Starting phenix.real_space_refine on Wed Feb 14 17:19:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyy_26199/02_2024/7tyy_26199.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyy_26199/02_2024/7tyy_26199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyy_26199/02_2024/7tyy_26199.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyy_26199/02_2024/7tyy_26199.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyy_26199/02_2024/7tyy_26199.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyy_26199/02_2024/7tyy_26199.pdb" } resolution = 3.0 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 6265 2.51 5 N 1676 2.21 5 O 1793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P GLU 15": "OE1" <-> "OE2" Residue "R GLU 106": "OE1" <-> "OE2" Residue "R GLU 210": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9802 Number of models: 1 Model: "" Number of chains: 11 Chain: "E" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 568 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 92} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 150 Chain: "P" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 239 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 2, 'TRANS': 29} Chain: "R" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2941 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 17, 'TRANS': 351} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 74 Chain: "A" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1895 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2598 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 413 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 174 Unusual residues: {'NAG': 1, 'PLM': 5, 'Y01': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.78, per 1000 atoms: 0.59 Number of scatterers: 9802 At special positions: 0 Unit cell: (82.82, 99.22, 156.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1793 8.00 N 1676 7.00 C 6265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS P 1 " - pdb=" SG CYS P 7 " distance=2.02 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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 Links applied NAG-ASN " NAG R 501 " - " ASN R 130 " Time building additional restraints: 4.18 Conformation dependent library (CDL) restraints added in 1.8 seconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 14 sheets defined 44.0% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'E' and resid 60 through 77 removed outlier: 3.513A pdb=" N PHE E 67 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN E 70 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN E 75 " --> pdb=" O HIS E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 5.238A pdb=" N LYS E 81 " --> pdb=" O PRO E 78 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP E 83 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 107 removed outlier: 3.805A pdb=" N SER E 94 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 96 " --> pdb=" O PRO E 92 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG E 97 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N CYS E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 100 " --> pdb=" O LEU E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 127 removed outlier: 3.678A pdb=" N ARG E 118 " --> pdb=" O PRO E 114 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ILE E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS E 127 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 149 removed outlier: 3.944A pdb=" N LEU E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET E 149 " --> pdb=" O VAL E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 165 removed outlier: 3.765A pdb=" N ILE E 157 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Proline residue: E 158 - end of helix removed outlier: 3.522A pdb=" N VAL E 165 " --> pdb=" O ILE E 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 21 Processing helix chain 'R' and resid 38 through 62 removed outlier: 3.707A pdb=" N GLN R 60 " --> pdb=" O TYR R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 