Starting phenix.real_space_refine on Sat Apr 13 21:10:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lnb_0929/04_2024/6lnb_0929.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lnb_0929/04_2024/6lnb_0929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lnb_0929/04_2024/6lnb_0929.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lnb_0929/04_2024/6lnb_0929.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lnb_0929/04_2024/6lnb_0929.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lnb_0929/04_2024/6lnb_0929.pdb" } resolution = 3.18 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= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 99 5.49 5 S 146 5.16 5 C 18473 2.51 5 N 5119 2.21 5 O 5746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 37": "NH1" <-> "NH2" Residue "G ARG 178": "NH1" <-> "NH2" Residue "G ARG 210": "NH1" <-> "NH2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F ARG 178": "NH1" <-> "NH2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "E TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 178": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "B TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "H ARG 21": "NH1" <-> "NH2" Residue "H ARG 24": "NH1" <-> "NH2" Residue "H ARG 67": "NH1" <-> "NH2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "H TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 234": "NH1" <-> "NH2" Residue "H ARG 243": "NH1" <-> "NH2" Residue "H ARG 259": "NH1" <-> "NH2" Residue "H PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 503": "NH1" <-> "NH2" Residue "H ARG 584": "NH1" <-> "NH2" Residue "H TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 628": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 125": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "J ARG 20": "NH1" <-> "NH2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 117": "NH1" <-> "NH2" Residue "J ARG 220": "NH1" <-> "NH2" Residue "J ARG 274": "NH1" <-> "NH2" Residue "J ARG 281": "NH1" <-> "NH2" Residue "J ARG 310": "NH1" <-> "NH2" Residue "J ARG 346": "NH1" <-> "NH2" Residue "J TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 5": "NH1" <-> "NH2" Residue "I ARG 20": "NH1" <-> "NH2" Residue "I ARG 58": "NH1" <-> "NH2" Residue "I TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 71": "NH1" <-> "NH2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "I ARG 117": "NH1" <-> "NH2" Residue "I ARG 220": "NH1" <-> "NH2" Residue "I ARG 249": "NH1" <-> "NH2" Residue "I TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 29583 Number of models: 1 Model: "" Number of chains: 13 Chain: "G" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2725 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2685 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 318} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2681 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 2 Chain: "D" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2659 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 315} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2443 Classifications: {'peptide': 301} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 284} Chain breaks: 3 Chain: "H" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4001 Classifications: {'peptide': 510} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 485} Chain breaks: 2 Chain: "A" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1611 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "J" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2937 Classifications: {'peptide': 359} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 339} Chain breaks: 3 Chain: "M" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1276 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 13, 'rna3p_pur': 21, 'rna3p_pyr': 17} Link IDs: {'rna2p': 22, 'rna3p': 37} Chain: "N" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 678 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "O" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 142 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "I" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3070 Classifications: {'peptide': 376} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 357} Chain breaks: 2 Time building chain proxies: 15.74, per 1000 atoms: 0.53 Number of scatterers: 29583 At special positions: 0 Unit cell: (194.4, 158.76, 163.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 146 16.00 P 99 15.00 O 5746 8.00 N 5119 7.00 C 18473 6.00 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: 11.60 Conformation dependent library (CDL) restraints added in 4.5 seconds 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6522 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 42 sheets defined 28.8% alpha, 12.4% beta 18 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 8.29 Creating SS restraints... Processing helix chain 'G' and resid 45 through 49 removed outlier: 3.542A pdb=" N LEU G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA G 49 " --> pdb=" O ALA G 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 49' Processing helix chain 'G' and resid 105 through 123 removed outlier: 3.742A pdb=" N THR G 111 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 137 removed outlier: 3.621A pdb=" N ARG G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU G 133 " --> pdb=" O ALA G 129 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE G 136 " --> pdb=" O TYR G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 183 removed outlier: 3.961A pdb=" N PHE G 181 " --> pdb=" O SER G 177 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS G 182 " --> pdb=" O ARG G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 199 removed outlier: 3.624A pdb=" N GLU G 192 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE G 194 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA G 197 " --> pdb=" O MET G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 269 removed outlier: 3.882A pdb=" N GLY G 265 " --> pdb=" O ALA G 261 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA G 269 " --> pdb=" O GLY G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 313 removed outlier: 4.294A pdb=" N LEU G 310 " --> pdb=" O PHE G 307 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLN G 311 " --> pdb=" O SER G 308 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA G 313 " --> pdb=" O LEU G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 321 removed outlier: 3.505A pdb=" N LEU G 320 " --> pdb=" O TYR G 316 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER G 321 " --> pdb=" O ILE G 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 316 through 321' Processing helix chain 'G' and resid 331 through 344 removed outlier: 3.658A pdb=" N LEU G 337 " --> pdb=" O ASP G 333 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU G 341 " --> pdb=" O LEU G 337 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE G 342 " --> pdb=" O MET G 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 49 removed outlier: 3.798A pdb=" N ALA F 49 " --> pdb=" O ALA F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 123 removed outlier: 3.675A pdb=" N GLN F 110 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR F 111 " --> pdb=" O LYS F 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR F 121 " --> pdb=" O GLU F 117 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 137 removed outlier: 3.807A pdb=" N ARG F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE F 136 " --> pdb=" O TYR F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 183 removed outlier: 3.702A pdb=" N LYS F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 200 removed outlier: 4.095A pdb=" N MET F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE F 194 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA F 197 " --> pdb=" O MET F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 269 removed outlier: 3.548A pdb=" N ILE F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 303 Processing helix chain 'F' and resid 306 through 311 removed outlier: 3.800A pdb=" N GLN F 311 " --> pdb=" O PHE F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 318 removed outlier: 3.527A pdb=" N TYR F 316 " --> pdb=" O GLN F 312 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 