimal weight: 20.0000 chunk 231 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 170 optimal weight: 20.0000 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 33077 Z= 0.338 Angle : 0.599 7.334 46500 Z= 0.352 Chirality : 0.041 0.168 5329 Planarity : 0.004 0.047 4905 Dihedral : 23.529 171.709 7697 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.53 % Favored : 95.44 % Rotamer: Outliers : 3.10 % Allowed : 19.25 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.15), residues: 3485 helix: 2.11 (0.13), residues: 1733 sheet: -0.76 (0.28), residues: 321 loop : -0.63 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 103 HIS 0.006 0.001 HIS A 228 PHE 0.014 0.002 PHE N 629 TYR 0.021 0.002 TYR M 147 ARG 0.009 0.001 ARG N 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue VAL 211 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 675 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 821 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue SER 896 is missing expected H atoms. Skipping. Residue LEU 899 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue LEU 984 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LEU 994 is missing expected H atoms. Skipping. Residue SER 997 is missing expected H atoms. Skipping. Residue TYR 999 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Evaluate side-chains 298 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 238 time to evaluate : 3.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 ASP cc_start: 0.8392 (t0) cc_final: 0.8131 (t0) REVERT: B 41 GLU cc_start: 0.8788 (tp30) cc_final: 0.8316 (tm-30) REVERT: B 195 LYS cc_start: 0.9653 (ttpt) cc_final: 0.9394 (ttmm) REVERT: B 284 MET cc_start: 0.9102 (mmp) cc_final: 0.8670 (mmm) REVERT: D 256 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9158 (ptmm) REVERT: M 262 PHE cc_start: 0.8549 (m-80) cc_final: 0.7696 (m-80) REVERT: N 403 MET cc_start: 0.9345 (tpp) cc_final: 0.8946 (tpp) REVERT: N 441 GLN cc_start: 0.8720 (tp40) cc_final: 0.8291 (tm-30) REVERT: N 458 GLN cc_start: 0.9160 (mm110) cc_final: 0.8782 (mm110) outliers start: 60 outliers final: 45 residues processed: 286 average time/residue: 0.7416 time to fit residues: 337.6865 Evaluate side-chains 273 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 227 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 67 ARG Chi-restraints excluded: chain M residue 225 ASN Chi-restraints excluded: chain M residue 252 ASP Chi-restraints excluded: chain M residue 309 LEU Chi-restraints excluded: chain M residue 356 VAL Chi-restraints excluded: chain M residue 439 ASP Chi-restraints excluded: chain M residue 447 SER Chi-restraints excluded: chain M residue 459 THR Chi-restraints excluded: chain M residue 465 GLU Chi-restraints excluded: chain M residue 545 THR Chi-restraints excluded: chain M residue 571 SER Chi-restraints excluded: chain M residue 577 GLU Chi-restraints excluded: chain M residue 605 LEU Chi-restraints excluded: chain M residue 662 SER Chi-restraints excluded: chain N residue 10 GLU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 114 LEU Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 609 THR Chi-restraints excluded: chain N residue 967 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 228 optimal weight: 0.9980 chunk 147 optimal weight: 20.0000 chunk 220 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 251 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 290 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33077 Z= 0.231 Angle : 0.554 7.184 46500 Z= 0.327 Chirality : 0.039 0.147 5329 Planarity : 0.003 0.045 4905 Dihedral : 23.482 170.050 7697 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 2.53 % Allowed : 20.02 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.15), residues: 3485 helix: 2.37 (0.13), residues: 1736 sheet: -0.68 (0.29), residues: 309 loop : -0.50 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 103 HIS 0.004 0.001 HIS N 123 PHE 0.020 0.001 PHE D 92 TYR 0.015 0.001 TYR M 147 ARG 0.006 0.000 ARG D 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue VAL 211 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 675 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 821 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue SER 896 is missing expected H atoms. Skipping. Residue LEU 899 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue LEU 984 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LEU 994 is missing expected H atoms. Skipping. Residue SER 997 is missing expected H atoms. Skipping. Residue TYR 999 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Evaluate side-chains 284 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 235 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 ASP cc_start: 0.8357 (t0) cc_final: 0.8060 (t0) REVERT: B 195 LYS cc_start: 0.9640 (ttpt) cc_final: 0.9384 (ttmm) REVERT: B 284 MET cc_start: 0.9068 (mmp) cc_final: 0.8636 (mmm) REVERT: M 262 PHE cc_start: 0.8541 (m-80) cc_final: 0.7710 (m-80) REVERT: M 284 MET cc_start: 0.9338 (mtp) cc_final: 0.9116 (mtt) REVERT: M 312 MET cc_start: 0.8120 (mtt) cc_final: 0.7875 (mtt) REVERT: N 403 MET cc_start: 0.9354 (tpp) cc_final: 0.9001 (tpp) REVERT: N 441 GLN cc_start: 0.8703 (tp40) cc_final: 0.8274 (tm-30) REVERT: N 458 GLN cc_start: 0.9160 (mm110) cc_final: 0.8759 (mm110) outliers start: 49 outliers final: 41 residues processed: 276 average time/residue: 0.7111 time to fit residues: 317.6712 Evaluate side-chains 263 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 222 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 110 TYR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 225 ASN Chi-restraints excluded: chain M residue 260 TRP Chi-restraints excluded: chain M residue 309 LEU Chi-restraints excluded: chain M residue 356 VAL Chi-restraints excluded: chain M residue 447 SER Chi-restraints excluded: chain M residue 459 THR Chi-restraints excluded: chain M residue 465 GLU Chi-restraints excluded: chain M residue 545 THR Chi-restraints excluded: chain M residue 571 SER Chi-restraints excluded: chain M residue 577 GLU Chi-restraints excluded: chain M residue 662 SER Chi-restraints excluded: chain N residue 10 GLU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 114 LEU Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 609 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 335 optimal weight: 2.9990 chunk 353 optimal weight: 6.9990 chunk 322 optimal weight: 0.0870 chunk 344 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 149 optimal weight: 30.0000 chunk 270 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 310 optimal weight: 2.9990 chunk 325 optimal weight: 1.9990 chunk 342 optimal weight: 0.5980 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33077 Z= 0.244 Angle : 0.554 7.282 46500 Z= 0.327 Chirality : 0.039 0.180 5329 Planarity : 0.003 0.045 4905 Dihedral : 23.439 170.453 7695 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.95 % Rotamer: Outliers : 2.37 % Allowed : 20.33 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.15), residues: 3485 helix: 2.41 (0.13), residues: 1738 sheet: -0.65 (0.29), residues: 304 loop : -0.47 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 103 HIS 0.012 0.001 HIS D 44 PHE 0.017 0.001 PHE D 92 TYR 0.017 0.001 TYR M 147 ARG 0.007 0.000 ARG D 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue VAL 211 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 675 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 821 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue SER 896 is missing expected H atoms. Skipping. Residue LEU 899 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue LEU 984 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LEU 994 is missing expected H atoms. Skipping. Residue SER 997 is missing expected H atoms. Skipping. Residue TYR 999 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Evaluate side-chains 273 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 227 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 ASP cc_start: 0.8392 (t0) cc_final: 0.8049 (t0) REVERT: B 195 LYS cc_start: 0.9632 (ttpt) cc_final: 0.9371 (ttmm) REVERT: B 284 MET cc_start: 0.9089 (mmp) cc_final: 0.8655 (mmm) REVERT: M 262 PHE cc_start: 0.8554 (m-80) cc_final: 0.7727 (m-80) REVERT: M 284 MET cc_start: 0.9341 (mtp) cc_final: 0.9124 (mtt) REVERT: N 403 MET cc_start: 0.9365 (tpp) cc_final: 0.9006 (tpp) REVERT: N 441 GLN cc_start: 0.8754 (tp40) cc_final: 0.8327 (tm-30) outliers start: 46 outliers final: 42 residues processed: 267 average time/residue: 0.7051 time to fit residues: 306.3633 Evaluate side-chains 267 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 225 time to evaluate : 3.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 110 TYR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 225 ASN Chi-restraints excluded: chain M residue 260 TRP Chi-restraints excluded: chain M residue 309 LEU Chi-restraints excluded: chain M residue 356 VAL Chi-restraints excluded: chain M residue 439 ASP Chi-restraints excluded: chain M residue 447 SER Chi-restraints excluded: chain M residue 459 THR Chi-restraints excluded: chain M residue 465 GLU Chi-restraints excluded: chain M residue 545 THR Chi-restraints excluded: chain M residue 571 SER Chi-restraints excluded: chain M residue 577 GLU Chi-restraints excluded: chain M residue 662 SER Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 114 LEU Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 609 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 225 optimal weight: 7.9990 chunk 363 optimal weight: 20.0000 chunk 222 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 252 optimal weight: 0.6980 chunk 381 optimal