removed outlier: 4.332A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.544A pdb=" N ILE R 160 " --> pdb=" O HIS R 156 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU R 163 " --> pdb=" O SER R 159 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER R 166 " --> pdb=" O THR R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.552A pdb=" N ASN R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.581A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG R 214 " --> pdb=" O GLU R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 249 removed outlier: 3.794A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 284 Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.519A pdb=" N TRP R 290 " --> pdb=" O ASP R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 329 Proline residue: R 304 - end of helix removed outlier: 3.555A pdb=" N ASN R 318 " --> pdb=" O PHE R 314 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG R 321 " --> pdb=" O LEU R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 353 removed outlier: 3.803A pdb=" N LEU R 339 " --> pdb=" O SER R 335 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS R 343 " --> pdb=" O LEU R 339 " (cutoff:3.500A) Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 381 removed outlier: 3.556A pdb=" N TYR R 374 " --> pdb=" O LYS R 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 405 Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.687A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.660A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 58' Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.550A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.869A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.116A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.527A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 4.389A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 24 removed outlier: 4.156A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.865A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AA2, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AA3, first strand: chain 'R' and resid 91 through 94 removed outlier: 3.532A pdb=" N SER R 91 " --> pdb=" O LYS R 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 120 through 121 removed outlier: 3.777A pdb=" N ARG R 126 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.962A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.949A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.513A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.520A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.734A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.717A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.701A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.552A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.106A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.88 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1597 1.32 - 1.44: 2766 1.44 - 1.57: 5558 1.57 - 1.69: 0 1.69 - 1.82: 94 Bond restraints: 10015 Sorted by residual: bond pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" N HIS R 302 " pdb=" CA HIS R 302 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.26e-02 6.30e+03 8.23e+00 bond pdb=" N ILE R 301 " pdb=" CA ILE R 301 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.23e-02 6.61e+03 7.38e+00 bond pdb=" N VAL R 305 " pdb=" CA VAL R 305 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.21e-02 6.83e+03 7.09e+00 bond pdb=" N THR P 27 " pdb=" CA THR P 27 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.08e-02 8.57e+03 6.68e+00 ... (remaining 10010 not shown) Histogram of bond angle deviations from ideal: 95.31 - 105.08: 163 105.08 - 114.86: 6085 114.86 - 124.64: 7158 124.64 - 134.41: 179 134.41 - 144.19: 1 Bond angle restraints: 13586 Sorted by residual: angle pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 112.00 95.31 16.69 1.40e+00 5.10e-01 1.42e+02 angle pdb=" C THR P 31 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 