312 through 318' Processing helix chain 'F' and resid 328 through 343 removed outlier: 3.722A pdb=" N PHE F 336 " --> pdb=" O ASN F 332 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 67 removed outlier: 3.946A pdb=" N GLN E 67 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 113 removed outlier: 3.794A pdb=" N GLN E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 123 removed outlier: 3.613A pdb=" N GLU E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU E 120 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 135 removed outlier: 3.717A pdb=" N ARG E 131 " --> pdb=" O GLU E 127 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 3.537A pdb=" N LEU E 142 " --> pdb=" O GLY E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 183 Processing helix chain 'E' and resid 187 through 200 removed outlier: 3.609A pdb=" N MET E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE E 194 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA E 197 " --> pdb=" O MET E 193 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 269 removed outlier: 3.533A pdb=" N ALA E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE E 268 " --> pdb=" O THR E 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA E 269 " --> pdb=" O GLY E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 311 removed outlier: 3.924A pdb=" N GLN E 311 " --> pdb=" O PHE E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 321 removed outlier: 3.716A pdb=" N GLU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 337 removed outlier: 3.734A pdb=" N ASP E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 344 removed outlier: 3.605A pdb=" N LYS E 343 " --> pdb=" O ALA E 339 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY E 344 " --> pdb=" O ASN E 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 66 removed outlier: 3.515A pdb=" N LEU D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 66' Processing helix chain 'D' and resid 107 through 123 removed outlier: 3.622A pdb=" N VAL D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU D 120 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.666A pdb=" N ARG D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE D 136 " --> pdb=" O TYR D 132 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN D 138 " --> pdb=" O MET D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 removed outlier: 3.818A pdb=" N LEU D 142 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP D 143 " --> pdb=" O LYS D 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 139 through 143' Processing helix chain 'D' and resid 177 through 182 removed outlier: 3.517A pdb=" N PHE D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 177 through 182' Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'D' and resid 191 through 200 removed outlier: 3.581A pdb=" N LYS D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA D 197 " --> pdb=" O MET D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 266 removed outlier: 3.603A pdb=" N THR D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 311 Processing helix chain 'D' and resid 312 through 320 removed outlier: 3.652A pdb=" N GLU D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 339 Processing helix chain 'D' and resid 339 through 344 removed outlier: 3.535A pdb=" N LYS D 343 " --> pdb=" O ALA D 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 105 through 123 removed outlier: 3.814A pdb=" N GLN C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C 123 " --> pdb=" O TYR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 137 removed outlier: 3.912A pdb=" N THR C 130 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 136 " --> pdb=" O TYR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 removed outlier: 4.072A pdb=" N PHE C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN C 183 " --> pdb=" O GLN C 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 183' Processing helix chain 'C' and resid 190 through 198 removed outlier: 3.825A pdb=" N LYS C 195 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA C 197 " --> pdb=" O MET C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 269 removed outlier: 3.780A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 311 removed outlier: 3.517A pdb=" N ILE C 309 " --> pdb=" O ASP C 305 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN C 311 " --> pdb=" O PHE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.649A pdb=" N GLU C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU C 320 " --> pdb=" O TYR C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 344 removed outlier: 3.619A pdb=" N PHE C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 341 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 342 " --> pdb=" O MET C 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 123 removed outlier: 3.678A pdb=" N THR B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.894A pdb=" N ARG B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 136 " --> pdb=" O TYR B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 175 Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.671A pdb=" N PHE B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 262 through 269 removed outlier: 3.638A pdb=" N ALA B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 removed outlier: 3.794A pdb=" N GLN B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 321 removed outlier: 4.301A pdb=" N GLU B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL B 319 " --> pdb=" O HIS B 315 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 320 " --> pdb=" O TYR B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 342 Processing helix chain 'H' and resid 15 through 18 removed outlier: 4.030A pdb=" N GLU H 18 " --> pdb=" O LEU H 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 15 through 18' Processing helix chain 'H' and resid 19 through 24 removed outlier: 3.719A pdb=" N ARG H 24 " --> pdb=" O LYS H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 44 removed outlier: 4.250A pdb=" N ILE H 42 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL H 44 " --> pdb=" O LEU H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 77 removed outlier: 3.961A pdb=" N SER H 74 " --> pdb=" O LYS H 70 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN H 77 " --> pdb=" O ALA H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 131 removed outlier: 3.664A pdb=" N VAL H 130 " --> pdb=" O SER H 127 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASN H 131 " --> pdb=" O LYS H 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 127 through 131' Processing helix chain 'H' and resid 174 through 181 removed outlier: 3.781A pdb=" N ALA H 178 " --> pdb=" O CYS H 174 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 227 Processing helix chain 'H' and resid 249 through 254 removed outlier: 3.830A pdb=" N CYS H 254 " --> pdb=" O THR H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 427 removed outlier: 3.751A pdb=" N PHE H 415 " --> pdb=" O SER H 411 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL H 419 " --> pdb=" O PHE H 415 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE H 422 " --> pdb=" O PHE H 418 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN H 425 " --> pdb=" O ALA H 421 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE H 426 " --> pdb=" O PHE H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 499 Processing helix chain 'H' and resid 527 through 531 removed outlier: 3.563A pdb=" N SER H 531 " --> pdb=" O ALA H 528 " (cutoff:3.500A) Processing helix chain 'H' and resid 549 through 561 removed outlier: 4.102A pdb=" N LEU H 553 " --> pdb=" O ASN H 549 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU H 559 " --> pdb=" O ALA H 555 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP H 560 " --> pdb=" O ALA H 556 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 586 removed outlier: 4.260A pdb=" N TYR H 586 " --> pdb=" O LEU H 583 " (cutoff:3.500A) Processing helix chain 'H' and resid 608 through 612 removed outlier: 3.608A pdb=" N THR H 611 " --> pdb=" O ASP H 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 30 removed outlier: 3.634A pdb=" N LEU A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 28 " --> pdb=" O