Starting phenix.real_space_refine on Mon Sep 14 04:07:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v9q_21126/09_2026/6v9q_21126_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v9q_21126/09_2026/6v9q_21126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6v9q_21126/09_2026/6v9q_21126_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v9q_21126/09_2026/6v9q_21126_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v9q_21126/09_2026/6v9q_21126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v9q_21126/09_2026/6v9q_21126.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 60 5.49 5 S 151 5.16 5 C 17670 2.51 5 N 4836 2.21 5 O 5369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28090 Number of models: 1 Model: "" Number of chains: 13 Chain: "K" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1275 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 15, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 24, 'rna3p': 36} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3573 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 8 Chain: "J" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3075 Classifications: {'peptide': 378} Link IDs: {'PCIS': 4, 'PTRANS': 14, 'TRANS': 359} Chain breaks: 2 Chain: "I" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3050 Classifications: {'peptide': 374} Link IDs: {'PCIS': 4, 'PTRANS': 14, 'TRANS': 355} Chain breaks: 3 Chain: "G" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2453 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 15, 'TRANS': 287} Chain breaks: 2 Chain: "B" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2731 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 17, 'TRANS': 323} Chain breaks: 1 Chain: "C" Number of atoms: 2713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2713 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 17, 'TRANS': 321} Chain breaks: 1 Chain: "D" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2704 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Chain: "E" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2695 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain breaks: 1 Chain: "F" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2704 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Chain: "H" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1113 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain breaks: 4 Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6062 SG CYS J 150 47.157 20.700 66.358 1.00102.18 S ATOM 6146 SG CYS J 161 42.892 16.042 84.318 1.00100.75 S ATOM 8946 SG CYS I 128 72.664 48.965 21.648 1.00 93.85 S ATOM 8967 SG CYS I 131 68.984 48.100 23.124 1.00 93.80 S ATOM 9137 SG CYS I 150 71.768 45.717 24.459 1.00 94.95 S ATOM 9221 SG CYS I 161 79.152 60.111 14.422 1.00 97.87 S ATOM 9349 SG CYS I 178 77.076 63.435 15.202 1.00 94.48 S ATOM 9370 SG CYS I 181 77.859 62.368 11.483 1.00 96.74 S Time building chain proxies: 6.17, per 1000 atoms: 0.22 Number of scatterers: 28090 At special positions: 0 Unit cell: (125.28, 201.96, 174.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 151 16.00 P 60 15.00 O 5369 8.00 N 4836 7.00 C 17670 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 - 3.00 Amino acid : True - 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: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 401 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 128 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 150 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 131 " pdb=" ZN I 402 " pdb="ZN ZN I 402 " - pdb=" SG CYS I 178 " pdb="ZN ZN I 402 " - pdb=" SG CYS I 181 " pdb="ZN ZN I 402 " - pdb=" SG CYS I 161 " pdb=" ZN J 401 " pdb="ZN ZN J 401 " - pdb=" ND1 HIS J 153 " pdb="ZN ZN J 401 " - pdb=" SG CYS J 150 " pdb=" ZN J 402 " pdb="ZN ZN J 402 " - pdb=" SG CYS J 161 " 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6358 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 50 sheets defined 33.3% alpha, 15.5% beta 5 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 16 through 23 removed outlier: 3.561A pdb=" N ALA A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 46 removed outlier: 3.735A pdb=" N LEU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 81 removed outlier: 3.625A pdb=" N TRP A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 removed outlier: 4.533A pdb=" N THR A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.563A pdb=" N GLY A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 411 through 427 removed outlier: 3.541A pdb=" N ASN A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'A' and resid 512 through 519 removed outlier: 4.352A pdb=" N LYS A 517 " --> pdb=" O ASP A 514 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 519 " --> pdb=" O PHE A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.717A pdb=" N ALA A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.606A pdb=" N ALA A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'J' and resid 13 through 25 removed outlier: 3.839A pdb=" N ILE J 19 " --> pdb=" O GLU J 15 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG J 20 " --> pdb=" O SER J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 44 Processing helix chain 'J' and resid 48 through 52 removed outlier: 3.552A pdb=" N THR J 51 " --> pdb=" O GLY J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 82 removed outlier: 3.551A pdb=" N ALA J 79 " --> pdb=" O PHE J 75 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN J 80 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU J 81 " --> pdb=" O LYS J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 93 removed outlier: 3.537A pdb=" N ALA J 93 " --> pdb=" O LEU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 135 Processing helix chain 'J' and resid 139 through 144 removed outlier: 3.632A pdb=" N TRP J 142 " --> pdb=" O SER J 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE J 144 " --> pdb=" O LEU J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 173 Processing helix chain 'J' and resid 195 through 205 removed outlier: 3.537A pdb=" N VAL J 200 " --> pdb=" O ALA J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 231 removed outlier: 3.766A pdb=" N TRP J 221 " --> pdb=" O LYS J 217 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY J 222 " --> pdb=" O SER J 218 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL J 224 " --> pdb=" O ARG J 220 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS J 231 " --> pdb=" O TRP J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 246 removed outlier: 3.677A pdb=" N VAL J 241 " --> pdb=" O HIS J 237 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE J 244 " --> pdb=" O PHE J 240 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN J 246 " --> pdb=" O GLN J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 248 through 265 removed outlier: 3.593A pdb=" N ILE J 255 " --> pdb=" O PHE J 251 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU J 264 " --> pdb=" O GLU J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 274 through 279 Processing helix chain 'J' and resid 297 through 307 Processing helix chain 'J' and resid 325 through 333 removed outlier: 3.615A pdb=" N THR J 329 " --> pdb=" O ALA J 325 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL J 330 " --> pdb=" O LEU J 326 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET J 331 " --> pdb=" O GLU J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 342 Processing helix chain 'J' and resid 369 through 380 Processing helix chain 'J' and resid 386 through 390 removed outlier: 4.050A pdb=" N PHE J 389 " --> pdb=" O ASN J 386 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR J 390 " --> pdb=" O ARG J 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 386 through 390' Processing helix chain 'I' and resid 13 through 25 removed outlier: 3.839A pdb=" N ILE I 19 " --> pdb=" O GLU I 15 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG I 20 " --> pdb=" O SER I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 44 removed outlier: 3.604A pdb=" N PHE I 33 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 52 removed outlier: 3.551A pdb=" N THR I 51 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.552A pdb=" N ALA I 79 " --> pdb=" O PHE I 75 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN I 80 " --> pdb=" O LEU I 76 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU I 81 " --> pdb=" O LYS I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 93 removed outlier: 3.536A pdb=" N ALA I 93 " --> pdb=" O LEU I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 135 Processing helix chain 'I' and resid 139 through 144 removed outlier: 3.632A pdb=" N TRP I 142 " --> pdb=" O SER I 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE I 144 " --> pdb=" O LEU I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 173 Processing helix chain 'I' and resid 195 through 205 removed outlier: 3.536A pdb=" N VAL I 200 " --> pdb=" O ALA I 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 231 removed outlier: 3.766A pdb=" N TRP I 221 " --> pdb=" O LYS I 217 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY I 222 " --> pdb=" O SER I 218 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL I 224 " --> pdb=" O ARG I 220 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS I 231 " --> pdb=" O TRP I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 246 removed outlier: 3.678A pdb=" N VAL I 241 " --> pdb=" O HIS I 237 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE I 244 " --> pdb=" O PHE I 240 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN I 246 " --> pdb=" O GLN I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 265 removed outlier: 3.594A pdb=" N ILE I 255 " --> pdb=" O PHE I 251 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU I 264 " --> pdb=" O GLU I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 279 Processing helix chain 'I' and resid 297 through 307 Processing helix chain 'I' and resid 325 through 333 removed outlier: 3.614A pdb=" N THR I 329 " --> pdb=" O ALA I 325 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL I 330 " --> pdb=" O LEU I 326 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET I 331 " --> pdb=" O GLU I 327 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 342 Processing helix chain 'I' and resid 369 through 380 Processing helix chain 'I' and resid 386 through 390 removed outlier: 4.050A pdb=" N PHE I 389 " --> pdb=" O ASN I 386 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR I 390 " --> pdb=" O ARG I 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 386 through 390' Processing helix chain 'G' and resid 105 through 123 Processing helix chain 'G' and resid 125 through 138 removed outlier: 3.930A pdb=" N ASN G 135 " --> pdb=" O ARG G 131 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE G 136 " --> pdb=" O TYR G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 183 removed