125.00 144.19 -19.19 4.10e+00 5.95e-02 2.19e+01 angle pdb=" N LEU R 298 " pdb=" CA LEU R 298 " pdb=" C LEU R 298 " ideal model delta sigma weight residual 113.18 107.94 5.24 1.21e+00 6.83e-01 1.88e+01 angle pdb=" O THR P 31 " pdb=" C THR P 31 " pdb=" N PRO P 32 " ideal model delta sigma weight residual 121.66 125.45 -3.79 9.40e-01 1.13e+00 1.62e+01 angle pdb=" N THR P 27 " pdb=" CA THR P 27 " pdb=" C THR P 27 " ideal model delta sigma weight residual 112.30 107.07 5.23 1.36e+00 5.41e-01 1.48e+01 ... (remaining 13581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5576 17.72 - 35.44: 356 35.44 - 53.16: 98 53.16 - 70.88: 20 70.88 - 88.60: 12 Dihedral angle restraints: 6062 sinusoidal: 2413 harmonic: 3649 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 173.02 -80.02 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS P 1 " pdb=" SG CYS P 1 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual -86.00 -128.76 42.76 1 1.00e+01 1.00e-02 2.55e+01 dihedral pdb=" CB CYS E 68 " pdb=" SG CYS E 68 " pdb=" SG CYS E 99 " pdb=" CB CYS E 99 " ideal model delta sinusoidal sigma weight residual -86.00 -47.08 -38.92 1 1.00e+01 1.00e-02 2.13e+01 ... (remaining 6059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1174 0.043 - 0.087: 259 0.087 - 0.130: 75 0.130 - 0.174: 6 0.174 - 0.217: 4 Chirality restraints: 1518 Sorted by residual: chirality pdb=" CB VAL P 8 " pdb=" CA VAL P 8 " pdb=" CG1 VAL P 8 " pdb=" CG2 VAL P 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA PHE R 359 " pdb=" N PHE R 359 " pdb=" C PHE R 359 " pdb=" CB PHE R 359 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.21 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ALA R 307 " pdb=" N ALA R 307 " pdb=" C ALA R 307 " pdb=" CB ALA R 307 " both_signs ideal model delta sigma weight residual False 2.48 2.69 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1515 not shown) Planarity restraints: 1726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN P 26 " 0.014 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C ASN P 26 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN P 26 " 0.017 2.00e-02 2.50e+03 pdb=" N THR P 27 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 299 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C TYR R 299 " 0.033 2.00e-02 2.50e+03 pdb=" O TYR R 299 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE R 300 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR P 31 " -0.033 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO P 32 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO P 32 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO P 32 " -0.026 5.00e-02 4.00e+02 ... (remaining 1723 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 330 2.72 - 3.26: 9996 3.26 - 3.81: 16541 3.81 - 4.35: 22015 4.35 - 4.90: 35463 Nonbonded interactions: 84345 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.174 2.440 nonbonded pdb=" O TYR R 374 " pdb=" OG SER R 378 " model vdw 2.229 2.440 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.234 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.252 2.440 nonbonded pdb=" OH TYR B 289 " pdb=" NE1 TRP B 297 " model vdw 2.265 2.520 ... (remaining 84340 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.990 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: 0.010 Extract box with map and model: 5.600 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.440 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 : 0.003 0.057 10015 Z= 0.201 Angle : 0.575 19.189 13586 Z= 0.350 Chirality : 0.041 0.217 1518 Planarity : 0.003 0.045 1725 Dihedral : 13.400 88.597 3675 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.03 % Allowed : 14.04 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.20), residues: 1230 helix: -2.79 (0.17), residues: 473 sheet: -2.22 (0.30), residues: 215 loop : -1.51 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 76 HIS 0.003 0.000 HIS R 302 PHE 0.008 0.001 PHE E 128 TYR 0.009 0.001 TYR N 60 ARG 0.002 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 222 