CYS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 69 Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.801A pdb=" N ARG A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 21 removed outlier: 3.929A pdb=" N PHE J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE J 19 " --> pdb=" O GLU J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 43 Processing helix chain 'J' and resid 48 through 52 removed outlier: 4.218A pdb=" N THR J 51 " --> pdb=" O GLY J 48 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE J 52 " --> pdb=" O TYR J 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 48 through 52' Processing helix chain 'J' and resid 67 through 77 removed outlier: 3.898A pdb=" N ALA J 73 " --> pdb=" O SER J 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS J 77 " --> pdb=" O ALA J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 206 removed outlier: 3.615A pdb=" N VAL J 200 " --> pdb=" O ALA J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 231 removed outlier: 3.812A pdb=" N HIS J 225 " --> pdb=" O TRP J 221 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TRP J 226 " --> pdb=" O GLY J 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 242 removed outlier: 3.644A pdb=" N GLN J 242 " --> pdb=" O PHE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 255 removed outlier: 4.382A pdb=" N PHE J 251 " --> pdb=" O TRP J 247 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N HIS J 252 " --> pdb=" O PRO J 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 308 Processing helix chain 'J' and resid 328 through 333 Processing helix chain 'J' and resid 338 through 343 removed outlier: 3.541A pdb=" N VAL J 343 " --> pdb=" O ILE J 339 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 380 removed outlier: 3.517A pdb=" N CYS J 374 " --> pdb=" O GLY J 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 24 removed outlier: 3.563A pdb=" N PHE I 17 " --> pdb=" O SER I 13 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE I 18 " --> pdb=" O LEU I 14 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS I 24 " --> pdb=" O ARG I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 45 Processing helix chain 'I' and resid 46 through 50 removed outlier: 4.183A pdb=" N GLN I 50 " --> pdb=" O ASN I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 81 removed outlier: 3.621A pdb=" N GLN I 80 " --> pdb=" O LEU I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 135 removed outlier: 3.511A pdb=" N LEU I 132 " --> pdb=" O CYS I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 144 removed outlier: 3.868A pdb=" N TRP I 142 " --> pdb=" O SER I 139 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS I 143 " --> pdb=" O TYR I 140 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE I 144 " --> pdb=" O LEU I 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 139 through 144' Processing helix chain 'I' and resid 196 through 202 Processing helix chain 'I' and resid 219 through 232 removed outlier: 3.555A pdb=" N LYS I 231 " --> pdb=" O TRP I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 246 Processing helix chain 'I' and resid 248 through 265 removed outlier: 3.923A pdb=" N HIS I 252 " --> pdb=" O PRO I 248 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER I 253 " --> pdb=" O ARG I 249 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE I 254 " --> pdb=" O SER I 250 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU I 263 " --> pdb=" O VAL I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 302 removed outlier: 3.553A pdb=" N GLY I 301 " --> pdb=" O ASN I 297 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 310 removed outlier: 3.522A pdb=" N ARG I 310 " --> pdb=" O TYR I 306 " (cutoff:3.500A) Processing helix chain 'I' and resid 325 through 332 removed outlier: 3.995A pdb=" N THR I 329 " --> pdb=" O ALA I 325 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 345 removed outlier: 3.553A pdb=" N ALA I 340 " --> pdb=" O LEU I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 374 removed outlier: 3.645A pdb=" N CYS I 374 " --> pdb=" O GLY I 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 391 removed outlier: 3.775A pdb=" N TYR I 390 " --> pdb=" O ARG I 387 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL I 391 " --> pdb=" O SER I 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 387 through 391' Processing sheet with id=AA1, first strand: chain 'G' and resid 29 through 31 removed outlier: 3.863A pdb=" N HIS G 84 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA G 211 " --> pdb=" O CYS G 87 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS G 151 " --> pdb=" O HIS G 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 35 through 40 removed outlier: 3.539A pdb=" N ASN G 35 " --> pdb=" O PHE G 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 248 through 251 Processing sheet with id=AA4, first strand: chain 'G' and resid 270 through 272 removed outlier: 3.521A pdb=" N ASP G 272 " --> pdb=" O LEU G 282 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 13 through 14 Processing sheet with id=AA6, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.995A pdb=" N CYS F 151 " --> pdb=" O HIS F 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 35 through 41 Processing sheet with id=AA8, first strand: chain 'F' and resid 248 through 249 Processing sheet with id=AA9, first strand: chain 'F' and resid 270 through 272 Processing sheet with id=AB1, first strand: chain 'E' and resid 8 through 9 Processing sheet with id=AB2, first strand: chain 'E' and resid 13 through 15 removed outlier: 3.691A pdb=" N HIS E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 13 through 15 removed outlier: 3.515A pdb=" N CYS E 151 " --> pdb=" O HIS E 214 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AB5, first strand: chain 'E' and resid 248 through 251 Processing sheet with id=AB6, first strand: chain 'E' and resid 270 through 272 Processing sheet with id=AB7, first strand: chain 'D' and resid 8 through 9 removed outlier: 3.865A pdb=" N GLY D 345 " --> pdb=" O TYR D 9 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 28 through 31 removed outlier: 3.747A pdb=" N ARG D 28 " --> pdb=" O TRP D 24 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS D 84 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS D 151 " --> pdb=" O HIS D 214 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 35 through 40 Processing sheet with id=AC1, first strand: chain 'D' and resid 248 through 251 Processing sheet with id=AC2, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AC3, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.796A pdb=" N CYS C 151 " --> pdb=" O HIS C 214 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 35 through 41 removed outlier: 3.757A pdb=" N HIS C 71 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 248 through 251 Processing sheet with id=AC6, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AC7, first strand: chain 'B' and resid 8 through 9 removed outlier: 3.574A pdb=" N GLY B 345 " --> pdb=" O TYR B 9 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.560A pdb=" N CYS B 19 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 88 " --> pdb=" O CYS B 19 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS B 84 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N CYS B 151 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 166 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.598A pdb=" N THR A 144 " --> pdb=" O SER B 36 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 248 through 251 removed outlier: 3.520A pdb=" N GLU B 254 " --> pdb=" O ILE B 251 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 270 through 272 Processing sheet with id=AD3, first strand: chain 'H' and resid 85 through 86 removed outlier: 4.017A pdb=" N ALA H 217 " --> pdb=" O ASN H 86 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 97 through 98 Processing sheet with id=AD5, first strand: chain 'H' and resid 201 through 204 removed outlier: 8.603A pdb=" N ALA H 589 " --> pdb=" O TYR H 210 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER H 212 " --> pdb=" O ALA H 589 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ALA H 591 " --> pdb=" O SER H 212 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N