weight: 8.9990 chunk 351 optimal weight: 2.9990 chunk 303 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.6436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 33077 Z= 0.330 Angle : 0.590 7.304 46500 Z= 0.347 Chirality : 0.041 0.200 5329 Planarity : 0.004 0.122 4905 Dihedral : 23.456 170.530 7695 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.73 % Favored : 95.21 % Rotamer: Outliers : 2.37 % Allowed : 20.43 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.15), residues: 3485 helix: 2.14 (0.13), residues: 1737 sheet: -0.75 (0.29), residues: 302 loop : -0.64 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 103 HIS 0.009 0.001 HIS D 44 PHE 0.013 0.002 PHE M 619 TYR 0.020 0.002 TYR M 147 ARG 0.010 0.000 ARG M 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue LEU 193 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue TYR 207 is missing expected H atoms. Skipping. Residue VAL 211 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue MET 284 is missing expected H atoms. Skipping. Residue MET 309 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue THR 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue TYR 16 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue ILE 74 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue TYR 97 is missing expected H atoms. Skipping. Residue THR 100 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue MET 3 is missing expected H atoms. Skipping. Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 12 is missing expected H atoms. Skipping. Residue VAL 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 24 is missing expected H atoms. Skipping. Residue LEU 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue TYR 57 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LEU 88 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 675 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 821 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 894 is missing expected H atoms. Skipping. Residue SER 896 is missing expected H atoms. Skipping. Residue LEU 899 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue LEU 984 is missing expected H atoms. Skipping. Residue LEU 985 is missing expected H atoms. Skipping. Residue LEU 994 is missing expected H atoms. Skipping. Residue SER 997 is missing expected H atoms. Skipping. Residue TYR 999 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue SER 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue LEU 327 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 338 is missing expected H atoms. Skipping. Residue SER 342 is missing expected H atoms. Skipping. Residue LYS 344 is missing expected H atoms. Skipping. Residue LEU 345 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue LEU 486 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 497 is missing expected H atoms. Skipping. Residue SER 499 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue VAL 512 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 702 is missing expected H atoms. Skipping. Residue MET 714 is missing expected H atoms. Skipping. Residue LEU 717 is missing expected H atoms. Skipping. Residue ILE 740 is missing expected H atoms. Skipping. Residue LEU 743 is missing expected H atoms. Skipping. Residue ILE 744 is missing expected H atoms. Skipping. Residue LEU 746 is missing expected H atoms. Skipping. Residue ILE 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue LEU 759 is missing expected H atoms. Skipping. Residue VAL 761 is missing expected H atoms. Skipping. Residue LEU 763 is missing expected H atoms. Skipping. Residue VAL 765 is missing expected H atoms. Skipping. Residue TYR 766 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue VAL 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue ILE 778 is missing expected H atoms. Skipping. Residue LEU 782 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 796 is missing expected H atoms. Skipping. Residue THR 801 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue VAL 823 is missing expected H atoms. Skipping. Residue VAL 826 is missing expected H atoms. Skipping. Residue TYR 832 is missing expected H atoms. Skipping. Residue ILE 836 is missing expected H atoms. Skipping. Residue VAL 837 is missing expected H atoms. Skipping. Residue SER 840 is missing expected H atoms. Skipping. Residue SER 841 is missing expected H atoms. Skipping. Residue MET 842 is missing expected H atoms. Skipping. Residue SER 844 is missing expected H atoms. Skipping. Residue ILE 845 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue ILE 852 is missing expected H atoms. Skipping. Residue LEU 865 is missing expected H atoms. Skipping. Residue TYR 866 is missing expected H atoms. Skipping. Residue LEU 867 is missing expected H atoms. Skipping. Residue LEU 868 is missing expected H atoms. Skipping. Residue