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: E 103 PHE cc_start: 0.6332 (m-10) cc_final: 0.5854 (m-80) REVERT: R 48 MET cc_start: 0.6999 (ttm) cc_final: 0.6506 (ttt) REVERT: R 49 MET cc_start: 0.7668 (mmm) cc_final: 0.6923 (mpp) REVERT: R 99 PHE cc_start: 0.7522 (m-80) cc_final: 0.7304 (m-80) REVERT: R 143 LYS cc_start: 0.7028 (tttt) cc_final: 0.6359 (mtmt) REVERT: R 213 ARG cc_start: 0.5391 (mtt90) cc_final: 0.4915 (mtp-110) REVERT: R 230 MET cc_start: 0.7091 (mtm) cc_final: 0.6770 (ttp) REVERT: R 346 MET cc_start: 0.6678 (mmp) cc_final: 0.6055 (ptp) REVERT: A 221 MET cc_start: 0.7775 (ttm) cc_final: 0.7419 (ttp) REVERT: A 265 ARG cc_start: 0.6230 (mmt180) cc_final: 0.5878 (mtt90) REVERT: B 19 ARG cc_start: 0.6639 (mtm180) cc_final: 0.6247 (mtm180) REVERT: G 17 GLU cc_start: 0.6131 (mm-30) cc_final: 0.5790 (pt0) REVERT: G 21 MET cc_start: 0.6199 (mmm) cc_final: 0.5976 (ttt) REVERT: N 106 ASP cc_start: 0.6811 (p0) cc_final: 0.6401 (p0) outliers start: 20 outliers final: 9 residues processed: 239 average time/residue: 1.2047 time to fit residues: 307.9290 Evaluate side-chains 170 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 161 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 305 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 57 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.0980 chunk 70 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 186 ASN R 286 ASN R 399 GLN ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 264 ASN A 278 ASN A 294 GLN A 357 HIS A 371 ASN B 156 GLN B 175 GLN B 266 HIS B 268 ASN N 31 ASN N 77 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10015 Z= 0.172 Angle : 0.521 7.390 13586 Z= 0.275 Chirality : 0.040 0.168 1518 Planarity : 0.004 0.043 1725 Dihedral : 6.801 59.542 1596 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.26 % Allowed : 18.72 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.23), residues: 1230 helix: -0.53 (0.22), residues: 487 sheet: -1.62 (0.31), residues: 222 loop : -1.00 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 169 HIS 0.008 0.001 HIS R 277 PHE 0.021 0.001 PHE R 359 TYR 0.020 0.001 TYR A 358 ARG 0.010 0.001 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 1.142 Fit side-chains REVERT: E 103 PHE cc_start: 0.6619 (m-10) cc_final: 0.6095 (m-80) REVERT: R 49 MET cc_start: 0.7793 (mmm) cc_final: 0.6304 (mpp) REVERT: R 52 GLN cc_start: 0.7403 (tt0) cc_final: 0.7138 (tm-30) REVERT: R 99 PHE cc_start: 0.7548 (m-80) cc_final: 0.7344 (m-80) REVERT: R 137 PHE cc_start: 0.7275 (m-80) cc_final: 0.6856 (m-80) REVERT: R 143 LYS cc_start: 0.6789 (tttt) cc_final: 0.6166 (mtmt) REVERT: R 230 MET cc_start: 0.7220 (mtm) cc_final: 0.6929 (ttp) REVERT: R 240 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6932 (mm-30) REVERT: R 306 MET cc_start: 0.8101 (mmm) cc_final: 0.7716 (mmt) REVERT: R 332 GLU cc_start: 0.6560 (tt0) cc_final: 0.6174 (tt0) REVERT: A 31 GLN cc_start: 0.7435 (tp40) cc_final: 0.6858 (tt0) REVERT: A 221 MET cc_start: 0.7875 (ttm) cc_final: 0.7541 (ttp) REVERT: A 299 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5765 (tt0) REVERT: N 5 GLN cc_start: 0.6660 (OUTLIER) cc_final: 0.6055 (mm-40) REVERT: N 106 ASP cc_start: 0.7031 (p0) cc_final: 0.6638 (p0) outliers start: 32 outliers final: 11 residues processed: 184 average time/residue: 1.0579 time to fit residues: 211.1003 Evaluate side-chains 151 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 92 TYR Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 336 HIS A 12 GLN ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 357 HIS B 156 GLN B 268 ASN N 31 ASN N 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10015 Z= 0.306 Angle : 0.585 7.514 13586 Z= 0.307 Chirality : 0.043 0.200 1518 Planarity : 0.004 0.040 1725 Dihedral : 7.251 59.464 1588 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.27 % Allowed : 18.72 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.23), residues: 1230 helix: 0.04 (0.23), residues: 485 sheet: -1.25 (0.31), residues: 230 loop : -0.80 