outlier: 3.615A pdb=" N PHE G 181 " --> pdb=" O SER G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 199 removed outlier: 3.812A pdb=" N MET G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE G 194 " --> pdb=" O ILE G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 269 removed outlier: 3.526A pdb=" N ALA G 267 " --> pdb=" O LYS G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 312 removed outlier: 3.737A pdb=" N GLN G 311 " --> pdb=" O PHE G 307 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN G 312 " --> pdb=" O SER G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 321 removed outlier: 4.117A pdb=" N GLU G 318 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL G 319 " --> pdb=" O HIS G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 344 removed outlier: 3.545A pdb=" N ASN G 340 " --> pdb=" O PHE G 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 123 removed outlier: 3.558A pdb=" N VAL B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 137 removed outlier: 3.873A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.880A pdb=" N PHE B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 200 removed outlier: 3.781A pdb=" N MET B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 194 " --> pdb=" O ILE B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 269 removed outlier: 3.576A pdb=" N ALA B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 removed outlier: 3.508A pdb=" N GLN B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 321 removed outlier: 4.054A pdb=" N GLU B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 319 " --> pdb=" O HIS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 344 removed outlier: 3.897A pdb=" N ASP B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 123 Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.837A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 136 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 138 " --> pdb=" O MET C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.857A pdb=" N PHE C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 199 removed outlier: 3.680A pdb=" N MET C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 269 removed outlier: 3.554A pdb=" N ALA C 267 " --> pdb=" O LYS C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 311 removed outlier: 3.853A pdb=" N GLN C 311 " --> pdb=" O PHE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 321 removed outlier: 3.554A pdb=" N ILE C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL C 319 " --> pdb=" O HIS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 344 removed outlier: 3.604A pdb=" N ASP C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N MET C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 340 " --> pdb=" O PHE C 336 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 341 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 123 Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.890A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE D 136 " --> pdb=" O TYR D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 183 removed outlier: 3.782A pdb=" N PHE D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 199 removed outlier: 3.620A pdb=" N MET D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 314 through 321 removed outlier: 4.017A pdb=" N GLU D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 319 " --> pdb=" O HIS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 344 removed outlier: 3.691A pdb=" N LEU D 341 " --> pdb=" O LEU D 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 123 Processing helix chain 'E' and resid 125 through 137 removed outlier: 3.906A pdb=" N ASN E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 136 " --> pdb=" O TYR E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 183 removed outlier: 3.829A pdb=" N PHE E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 199 removed outlier: 3.754A pdb=" N MET E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 269 removed outlier: 3.529A pdb=" N ALA E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 311 removed outlier: 3.593A pdb=" N GLN E 311 " --> pdb=" O PHE E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 321 removed outlier: 4.034A pdb=" N GLU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL E 319 " --> pdb=" O HIS E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 344 removed outlier: 3.770A pdb=" N ASP E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N MET E 334 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU E 341 " --> pdb=" O LEU E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 67 removed outlier: 4.020A pdb=" N GLN F 67 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 123 Processing helix chain 'F' and resid 125 through 137 removed outlier: 3.838A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE F 136 " --> pdb=" O TYR F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 183 removed outlier: 3.823A pdb=" N PHE F 181 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 200 removed outlier: 3.935A pdb=" N MET F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 194 " --> pdb=" O ILE F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 269 removed outlier: 3.546A pdb=" N ALA F 267 " --> pdb=" O LYS F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 311 removed outlier: 3.628A pdb=" N GLN F 311 " --> pdb=" O PHE F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 321 removed outlier: 4.091A