SER 869 is missing expected H atoms. Skipping. Residue ILE 872 is missing expected H atoms. Skipping. Residue SER 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 889 is missing expected H atoms. Skipping. Residue LEU 907 is missing expected H atoms. Skipping. Residue LEU 908 is missing expected H atoms. Skipping. Residue ILE 911 is missing expected H atoms. Skipping. Residue VAL 918 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue VAL 930 is missing expected H atoms. Skipping. Residue LEU 932 is missing expected H atoms. Skipping. Residue SER 948 is missing expected H atoms. Skipping. Residue SER 949 is missing expected H atoms. Skipping. Residue LEU 950 is missing expected H atoms. Skipping. Residue LYS 978 is missing expected H atoms. Skipping. Residue TYR 982 is missing expected H atoms. Skipping. Residue SER 1005 is missing expected H atoms. Skipping. Residue LEU 1010 is missing expected H atoms. Skipping. Residue LEU 1011 is missing expected H atoms. Skipping. Residue THR 1024 is missing expected H atoms. Skipping. Residue THR 1027 is missing expected H atoms. Skipping. Residue VAL 1028 is missing expected H atoms. Skipping. Residue TYR 1030 is missing expected H atoms. Skipping. Residue LEU 1034 is missing expected H atoms. Skipping. Residue VAL 1035 is missing expected H atoms. Skipping. Residue MET 1037 is missing expected H atoms. Skipping. Residue LEU 1043 is missing expected H atoms. Skipping. Residue LEU 1045 is missing expected H atoms. Skipping. Residue MET 1050 is missing expected H atoms. Skipping. Residue TYR 1052 is missing expected H atoms. Skipping. Residue VAL 1055 is missing expected H atoms. Skipping. Residue LEU 1057 is missing expected H atoms. Skipping. Evaluate side-chains 269 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 223 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 ASP cc_start: 0.8420 (t0) cc_final: 0.8143 (t0) REVERT: B 195 LYS cc_start: 0.9643 (ttpt) cc_final: 0.9374 (ttmm) REVERT: B 284 MET cc_start: 0.9173 (mmp) cc_final: 0.8754 (mmm) REVERT: C 244 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9266 (tt) REVERT: M 262 PHE cc_start: 0.8574 (m-80) cc_final: 0.7813 (m-80) REVERT: M 312 MET cc_start: 0.8344 (mtt) cc_final: 0.8091 (mtt) REVERT: M 393 ARG cc_start: 0.9192 (ttm170) cc_final: 0.8934 (mtp85) REVERT: N 403 MET cc_start: 0.9364 (tpp) cc_final: 0.8979 (tpp) REVERT: N 411 GLU cc_start: 0.8367 (tt0) cc_final: 0.7541 (tt0) outliers start: 46 outliers final: 40 residues processed: 264 average time/residue: 0.7421 time to fit residues: 320.5257 Evaluate side-chains 259 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 218 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 110 TYR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 225 ASN Chi-restraints excluded: chain M residue 249 ARG Chi-restraints excluded: chain M residue 260 TRP Chi-restraints excluded: chain M residue 309 LEU Chi-restraints excluded: chain M residue 356 VAL Chi-restraints excluded: chain M residue 439 ASP Chi-restraints excluded: chain M residue 447 SER Chi-restraints excluded: chain M residue 459 THR Chi-restraints excluded: chain M residue 465 GLU Chi-restraints excluded: chain M residue 545 THR Chi-restraints excluded: chain M residue 571 SER Chi-restraints excluded: chain M residue 662 SER Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 114 LEU Chi-restraints excluded: chain N residue 279 LEU Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 609 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 241 optimal weight: 6.9990 chunk 323 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 280 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 304 optimal weight: 4.9990 chunk 127 optimal weight: 50.0000 chunk 312 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 221 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.121860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.073660 restraints weight = 209532.232| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.58 r_work: 0.2800 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.6537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33077 Z= 0.203 Angle : 0.550 7.251 46500 Z= 0.323 Chirality : 0.038 0.184 5329 Planarity : 0.003 0.047 4905 Dihedral : 23.402 170.128 7695 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.36 % Rotamer: Outliers : 2.32 % Allowed : 20.38 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.15), residues: 3485 helix: 2.46 (0.13), residues: 1737 sheet: -0.63 (0.30), residues: 290 loop : -0.46 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 103 HIS 0.008 0.001 HIS D 44 PHE 0.011 0.001 PHE D 308 TYR 0.019 0.001 TYR M 147 ARG 0.005 0.000 ARG N 308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11145.12 seconds wall clock time: 193 minutes 6.77 seconds (11586.77 seconds total)