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 236 HIS 0.005 0.001 HIS A 41 PHE 0.018 0.002 PHE R 119 TYR 0.019 0.002 TYR A 358 ARG 0.006 0.001 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 147 time to evaluate : 1.146 Fit side-chains REVERT: E 103 PHE cc_start: 0.6596 (m-10) cc_final: 0.6131 (m-80) REVERT: R 49 MET cc_start: 0.7815 (mmm) cc_final: 0.6763 (mpp) REVERT: R 52 GLN cc_start: 0.7579 (tt0) cc_final: 0.7153 (tt0) REVERT: R 77 ASP cc_start: 0.7735 (p0) cc_final: 0.7515 (p0) REVERT: R 99 PHE cc_start: 0.7682 (m-80) cc_final: 0.7452 (m-80) REVERT: R 143 LYS cc_start: 0.6849 (tttt) cc_final: 0.6193 (mtmt) REVERT: R 321 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6599 (ttm170) REVERT: R 346 MET cc_start: 0.6973 (mmm) cc_final: 0.6436 (ptp) REVERT: A 31 GLN cc_start: 0.7249 (tp40) cc_final: 0.6723 (tt0) REVERT: A 221 MET cc_start: 0.8010 (ttm) cc_final: 0.7557 (ttp) REVERT: A 372 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7756 (mp) REVERT: B 59 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.6921 (t80) REVERT: B 130 GLU cc_start: 0.5054 (OUTLIER) cc_final: 0.4728 (mp0) REVERT: B 262 MET cc_start: 0.7691 (tpt) cc_final: 0.7466 (tpt) REVERT: N 1 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6793 (tt0) REVERT: N 106 ASP cc_start: 0.7107 (p0) cc_final: 0.6898 (p0) outliers start: 42 outliers final: 15 residues processed: 176 average time/residue: 0.9836 time to fit residues: 188.4354 Evaluate side-chains 146 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 104 optimal weight: 0.0170 chunk 31 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 GLN ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10015 Z= 0.172 Angle : 0.500 6.827 13586 Z= 0.261 Chirality : 0.041 0.188 1518 Planarity : 0.003 0.045 1725 Dihedral : 6.805 59.915 1587 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.66 % Allowed : 21.16 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.24), residues: 1230 helix: 0.52 (0.24), residues: 494 sheet: -1.22 (0.32), residues: 228 loop : -0.54 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.006 0.001 HIS R 302 PHE 0.012 0.001 PHE A 222 TYR 0.018 0.001 TYR R 372 ARG 0.004 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 139 time to evaluate : 0.967 Fit side-chains REVERT: E 103 PHE cc_start: 0.6490 (m-80) cc_final: 0.5976 (m-80) REVERT: R 49 MET cc_start: 0.7742 (mmm) cc_final: 0.6264 (mpp) REVERT: R 52 GLN cc_start: 0.7558 (tt0) cc_final: 0.7043 (tt0) REVERT: R 77 ASP cc_start: 0.7786 (p0) cc_final: 0.7571 (p0) REVERT: R 99 PHE cc_start: 0.7617 (m-80) cc_final: 0.7407 (m-80) REVERT: R 137 PHE cc_start: 0.7176 (m-80) cc_final: 0.6926 (m-80) REVERT: R 143 LYS cc_start: 0.6805 (tttt) cc_final: 0.6130 (mtmt) REVERT: R 321 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6246 (ttm170) REVERT: R 346 MET cc_start: 0.6778 (mmm) cc_final: 0.6340 (ptp) REVERT: A 31 GLN cc_start: 0.7219 (tp40) cc_final: 0.6718 (tt0) REVERT: A 221 MET cc_start: 0.8045 (ttm) cc_final: 0.7599 (ttp) REVERT: A 299 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5840 (tt0) REVERT: B 59 TYR cc_start: 0.7642 (OUTLIER) cc_final: 0.6751 (t80) REVERT: B 197 ARG cc_start: 0.7283 (mtm110) cc_final: 0.6943 (mtp180) REVERT: N 1 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6823 (tt0) REVERT: N 106 ASP cc_start: 0.7285 (p0) cc_final: 0.6914 (p0) outliers start: 36 outliers final: 15 residues processed: 165 average time/residue: 1.0409 time to fit residues: 186.4766 Evaluate side-chains 146 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 92 TYR Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 104 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN A 12 GLN A 357 HIS N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10015 Z= 0.174 Angle : 0.496 6.785 13586 Z= 0.259 Chirality : 0.041 0.192 1518 Planarity : 0.003 0.050 1725 Dihedral : 6.672 57.783 1587 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.17 % Allowed : 21.77 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.24), residues: 1230 helix: 0.75 (0.24), residues: 