SER H 214 " --> pdb=" O ALA H 591 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N CYS H 593 " --> pdb=" O SER H 214 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE H 590 " --> pdb=" O LEU H 572 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU H 572 " --> pdb=" O ILE H 590 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLU H 592 " --> pdb=" O TYR H 570 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR H 570 " --> pdb=" O GLU H 592 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE H 594 " --> pdb=" O VAL H 568 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER H 566 " --> pdb=" O GLY H 596 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 439 through 444 removed outlier: 6.494A pdb=" N VAL H 478 " --> pdb=" O HIS H 443 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU H 481 " --> pdb=" O PRO H 391 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU H 483 " --> pdb=" O VAL H 389 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL H 389 " --> pdb=" O LEU H 483 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 398 through 399 Processing sheet with id=AD8, first strand: chain 'H' and resid 457 through 458 removed outlier: 3.635A pdb=" N SER H 465 " --> pdb=" O VAL H 457 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 614 through 616 removed outlier: 3.720A pdb=" N GLN H 626 " --> pdb=" O SER H 615 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 4 through 5 removed outlier: 3.575A pdb=" N TYR A 5 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL A 90 " --> pdb=" O TYR A 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'A' and resid 101 through 103 removed outlier: 4.360A pdb=" N ARG A 102 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG A 168 " --> pdb=" O ARG A 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'A' and resid 152 through 155 Processing sheet with id=AE4, first strand: chain 'J' and resid 108 through 109 removed outlier: 4.325A pdb=" N VAL J 108 " --> pdb=" O PHE J 115 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 94 through 96 Processing sheet with id=AE6, first strand: chain 'I' and resid 273 through 274 removed outlier: 6.629A pdb=" N LEU I 273 " --> pdb=" O LYS I 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 672 hydrogen bonds defined for protein. 1836 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 8.85 Time building geometry restraints manager: 12.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7733 1.33 - 1.45: 7137 1.45 - 1.58: 15267 1.58 - 1.70: 197 1.70 - 1.82: 209 Bond restraints: 30543 Sorted by residual: bond pdb=" C1' U M 39 " pdb=" N1 U M 39 " ideal model delta sigma weight residual 1.480 1.560 -0.080 1.50e-02 4.44e+03 2.85e+01 bond pdb=" C LYS I 210 " pdb=" N PRO I 211 " ideal model delta sigma weight residual 1.334 1.363 -0.029 8.40e-03 1.42e+04 1.20e+01 bond pdb=" N VAL J 30 " pdb=" CA VAL J 30 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.31e+00 bond pdb=" N ASP J 29 " pdb=" CA ASP J 29 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.82e+00 bond pdb=" N TYR J 27 " pdb=" CA TYR J 27 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 7.02e+00 ... (remaining 30538 not shown) Histogram of bond angle deviations from ideal: 96.78 - 105.71: 1106 105.71 - 114.64: 17962 114.64 - 123.57: 20991 123.57 - 132.49: 1749 132.49 - 141.42: 90 Bond angle restraints: 41898 Sorted by residual: angle pdb=" C GLU H 575 " pdb=" N PRO H 576 " pdb=" CA PRO H 576 " ideal model delta sigma weight residual 127.00 141.42 -14.42 2.40e+00 1.74e-01 3.61e+01 angle pdb=" C CYS G 103 " pdb=" N ASN G 104 " pdb=" CA ASN G 104 " ideal model delta sigma weight residual 123.93 132.82 -8.89 1.54e+00 4.22e-01 3.33e+01 angle pdb=" C GLU H 575 " pdb=" N PRO H 576 " pdb=" CD PRO H 576 " ideal model delta sigma weight residual 120.60 107.91 12.69 2.20e+00 2.07e-01 3.33e+01 angle pdb=" C LEU C 142 " pdb=" N TRP C 143 " pdb=" CA TRP C 143 " ideal model delta sigma weight residual 121.54 131.83 -10.29 1.91e+00 2.74e-01 2.90e+01 angle pdb=" N ARG J 39 " pdb=" CA ARG J 39 " pdb=" C ARG J 39 " ideal model delta sigma weight residual 111.69 105.14 6.55 1.23e+00 6.61e-01 2.83e+01 ... (remaining 41893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 17705 35.63 - 71.26: 389 71.26 - 106.89: 30 106.89 - 142.53: 1 142.53 - 178.16: 3 Dihedral angle restraints: 18128 sinusoidal: 8090 harmonic: 10038 Sorted by residual: dihedral pdb=" CA LYS J 7 " pdb=" C LYS J 7 " pdb=" N PRO J 8 " pdb=" CA PRO J 8 " ideal model delta harmonic sigma weight residual -180.00 -131.59 -48.41 0 5.00e+00 4.00e-02 9.37e+01 dihedral pdb=" O4' C M 20 " pdb=" C1' C M 20 " pdb=" N1 C M 20 " pdb=" C2 C M 20 " ideal model delta sinusoidal sigma weight residual -128.00 50.16 -178.16 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C M 38 " pdb=" C1' C M 38 " pdb=" N1 C M 38 " pdb=" C2 C M 38 " ideal model delta sinusoidal sigma weight residual 232.00 78.43 153.57 1 1.70e+01 3.46e-03 6.30e+01 ... (remaining 18125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 4136 0.092 - 0.184: 466 0.184 - 0.276: 26 0.276 - 0.368: 1 0.368 - 0.460: 2 Chirality restraints: 4631 Sorted by residual: chirality pdb=" CB ILE J 94 " pdb=" CA ILE J 94 " pdb=" CG1 ILE J 94 " pdb=" CG2 ILE J 94 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" CB ILE H 534 " pdb=" CA ILE H 534 " pdb=" CG1 ILE H 534 " pdb=" CG2 ILE H 534 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CA ASP J 29 " pdb=" N ASP J 29 " pdb=" C ASP J 29 " pdb=" CB ASP J 29 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 4628 not shown) Planarity restraints: 5001 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 9 " 0.019 2.00e-02 2.50e+03 2.18e-02 9.49e+00 pdb=" CG TYR D 9 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR D 9 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR D 9 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 9 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR D 9 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR D 9 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 9 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU J 289 " -0.045 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO J 290 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO J 290 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO J 290 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 9 " -0.016 2.00e-02 2.50e+03 1.84e-02 6.81e+00 pdb=" CG TYR F 9 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR F 9 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR F 9 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 9 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR F 9 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR F 9 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 9 " -0.000 2.00e-02 2.50e+03 ... (remaining 4998 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2739 2.74 - 3.28: 26326 3.28 - 3.82: 46427 3.82 - 4.36: 56459 4.36 - 4.90: 95932 Nonbonded interactions: 227883 Sorted by model distance: nonbonded pdb=" OG SER A 187 " pdb=" O GLN A 194 " model vdw 2.202 2.440 nonbonded pdb=" CD2 LEU J 3 " pdb=" CZ PHE J 33 " model vdw 2.223 3.760 nonbonded pdb=" O TYR G 9 " pdb=" O2' U M 5 " model vdw 2.246 2.440 nonbonded pdb=" O SER H 133 " pdb=" OG1 THR H 137 " model vdw 2.262 2.440 nonbonded pdb=" OG SER J 102 " pdb=" O ILE J 287 " model vdw 2.262 2.440 ... (remaining 227878 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 'B' and (resid 2 through 228 or resid 243 through 349)) selection = (chain 'C' and (resid 2 through 38 or resid 70 through 228 or resid 243 through \ 321 or resid 326 through 349)) selection = (chain 'D' and (resid 2 through 38 or resid 70 through 228 or resid 243 through \ 321 or resid 326 through 349)) selection = (chain 'E' and (resid 2 through 38 or resid 70 through 228 or resid 243 through \ 321 or resid 326 through 349)) selection = (chain 'F' and (resid 2 through 38 or resid 70 through 228 or resid 243 through \ 321 or resid 326 through 349)) selection = (chain 'G' and (resid 2 through 38 or resid 70 through 228 or resid 243 through \ 321 or resid 326 through 349)) } ncs_group { reference = (chain 'I' and (resid 1 through 172 or resid 195 through 232 or resid 236 throug \ h 393)) selection = chain 'J' } 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.040 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 77.010 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 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 : 0.006 0.080 30543 Z= 0.398 Angle : 1.070 14.792 41898 Z= 0.576 Chirality : 0.059 0.460 4631 Planarity : 0.008 0.069 5001 Dihedral : 14.600 178.157 11606 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 0.50 % Allowed : 3.64 % Favored : 95.