494 sheet: -1.10 (0.33), residues: 224 loop : -0.52 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.008 0.001 HIS R 302 PHE 0.023 0.001 PHE R 359 TYR 0.018 0.001 TYR N 32 ARG 0.003 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 139 time to evaluate : 1.043 Fit side-chains REVERT: E 103 PHE cc_start: 0.6456 (m-80) cc_final: 0.5936 (m-80) REVERT: R 49 MET cc_start: 0.7743 (mmm) cc_final: 0.6283 (mpp) REVERT: R 52 GLN cc_start: 0.7552 (tt0) cc_final: 0.7076 (tt0) REVERT: R 143 LYS cc_start: 0.6813 (tttt) cc_final: 0.6156 (mtmt) REVERT: R 240 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6948 (mm-30) REVERT: R 321 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6208 (ttm170) REVERT: R 346 MET cc_start: 0.6685 (mmm) cc_final: 0.6312 (ptp) REVERT: A 31 GLN cc_start: 0.7130 (tp40) cc_final: 0.6737 (tt0) REVERT: A 221 MET cc_start: 0.8020 (ttm) cc_final: 0.7557 (ttp) REVERT: A 299 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.5949 (tt0) REVERT: B 59 TYR cc_start: 0.7674 (OUTLIER) cc_final: 0.6772 (t80) REVERT: B 130 GLU cc_start: 0.5041 (OUTLIER) cc_final: 0.4729 (mp0) REVERT: B 214 ARG cc_start: 0.7771 (mpt-90) cc_final: 0.7436 (mmt-90) REVERT: N 1 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.6765 (tt0) REVERT: N 5 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6607 (mm-40) outliers start: 41 outliers final: 18 residues processed: 169 average time/residue: 1.0470 time to fit residues: 191.8288 Evaluate side-chains 152 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 68 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 97 optimal weight: 0.0170 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 30.0000 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN A 12 GLN A 357 HIS N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10015 Z= 0.174 Angle : 0.498 8.864 13586 Z= 0.258 Chirality : 0.040 0.169 1518 Planarity : 0.003 0.051 1725 Dihedral : 6.573 56.059 1587 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.15 % Allowed : 21.87 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.24), residues: 1230 helix: 0.84 (0.24), residues: 503 sheet: -1.16 (0.32), residues: 239 loop : -0.42 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.007 0.001 HIS R 302 PHE 0.016 0.001 PHE R 359 TYR 0.018 0.001 TYR R 372 ARG 0.005 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 1.122 Fit side-chains REVERT: E 103 PHE cc_start: 0.6396 (m-80) cc_final: 0.5862 (m-80) REVERT: R 49 MET cc_start: 0.7726 (mmm) cc_final: 0.6290 (mpp) REVERT: R 52 GLN cc_start: 0.7554 (tt0) cc_final: 0.7303 (tt0) REVERT: R 143 LYS cc_start: 0.6807 (tttt) cc_final: 0.6167 (mtmt) REVERT: R 240 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6968 (mm-30) REVERT: R 321 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6225 (ttm170) REVERT: R 346 MET cc_start: 0.6671 (mmm) cc_final: 0.6323 (ptp) REVERT: A 31 GLN cc_start: 0.7023 (tp40) cc_final: 0.6610 (tt0) REVERT: A 221 MET cc_start: 0.7984 (ttm) cc_final: 0.7535 (ttp) REVERT: A 299 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.5977 (tt0) REVERT: B 59 TYR cc_start: 0.7691 (OUTLIER) cc_final: 0.6728 (t80) REVERT: B 130 GLU cc_start: 0.5050 (OUTLIER) cc_final: 0.4711 (mp0) REVERT: B 214 ARG cc_start: 0.7649 (mpt-90) cc_final: 0.7421 (mmt-90) REVERT: N 5 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6718 (mm-40) outliers start: 31 outliers final: 18 residues processed: 159 average time/residue: 1.0047 time to fit residues: 173.8200 Evaluate side-chains 151 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 116 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN A 12 GLN A 357 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10015 Z= 0.185 Angle : 0.503 9.034 13586 Z= 0.260 Chirality : 0.041 0.203 1518 Planarity : 0.003 0.052 1725 Dihedral : 6.573 58.372 1587 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.56 % Allowed : 22.08 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.24), residues: 1230 helix: 0.94 (0.24), residues: 502 sheet: -1.16 (0.32), residues: 241 loop : -0.41 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.007 0.001 HIS R 302 PHE 0.029 0.001 PHE R 359 TYR 0.016 0.001 TYR R 372 ARG 0.004 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 131 time to evaluate : 1.226 Fit side-chains REVERT: E 103 PHE cc_start: 0.6312 (m-80) cc_final: 0.5811 (m-80) REVERT: R 49 MET cc_start: 0.7700 (mmm) cc_final: 0.6284 (mpp) REVERT: R 52 GLN cc_start: 0.7517 (tt0) cc_final: 0.7108 (tt0) REVERT: R 143 LYS cc_start: 0.6804 (tttt) cc_final: 0.6162 (mtmt) REVERT: R 240 GLU cc_start: 0.7411 (mm-30) cc_final: 0.6917 (mm-30) REVERT: R 321 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6235 (ttm170) REVERT: R 346 MET cc_start: 0.6667 (mmm) cc_final: 0.6332 (ptp) REVERT: A 31 GLN cc_start: 0.6977 (tp40) cc_final: 0.6609 (tt0) REVERT: A 221 MET cc_start: 0.7979 (ttm) cc_final: 0.7536 (ttp) REVERT: A 299 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.5983 (tt0) REVERT: A 334 VAL cc_start: 0.7731 (t) cc_final: 0.7434 (p) REVERT: B 59 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.6747 (t80) REVERT: B 130 GLU cc_start: 0.5099 (OUTLIER) cc_final: 0.4753 (mp0) REVERT: N 5 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6774 (mm-40) outliers start: 35 outliers final: 19 residues processed: 157 average time/residue: 1.0327 time to fit residues: 176.5554 Evaluate side-chains 151 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 0.0050 chunk 79 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 108 optimal weight: 0.3980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN A 12 GLN A 357 HIS A 387 HIS N 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10015 Z= 0.154 Angle : 0.487 9.708 13586 Z= 0.252 Chirality : 0.040 0.189 1518 Planarity : 0.003 0.053 1725 Dihedral : 6.376 58.359 1587 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.85 % Allowed : 23.19 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1230 helix: 1.08 (0.24), residues: 503 sheet: -1.16 (0.32), residues: 242 loop : -0.25 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.006 0.001 HIS R 302 PHE 0.023 0.001 PHE R 359 TYR 0.021 0.001 TYR R 284 ARG 0.004 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 1.085 Fit side-chains REVERT: E 103 PHE cc_start: 0.6310 (m-80) cc_final: 0.5797 (m-80) REVERT: R 49 MET cc_start: 0.7663 (mmm) cc_final: 0.6336 (mpp) REVERT: R 52 GLN cc_start: 0.7521 (tt0) cc_final: 0.7119 (tt0) REVERT: R 143 LYS cc_start: 0.6804 (tttt) cc_final: 0.6165 (mtmt) REVERT: R 321 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6193 (ttm170) REVERT: R 346 MET cc_start: 0.6595 (mmm) cc_final: 0.6275 (ptp) REVERT: A 31 GLN cc_start: 0.6977 (tp40) cc_final: 0.6628 (tt0) REVERT: A 221 MET cc_start: 0.7914 (ttm) cc_final: 0.7563 (ttp) REVERT: A 299 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.5940 (tt0) REVERT: A 334 VAL cc_start: 0.7681 (t) cc_final: 0.7391 (p) REVERT: B 59 TYR cc_start: 0.7683 (OUTLIER) cc_final: 0.6689 (t80) REVERT: B 130 GLU cc_start: 0.5125 (OUTLIER) cc_final: 0.4696 (mp0) REVERT: N 5 GLN cc_start: 0.6991 (OUTLIER) cc_final: 0.6582 (mm-40) outliers start: 28 outliers final: 17 residues processed: 159 average time/residue: 1.1366 time to fit residues: 196.1214 Evaluate side-chains 156 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10015 Z= 0.206 Angle : 0.514 9.070 13586 Z= 0.266 Chirality : 0.041 0.190 1518 Planarity : 0.003 0.052 1725 Dihedral : 6.495 55.695 1587 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.95 % Allowed : 22.58 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1230 helix: 1.07 (0.24), residues: 505 sheet: -1.16 (0.32), residues: 248 loop : -0.14 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.006 0.001 HIS R 302 PHE 0.022 0.001 PHE R 119 TYR 0.015 0.001 TYR R 372 ARG 0.006 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.123 Fit side-chains REVERT: E 103 PHE cc_start: 0.6272 (m-80) cc_final: 0.5739 (m-80) REVERT: R 49 MET cc_start: 0.7635 (mmm) cc_final: 0.6310 (mpp) REVERT: R 106 GLU cc_start: 0.4180 (mp0) cc_final: 0.3386 (mm-30) REVERT: R 143 LYS cc_start: 0.6795 (tttt) cc_final: 0.6169 (mtmt) REVERT: R 215 ASP cc_start: 0.6375 (p0) cc_final: 0.5996 (t0) REVERT: R 240 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6893 (mm-30) REVERT: R 321 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6275 (ttm170) REVERT: R 346 MET cc_start: 0.6639 (mmm) cc_final: 0.6312 (ptp) REVERT: A 31 GLN cc_start: 0.6977 (tp40) cc_final: 0.6597 (tt0) REVERT: A 221 MET cc_start: 0.7964 (ttm) cc_final: 0.7581 (ttp) REVERT: A 299 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.5953 (tt0) REVERT: A 334 VAL cc_start: 0.7730 (t) cc_final: 0.7443 (p) REVERT: B 59 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.6777 (t80) REVERT: B 130 GLU cc_start: 0.5116 (OUTLIER) cc_final: 0.4773 (mp0) REVERT: B 334 SER cc_start: 0.7889 (OUTLIER) cc_final: 0.7612 (p) REVERT: N 1 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.6692 (tt0) REVERT: N 5 GLN cc_start: 0.7071 (OUTLIER) cc_final: 0.6700 (mm-40) outliers start: 29 outliers final: 18 residues processed: 153 average time/residue: 0.9746 time to fit residues: 162.6246 Evaluate side-chains 156 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 30.0000 chunk 74 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10015 Z= 0.180 Angle : 0.505 8.832 13586 Z= 0.261 Chirality : 0.041 0.188 1518 Planarity : 0.003 0.053 1725 Dihedral : 6.406 57.601 1587 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.85 % Allowed : 22.58 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1230 helix: 1.15 (0.24), residues: 507 sheet: -1.17 (0.32), residues: 245 loop : -0.14 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.007 0.001 HIS R 302 PHE 0.022 0.001 PHE R 119 TYR 0.019 0.001 TYR R 284 ARG 0.007 0.000 ARG N 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 1.060 Fit side-chains REVERT: E 103 PHE cc_start: 0.6252 (m-80) cc_final: 0.5715 (m-80) REVERT: R 49 MET cc_start: 0.7581 (mmm) cc_final: 0.6398 (mpp) REVERT: R 106 GLU cc_start: 0.3818 (mp0) cc_final: 0.3218 (mt-10) REVERT: R 143 LYS cc_start: 0.6779 (tttt) cc_final: 0.6136 (mtmt) REVERT: R 215 ASP cc_start: 0.6289 (p0) cc_final: 0.5992 (t0) REVERT: R 240 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6897 (mm-30) REVERT: R 321 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6182 (ttm170) REVERT: R 346 MET cc_start: 0.6627 (mmm) cc_final: 0.6308 (ptp) REVERT: A 31 GLN cc_start: 0.6962 (tp40) cc_final: 0.6591 (tt0) REVERT: A 221 MET cc_start: 0.7951 (ttm) cc_final: 0.7524 (ttp) REVERT: A 299 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.5942 (tt0) REVERT: A 334 VAL cc_start: 0.7701 (t) cc_final: 0.7390 (p) REVERT: B 59 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.6677 (t80) REVERT: B 130 GLU cc_start: 0.5134 (OUTLIER) cc_final: 0.4700 (mp0) REVERT: B 334 SER cc_start: 0.7855 (OUTLIER) cc_final: 0.7575 (p) REVERT: N 5 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6657 (mm-40) outliers start: 28 outliers final: 17 residues processed: 159 average time/residue: 1.0293 time to fit residues: 178.2763 Evaluate side-chains 160 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 52 GLN ** R 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.168522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.133198 restraints weight = 11345.860| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.41 r_work: 0.3443 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10015 Z= 0.258 Angle : 0.551 8.686 13586 Z= 0.286 Chirality : 0.042 0.197 1518 Planarity : 0.004 0.051 1725 Dihedral : 6.676 58.881 1586 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.85 % Allowed : 22.79 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1230 helix: 1.09 (0.24), residues: 501 sheet: -1.14 (0.32), residues: 245 loop : -0.10 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.008 0.001 HIS R 302 PHE 0.019 0.002 PHE R 119 TYR 0.014 0.002 TYR N 95 ARG 0.007 0.001 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4011.82 seconds wall clock time: 71 minutes 58.79 seconds (4318.79 seconds total)