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 1.22 % 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: -5.23 (0.11), residues: 3369 helix: -4.69 (0.06), residues: 887 sheet: -1.77 (0.21), residues: 533 loop : -3.50 (0.11), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 159 HIS 0.024 0.002 HIS C 290 PHE 0.033 0.003 PHE A 10 TYR 0.050 0.004 TYR D 9 ARG 0.017 0.001 ARG G 286 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 461 time to evaluate : 3.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 229 GLU cc_start: 0.6755 (tm-30) cc_final: 0.6460 (tt0) REVERT: G 301 SER cc_start: 0.8497 (p) cc_final: 0.8230 (m) REVERT: G 309 ILE cc_start: 0.8431 (mt) cc_final: 0.8160 (mm) REVERT: G 338 MET cc_start: 0.8325 (mmt) cc_final: 0.8012 (mmt) REVERT: G 349 HIS cc_start: 0.6045 (t70) cc_final: 0.5822 (t-170) REVERT: F 180 ASP cc_start: 0.7372 (m-30) cc_final: 0.7018 (m-30) REVERT: E 35 ASN cc_start: 0.8055 (m-40) cc_final: 0.7617 (m110) REVERT: E 63 GLU cc_start: 0.7555 (tp30) cc_final: 0.7119 (tt0) REVERT: E 202 ASP cc_start: 0.7124 (p0) cc_final: 0.6728 (t0) REVERT: D 110 GLN cc_start: 0.6972 (mp-120) cc_final: 0.6723 (mm-40) REVERT: D 217 THR cc_start: 0.8610 (p) cc_final: 0.8399 (t) REVERT: D 228 THR cc_start: 0.6964 (t) cc_final: 0.6759 (p) REVERT: C 74 ASP cc_start: 0.8123 (m-30) cc_final: 0.7870 (m-30) REVERT: C 165 LYS cc_start: 0.7742 (mtmm) cc_final: 0.7372 (mtmm) REVERT: C 210 ARG cc_start: 0.6961 (tpp80) cc_final: 0.6716 (ttm-80) REVERT: B 148 LYS cc_start: 0.7772 (mmtm) cc_final: 0.7072 (tppt) REVERT: H 63 LYS cc_start: 0.5679 (OUTLIER) cc_final: 0.4747 (mttt) REVERT: H 93 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6038 (ptt90) REVERT: H 526 GLU cc_start: 0.6849 (mp0) cc_final: 0.6417 (mp0) REVERT: H 535 GLU cc_start: 0.7345 (tm-30) cc_final: 0.7026 (mm-30) REVERT: H 558 THR cc_start: 0.5874 (t) cc_final: 0.5559 (m) outliers start: 15 outliers final: 4 residues processed: 475 average time/residue: 0.4865 time to fit residues: 350.0831 Evaluate side-chains 276 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 270 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain I residue 278 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 293 optimal weight: 40.0000 chunk 263 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 177 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 271 optimal weight: 0.3980 chunk 105 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 315 optimal weight: 50.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 72 GLN ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN G 184 ASN F 114 GLN F 135 ASN ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 GLN F 340 ASN E 183 ASN E 184 ASN E 290 HIS D 104 ASN ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 ASN D 299 HIS C 145 ASN C 162 ASN C 290 HIS C 340 ASN B 104 ASN B 174 ASN B 348 GLN B 349 HIS ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 420 HIS H 548 ASN H 581 ASN ** H 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 HIS A 85 HIS A 143 HIS A 150 HIS A 178 ASN J 153 HIS J 237 HIS J 351 ASN J 381 GLN I 23 ASN I 25 ASN I 31 HIS I 154 ASN I 207 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 30543 Z= 0.338 Angle : 0.766 10.376 41898 Z= 0.406 Chirality : 0.047 0.207 4631 Planarity : 0.007 0.084 5001 Dihedral : 16.800 174.370 5088 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.96 % Favored : 88.04 % Rotamer: Outliers : 2.18 % Allowed : 7.87 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 1.22 % 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: -4.37 (0.12), residues: 3369 helix: -3.35 (0.12), residues: 929 sheet: -1.13 (0.22), residues: 509 loop : -3.30 (0.12), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 159 HIS 0.013 0.002 HIS C 290 PHE 0.024 0.002 PHE A 10 TYR 0.028 0.002 TYR D 9 ARG 0.007 0.001 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 274 time to evaluate : 3.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 114 GLN cc_start: 0.7788 (tt0) cc_final: 0.7582 (tt0) REVERT: G 202 ASP cc_start: 0.6620 (m-30) cc_final: 0.6341 (m-30) REVERT: G 349 HIS cc_start: 0.5943 (t70) cc_final: 0.5718 (t-170) REVERT: F 180 ASP cc_start: 0.7205 (m-30) cc_final: 0.6907 (m-30) REVERT: E 63 GLU cc_start: 0.7681 (tp30) cc_final: 0.7250 (tt0) REVERT: C 165 LYS cc_start: 0.7626 (mtmm) cc_final: 0.7219 (mtmm) REVERT: C 346 MET cc_start: 0.8085 (mmm) cc_final: 0.7811 (mtt) REVERT: B 176 THR cc_start: 0.6640 (p) cc_final: 0.6398 (t) REVERT: H 63 LYS cc_start: 0.5877 (OUTLIER) cc_final: 0.4837 (mttt) REVERT: H 175 LYS cc_start: 0.6434 (mptt) cc_final: 0.5497 (tttm) REVERT: H 535 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6916 (mm-30) outliers start: 66 outliers final: 41 residues processed: 324 average time/residue: 0.4326 time to fit residues: 222.2807 Evaluate side-chains 289 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 247 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 269 SER Chi-restraints excluded: chain H residue 517 LYS Chi-restraints excluded: chain H residue 557 MET Chi-restraints excluded: chain H residue 583 LEU Chi-restraints excluded: chain H residue 617 LYS Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain I residue 278 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 262 optimal weight: 20.0000 chunk 214 optimal weight: 0.0980 chunk 86 optimal weight: 3.9990 chunk 315 optimal weight: 50.0000 chunk 341 optimal weight: 10.0000 chunk 281 optimal weight: 50.0000 chunk 313 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 253 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN D 174 ASN C 162 ASN C 349 HIS B 332 ASN B 335 HIS ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 484 ASN H 548 ASN ** H 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30543 Z= 0.286 Angle : 0.691 9.345 41898 Z= 0.366 Chirality : 0.045 0.206 4631 Planarity : 0.006 0.069 5001 Dihedral : 16.678 175.252 5087 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 2.78 % Allowed : 9.65 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 1.22 % 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: -3.76 (0.13), residues: 3369 helix: -2.48 (0.15), residues: 929 sheet: -0.87 (0.22), residues: 517 loop : -3.10 (0.12), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 143 HIS 0.008 0.001 HIS B 84 PHE 0.024 0.002 PHE A 10 TYR 0.022 0.002 TYR J 62 ARG 0.006 0.001 ARG D 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 270 time to evaluate : 3.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 114 GLN cc_start: 0.7837 (tt0) cc_final: 0.7586 (tt0) REVERT: G 117 GLU cc_start: 0.6184 (mm-30) cc_final: 0.5929 (mm-30) REVERT: G 349 HIS cc_start: 0.5997 (t70) cc_final: 0.5719 (t-170) REVERT: F 180 ASP cc_start: 0.7257 (m-30) cc_final: 0.6955 (m-30) REVERT: E 63 GLU cc_start: 0.7624 (tp30) cc_final: 0.7272 (tt0) REVERT: E 96 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: E 104 ASN cc_start: 0.8776 (OUTLIER) cc_final: 0.8540 (t0) REVERT: C 165 LYS cc_start: 0.7424 (mtmm) cc_final: 0.7024 (mtmm) REVERT: C 172 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6795 (mtt-85) REVERT: B 176 THR cc_start: 0.6615 (p) cc_final: 0.6396 (t) REVERT: H 63 LYS cc_start: 0.5941 (OUTLIER) cc_final: 0.4836 (mttt) REVERT: H 175 LYS cc_start: 0.6480 (mptt) cc_final: 0.5554 (tttm) REVERT: H 247 MET cc_start: 0.6335 (mmm) cc_final: 0.6120 (mtm) REVERT: H 458 GLU cc_start: 0.6783 (tp30) cc_final: 0.6207 (pm20) REVERT: H 535 GLU cc_start: 0.7340 (tm-30) cc_final: 0.6941 (mm-30) REVERT: H 614 TRP cc_start: 0.8200 (OUTLIER) cc_final: 0.7734 (m100) REVERT: A 125 ARG cc_start: 0.5348 (OUTLIER) cc_final: 0.4644 (ppp80) REVERT: I 321 LEU cc_start: 0.4357 (mm) cc_final: 0.4109 (mt) outliers start: 84 outliers final: 55 residues processed: 331 average time/residue: 0.4223 time to fit residues: 223.7119 Evaluate side-chains 295 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 234 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 334 MET Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 315 HIS Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 269 SER Chi-restraints excluded: chain H residue 517 LYS Chi-restraints excluded: chain H residue 557 MET Chi-restraints excluded: chain H residue 583 LEU Chi-restraints excluded: chain H residue 614 TRP Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain I residue 278 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 311 optimal weight: 30.0000 chunk 237 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 150 optimal weight: 0.1980 chunk 211 optimal weight: 9.9990 chunk 316 optimal weight: 20.0000 chunk 335 optimal weight: 9.9990 chunk 165 optimal weight: 0.9990 chunk 300 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 299 HIS ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN D 179 GLN D 183 ASN C 162 ASN B 214 HIS B 332 ASN ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 545 GLN H 548 ASN ** H 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30543 Z= 0.267 Angle : 0.668 8.987 41898 Z= 0.353 Chirality : 0.045 0.206 4631 Planarity : 0.006 0.065 5001 Dihedral : 16.606 175.282 5087 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 3.70 % Allowed : 9.95 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 1.22 % 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: -3.48 (0.13), residues: 3369 helix: -2.08 (0.16), residues: 947 sheet: -0.85 (0.22), residues: 541 loop : -3.00 (0.12), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 143 HIS 0.007 0.001 HIS B 84 PHE 0.022 0.002 PHE A 10 TYR 0.019 0.002 TYR J 62 ARG 0.006 0.001 ARG E 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 245 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 334 MET cc_start: 0.6569 (mtp) cc_final: 0.6261 (mtp) REVERT: G 349 HIS cc_start: 0.6056 (t70) cc_final: 0.5817 (t-170) REVERT: F 180 ASP cc_start: 0.7242 (m-30) cc_final: 0.6962 (m-30) REVERT: F 186 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7576 (m-40) REVERT: E 63 GLU cc_start: 0.7592 (tp30) cc_final: 0.7344 (tt0) REVERT: E 65 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8270 (mp) REVERT: E 96 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: E 104 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8532 (t0) REVERT: C 23 VAL cc_start: 0.8094 (OUTLIER) cc_final: 0.7856 (t) REVERT: C 165 LYS cc_start: 0.7437 (mtmm) cc_final: 0.7063 (mtmm) REVERT: C 172 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6717 (mtt-85) REVERT: H 63 LYS cc_start: 0.6119 (OUTLIER) cc_final: 0.4954 (mttt) REVERT: H 175 LYS cc_start: 0.6514 (mptt) cc_final: 0.6219 (tptp) REVERT: H 535 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6919 (mm-30) REVERT: A 125 ARG cc_start: 0.5474 (OUTLIER) cc_final: 0.4756 (ppp80) outliers start: 112 outliers final: 67 residues processed: 331 average time/residue: 0.4765 time to fit residues: 257.2232 Evaluate side-chains 314 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 239 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 334 MET Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 315 HIS Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 269 SER Chi-restraints excluded: chain H residue 517 LYS Chi-restraints excluded: chain H residue 557 MET Chi-restraints excluded: chain H residue 583 LEU Chi-restraints excluded: chain H residue 624 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 304 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 279 optimal weight: 7.9990 chunk 190 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 249 optimal weight: 20.0000 chunk 138 optimal weight: 1.9990 chunk 286 optimal weight: 5.9990 chunk 231 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 301 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN C 162 ASN H 83 GLN ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 548 ASN ** H 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30543 Z= 0.259 Angle : 0.656 8.699 41898 Z= 0.346 Chirality : 0.044 0.205 4631 Planarity : 0.005 0.062 5001 Dihedral : 16.559 175.392 5087 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 3.57 % Allowed : 11.31 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 1.22 % 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: -3.27 (0.13), residues: 3369 helix: -1.86 (0.16), residues: 945 sheet: -0.67 (0.23), residues: 529 loop : -2.91 (0.12), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 143 HIS 0.007 0.001 HIS B 84 PHE 0.017 0.001 PHE A 10 TYR 0.017 0.002 TYR J 62 ARG 0.007 0.000 ARG H 428 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 240 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 349 HIS cc_start: 0.6127 (t70) cc_final: 0.5894 (t-170) REVERT: F 11 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7735 (mtt90) REVERT: F 96 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.6726 (mt-10) REVERT: F 180 ASP cc_start: 0.7318 (m-30) cc_final: 0.7047 (m-30) REVERT: F 346 MET cc_start: 0.7442 (mtp) cc_final: 0.7162 (mtp) REVERT: E 63 GLU cc_start: 0.7572 (tp30) cc_final: 0.7284 (tt0) REVERT: E 65 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8255 (mp) REVERT: E 96 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6792 (mp0) REVERT: E 104 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8563 (t0) REVERT: D 110 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6241 (mp10) REVERT: C 17 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7807 (p0) REVERT: C 23 VAL cc_start: 0.8086 (OUTLIER) cc_final: 0.7854 (t) REVERT: C 165 LYS cc_start: 0.7438 (mtmm) cc_final: 0.7082 (mtmm) REVERT: C 172 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6719 (mtt-85) REVERT: H 63 LYS cc_start: 0.5937 (OUTLIER) cc_final: 0.4991 (mttt) REVERT: H 175 LYS cc_start: 0.6503 (mptt) cc_final: 0.6263 (tptp) REVERT: H 514 ASP cc_start: 0.5908 (p0) cc_final: 0.5690 (t0) REVERT: H 535 GLU cc_start: 0.7308 (tm-30) cc_final: 0.6883 (mm-30) REVERT: A 125 ARG cc_start: 0.5372 (OUTLIER) cc_final: 0.4603 (ppp80) outliers start: 108 outliers final: 77 residues processed: 325 average time/residue: 0.4213 time to fit residues: 220.2189 Evaluate side-chains 323 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 235 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 334 MET Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 269 SER Chi-restraints excluded: chain H residue 517 LYS Chi-restraints excluded: chain H residue 552 ASP Chi-restraints excluded: chain H residue 557 MET Chi-restraints excluded: chain H residue 575 GLU Chi-restraints excluded: chain H residue 583 LEU Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 624 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 304 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 112 optimal weight: 3.9990 chunk 302 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 196 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 335 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 chunk 155 optimal weight: 0.0980 chunk 27 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 176 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 ASN C 71 HIS C 162 ASN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 548 ASN I 265 HIS ** I 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30543 Z= 0.187 Angle : 0.595 8.029 41898 Z= 0.315 Chirality : 0.042 0.199 4631 Planarity : 0.005 0.061 5001 Dihedral : 16.387 175.693 5087 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer: Outliers : 3.50 % Allowed : 12.17 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 0.61 % 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: -3.00 (0.13), residues: 3369 helix: -1.56 (0.17), residues: 946 sheet: -0.53 (0.23), residues: 528 loop : -2.78 (0.13), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 143 HIS 0.006 0.001 HIS B 84 PHE 0.016 0.001 PHE G 89 TYR 0.017 0.001 TYR C 275 ARG 0.007 0.000 ARG H 428 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 260 time to evaluate : 3.162 Fit side-chains revert: symmetry clash REVERT: G 112 LEU cc_start: 0.8230 (mm) cc_final: 0.7830 (mm) REVERT: F 96 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6819 (mt-10) REVERT: F 180 ASP cc_start: 0.7319 (m-30) cc_final: 0.7062 (m-30) REVERT: F 346 MET cc_start: 0.7425 (mtp) cc_final: 0.7150 (mtp) REVERT: E 63 GLU cc_start: 0.7583 (tp30) cc_final: 0.7274 (tt0) REVERT: E 65 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8193 (mp) REVERT: E 96 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6423 (mp0) REVERT: D 110 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6276 (mp10) REVERT: D 210 ARG cc_start: 0.7413 (tpt170) cc_final: 0.7163 (tpt170) REVERT: C 17 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7737 (p0) REVERT: C 23 VAL cc_start: 0.8091 (OUTLIER) cc_final: 0.7851 (t) REVERT: C 165 LYS cc_start: 0.7407 (mtmm) cc_final: 0.7036 (mtmm) REVERT: C 172 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6913 (mtt-85) REVERT: H 63 LYS cc_start: 0.5937 (OUTLIER) cc_final: 0.4927 (mttt) REVERT: H 175 LYS cc_start: 0.6342 (mptt) cc_final: 0.5757 (tttm) REVERT: H 517 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7606 (ptmm) REVERT: H 535 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6873 (mm-30) REVERT: A 125 ARG cc_start: 0.5352 (OUTLIER) cc_final: 0.4581 (ppp80) REVERT: J 89 LEU cc_start: 0.2470 (OUTLIER) cc_final: 0.2220 (tm) outliers start: 106 outliers final: 63 residues processed: 342 average time/residue: 0.4283 time to fit residues: 232.8121 Evaluate side-chains 316 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 242 time to evaluate : 3.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 269 SER Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 517 LYS Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 575 GLU Chi-restraints excluded: chain H residue 583 LEU Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 624 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 304 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 323 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 245 optimal weight: 9.9990 chunk 189 optimal weight: 0.9980 chunk 282 optimal weight: 10.0000 chunk 187 optimal weight: 0.9990 chunk 334 optimal weight: 50.0000 chunk 209 optimal weight: 20.0000 chunk 203 optimal weight: 0.0270 chunk 154 optimal weight: 5.9990 overall best weight: 2.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 114 GLN G 349 HIS ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN C 162 ASN ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 548 ASN I 313 GLN I 381 GLN I 386 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 30543 Z= 0.321 Angle : 0.694 10.075 41898 Z= 0.366 Chirality : 0.046 0.205 4631 Planarity : 0.006 0.077 5001 Dihedral : 16.517 175.241 5087 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.35 % Favored : 87.65 % Rotamer: Outliers : 3.67 % Allowed : 12.76 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 0.61 % 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: -3.05 (0.13), residues: 3369 helix: -1.59 (0.16), residues: 942 sheet: -0.60 (0.23), residues: 521 loop : -2.78 (0.13), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 143 HIS 0.006 0.001 HIS H 272 PHE 0.020 0.002 PHE G 89 TYR 0.017 0.002 TYR J 62 ARG 0.009 0.001 ARG E 298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 239 time to evaluate : 3.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 220 MET cc_start: 0.6400 (mpp) cc_final: 0.5944 (mpp) REVERT: G 334 MET cc_start: 0.6541 (mtp) cc_final: 0.6287 (mtp) REVERT: F 96 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.6757 (mt-10) REVERT: F 180 ASP cc_start: 0.7309 (m-30) cc_final: 0.7046 (m-30) REVERT: F 346 MET cc_start: 0.7509 (mtp) cc_final: 0.7205 (mtp) REVERT: E 63 GLU cc_start: 0.7544 (tp30) cc_final: 0.7248 (tt0) REVERT: E 65 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8196 (mp) REVERT: E 96 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: E 104 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8346 (t0) REVERT: C 17 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7837 (p0) REVERT: C 165 LYS cc_start: 0.7515 (mtmm) cc_final: 0.7173 (mtmm) REVERT: C 172 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6754 (mtt-85) REVERT: A 125 ARG cc_start: 0.5381 (OUTLIER) cc_final: 0.4592 (ppp80) REVERT: J 89 LEU cc_start: 0.2533 (OUTLIER) cc_final: 0.2290 (tm) outliers start: 111 outliers final: 86 residues processed: 328 average time/residue: 0.4308 time to fit residues: 225.8083 Evaluate side-chains 324 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 230 time to evaluate : 3.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 349 HIS Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 334 MET Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 315 HIS Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 269 SER Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 517 LYS Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 552 ASP Chi-restraints excluded: chain H residue 575 GLU Chi-restraints excluded: chain H residue 583 LEU Chi-restraints excluded: chain H residue 624 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 304 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 206 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.0570 chunk 212 optimal weight: 8.9990 chunk 227 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN G 349 HIS ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN C 162 ASN B 110 GLN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 548 ASN ** H 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30543 Z= 0.245 Angle : 0.645 8.196 41898 Z= 0.341 Chirality : 0.044 0.208 4631 Planarity : 0.005 0.062 5001 Dihedral : 16.428 174.798 5087 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 3.37 % Allowed : 13.32 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 0.61 % 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: -2.97 (0.13), residues: 3369 helix: -1.50 (0.16), residues: 947 sheet: -0.55 (0.23), residues: 517 loop : -2.75 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 143 HIS 0.006 0.001 HIS B 84 PHE 0.018 0.001 PHE G 89 TYR 0.016 0.002 TYR J 62 ARG 0.006 0.000 ARG H 428 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 238 time to evaluate : 3.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 112 LEU cc_start: 0.8242 (mm) cc_final: 0.7804 (mm) REVERT: G 220 MET cc_start: 0.6351 (mpp) cc_final: 0.5882 (mpp) REVERT: G 241 GLN cc_start: 0.5967 (tp40) cc_final: 0.5618 (tp40) REVERT: G 334 MET cc_start: 0.6453 (mtp) cc_final: 0.6197 (mtp) REVERT: F 96 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6780 (mt-10) REVERT: F 180 ASP cc_start: 0.7305 (m-30) cc_final: 0.7056 (m-30) REVERT: F 346 MET cc_start: 0.7475 (mtp) cc_final: 0.7187 (mtp) REVERT: E 63 GLU cc_start: 0.7542 (tp30) cc_final: 0.7241 (tt0) REVERT: E 65 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8189 (mp) REVERT: E 96 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: E 104 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8254 (t0) REVERT: C 17 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7804 (p0) REVERT: C 23 VAL cc_start: 0.8126 (OUTLIER) cc_final: 0.7888 (t) REVERT: C 172 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6759 (mtt-85) REVERT: H 535 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6614 (mm-30) REVERT: A 125 ARG cc_start: 0.5218 (OUTLIER) cc_final: 0.4466 (ppp80) REVERT: J 89 LEU cc_start: 0.2436 (OUTLIER) cc_final: 0.2200 (tm) REVERT: I 279 LEU cc_start: 0.6646 (mt) cc_final: 0.6432 (mp) outliers start: 102 outliers final: 82 residues processed: 319 average time/residue: 0.4232 time to fit residues: 215.9720 Evaluate side-chains 325 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 234 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 349 HIS Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 334 MET Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 269 SER Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 517 LYS Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 552 ASP Chi-restraints excluded: chain H residue 575 GLU Chi-restraints excluded: chain H residue 583 LEU Chi-restraints excluded: chain H residue 624 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 304 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 304 optimal weight: 6.9990 chunk 320 optimal weight: 50.0000 chunk 292 optimal weight: 20.0000 chunk 311 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 281 optimal weight: 20.0000 chunk 294 optimal weight: 0.0000 chunk 310 optimal weight: 0.8980 overall best weight: 2.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 114 GLN G 349 HIS ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN C 162 ASN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 548 ASN ** H 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30543 Z= 0.297 Angle : 0.678 9.367 41898 Z= 0.357 Chirality : 0.045 0.204 4631 Planarity : 0.006 0.069 5001 Dihedral : 16.468 175.249 5087 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.53 % Favored : 87.47 % Rotamer: Outliers : 3.44 % Allowed : 13.52 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 0.61 % 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: -2.99 (0.13), residues: 3369 helix: -1.52 (0.16), residues: 955 sheet: -0.60 (0.23), residues: 519 loop : -2.76 (0.13), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 143 HIS 0.015 0.001 HIS G 349 PHE 0.019 0.002 PHE G 89 TYR 0.016 0.002 TYR J 62 ARG 0.008 0.001 ARG H 428 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 231 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 112 LEU cc_start: 0.8270 (mm) cc_final: 0.7809 (mm) REVERT: G 220 MET cc_start: 0.6360 (mpp) cc_final: 0.5887 (mpp) REVERT: G 334 MET cc_start: 0.6500 (mtp) cc_final: 0.6266 (mtp) REVERT: F 86 GLU cc_start: 0.7288 (tp30) cc_final: 0.6990 (mm-30) REVERT: F 96 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6679 (mt-10) REVERT: F 180 ASP cc_start: 0.7309 (m-30) cc_final: 0.7029 (m-30) REVERT: F 346 MET cc_start: 0.7504 (mtp) cc_final: 0.7217 (mtp) REVERT: E 63 GLU cc_start: 0.7538 (tp30) cc_final: 0.7242 (tt0) REVERT: E 65 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8205 (mp) REVERT: E 96 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: E 104 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8368 (t0) REVERT: C 17 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7822 (p0) REVERT: C 165 LYS cc_start: 0.7477 (mtmm) cc_final: 0.7148 (mtmm) REVERT: C 172 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6762 (mtt-85) REVERT: H 63 LYS cc_start: 0.5368 (OUTLIER) cc_final: 0.4949 (ttpt) REVERT: H 535 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6696 (mm-30) REVERT: A 125 ARG cc_start: 0.5217 (OUTLIER) cc_final: 0.4441 (ppp80) REVERT: J 89 LEU cc_start: 0.2420 (OUTLIER) cc_final: 0.2195 (tm) outliers start: 104 outliers final: 87 residues processed: 315 average time/residue: 0.4250 time to fit residues: 214.2467 Evaluate side-chains 325 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 229 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 292 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 334 MET Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 269 SER Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 517 LYS Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 552 ASP Chi-restraints excluded: chain H residue 575 GLU Chi-restraints excluded: chain H residue 583 LEU Chi-restraints excluded: chain H residue 624 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 304 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 204 optimal weight: 5.9990 chunk 329 optimal weight: 20.0000 chunk 201 optimal weight: 0.0070 chunk 156 optimal weight: 0.5980 chunk 229 optimal weight: 6.9990 chunk 345 optimal weight: 9.9990 chunk 318 optimal weight: 20.0000 chunk 275 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 212 optimal weight: 9.9990 chunk 168 optimal weight: 0.3980 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 349 HIS ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN C 162 ASN B 72 GLN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 548 ASN ** H 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 30543 Z= 0.317 Angle : 0.695 9.663 41898 Z= 0.365 Chirality : 0.046 0.205 4631 Planarity : 0.006 0.071 5001 Dihedral : 16.502 174.938 5087 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.44 % Favored : 87.56 % Rotamer: Outliers : 3.44 % Allowed : 13.59 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 0.61 % 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: -3.01 (0.13), residues: 3369 helix: -1.52 (0.16), residues: 956 sheet: -0.63 (0.23), residues: 519 loop : -2.77 (0.13), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 152 HIS 0.007 0.001 HIS H 272 PHE 0.019 0.002 PHE G 89 TYR 0.016 0.002 TYR E 275 ARG 0.008 0.001 ARG E 298 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 238 time to evaluate : 3.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 112 LEU cc_start: 0.8336 (mm) cc_final: 0.7893 (mm) REVERT: G 220 MET cc_start: 0.6365 (mpp) cc_final: 0.5872 (mpp) REVERT: G 334 MET cc_start: 0.6496 (mtp) cc_final: 0.6268 (mtp) REVERT: F 86 GLU cc_start: 0.7306 (tp30) cc_final: 0.7001 (mm-30) REVERT: F 96 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6677 (mt-10) REVERT: F 180 ASP cc_start: 0.7306 (m-30) cc_final: 0.7017 (m-30) REVERT: F 346 MET cc_start: 0.7479 (mtp) cc_final: 0.7188 (mtp) REVERT: E 63 GLU cc_start: 0.7506 (tp30) cc_final: 0.7210 (tt0) REVERT: E 65 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8174 (mp) REVERT: E 96 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6763 (mp0) REVERT: E 104 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8360 (t0) REVERT: C 17 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7834 (p0) REVERT: C 165 LYS cc_start: 0.7472 (mtmm) cc_final: 0.7132 (mtmm) REVERT: C 172 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6768 (mtt-85) REVERT: H 63 LYS cc_start: 0.5348 (OUTLIER) cc_final: 0.5021 (ttmt) REVERT: H 93 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6797 (ptt90) REVERT: H 535 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6623 (mm-30) REVERT: A 125 ARG cc_start: 0.5211 (OUTLIER) cc_final: 0.4433 (ppp80) REVERT: J 89 LEU cc_start: 0.2395 (OUTLIER) cc_final: 0.2175 (tm) REVERT: I 279 LEU cc_start: 0.6670 (mt) cc_final: 0.6430 (mp) outliers start: 104 outliers final: 88 residues processed: 321 average time/residue: 0.4151 time to fit residues: 214.1515 Evaluate side-chains 330 residues out of total 3035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 232 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 292 GLU Chi-restraints excluded: chain G residue 349 HIS Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 334 MET Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 269 SER Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 517 LYS Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 552 ASP Chi-restraints excluded: chain H residue 575 GLU Chi-restraints excluded: chain H residue 583 LEU Chi-restraints excluded: chain H residue 624 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 304 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 218 optimal weight: 5.9990 chunk 293 optimal weight: 50.0000 chunk 84 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 76 optimal weight: 0.0170 chunk 275 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 283 optimal weight: 50.0000 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN G 349 HIS ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 548 ASN ** H 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.209519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.155251 restraints weight = 37853.555| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.63 r_work: 0.3222 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30543 Z= 0.226 Angle : 0.633 7.952 41898 Z= 0.334 Chirality : 0.044 0.206 4631 Planarity : 0.005 0.062 5001 Dihedral : 16.412 174.676 5087 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.72 % Favored : 88.28 % Rotamer: Outliers : 3.24 % Allowed : 13.79 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.06 % Twisted Proline : 0.61 % 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: -2.85 (0.14), residues: 3369 helix: -1.37 (0.16), residues: 957 sheet: -0.52 (0.23), residues: 515 loop : -2.68 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 143 HIS 0.006 0.001 HIS B 84 PHE 0.017 0.001 PHE G 89 TYR 0.017 0.001 TYR C 275 ARG 0.008 0.000 ARG H 428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6200.56 seconds wall clock time: 114 minutes 28.70 seconds (6868.70 seconds total)