pdb=" N GLU F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL F 319 " --> pdb=" O HIS F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 344 removed outlier: 3.758A pdb=" N ASP F 333 " --> pdb=" O GLU F 329 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N MET F 334 " --> pdb=" O THR F 330 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN F 340 " --> pdb=" O PHE F 336 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 341 " --> pdb=" O LEU F 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 35 removed outlier: 4.406A pdb=" N LYS H 23 " --> pdb=" O SER H 19 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN H 32 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR H 33 " --> pdb=" O HIS H 29 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN H 34 " --> pdb=" O GLY H 30 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR H 35 " --> pdb=" O PHE H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 80 removed outlier: 3.952A pdb=" N LEU H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 124 removed outlier: 3.502A pdb=" N ALA H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU H 122 " --> pdb=" O LYS H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 138 removed outlier: 3.560A pdb=" N PHE H 138 " --> pdb=" O PRO H 135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'A' and resid 201 through 203 removed outlier: 4.646A pdb=" N LEU A 597 " --> pdb=" O TYR A 543 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 203 removed outlier: 7.206A pdb=" N ILE A 590 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU A 572 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLU A 592 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR A 570 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 594 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 16.048A pdb=" N SER A 566 " --> pdb=" O PRO A 627 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A 568 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 236 through 237 removed outlier: 5.973A pdb=" N LEU A 261 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 437 through 443 removed outlier: 4.013A pdb=" N SER A 437 " --> pdb=" O ASN A 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AA9, first strand: chain 'A' and resid 447 through 448 Processing sheet with id=AB1, first strand: chain 'J' and resid 95 through 100 removed outlier: 3.669A pdb=" N THR J 97 " --> pdb=" O ALA J 107 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA J 107 " --> pdb=" O THR J 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 322 through 323 removed outlier: 3.511A pdb=" N PHE J 367 " --> pdb=" O MET J 323 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 95 through 100 removed outlier: 3.669A pdb=" N THR I 97 " --> pdb=" O ALA I 107 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA I 107 " --> pdb=" O THR I 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 322 through 323 removed outlier: 3.511A pdb=" N PHE I 367 " --> pdb=" O MET I 323 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 102 through 103 Processing sheet with id=AB6, first strand: chain 'G' and resid 13 through 14 removed outlier: 3.506A pdb=" N HIS G 84 " --> pdb=" O VAL G 23 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 18 through 24 current: chain 'G' and resid 151 through 158 removed outlier: 6.448A pdb=" N TRP G 152 " --> pdb=" O ASP G 170 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP G 170 " --> pdb=" O TRP G 152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 28 through 31 removed outlier: 3.727A pdb=" N ARG G 28 " --> pdb=" O TRP G 24 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS G 84 " --> pdb=" O VAL G 23 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 84 through 93 current: chain 'G' and resid 248 through 251 Processing sheet with id=AB8, first strand: chain 'G' and resid 270 through 272 Processing sheet with id=AB9, first strand: chain 'G' and resid 289 through 290 removed outlier: 3.717A pdb=" N THR G 295 " --> pdb=" O HIS G 290 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AC2, first strand: chain 'B' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 18 through 23 current: chain 'B' and resid 151 through 155 removed outlier: 6.559A pdb=" N TRP B 152 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 170 " --> pdb=" O TRP B 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 93 current: chain 'B' and resid 248 through 251 Processing sheet with id=AC4, first strand: chain 'B' and resid 35 through 41 Processing sheet with id=AC5, first strand: chain 'B' and resid 270 through 272 Processing sheet with id=AC6, first strand: chain 'B' and resid 289 through 290 removed outlier: 3.718A pdb=" N THR B 295 " --> pdb=" O HIS B 290 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 102 through 103 Processing sheet with id=AC8, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.802A pdb=" N CYS C 151 " --> pdb=" O HIS C 214 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP C 152 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP C 170 " --> pdb=" O TRP C 152 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 29 through 31 removed outlier: 4.110A pdb=" N PHE C 20 " --> pdb=" O PRO C 257 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N VAL C 22 " --> pdb=" O ARG C 255 " (cutoff:3.500A) removed outlier: 14.136A pdb=" N ARG C 255 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 35 through 41 removed outlier: 8.473A pdb=" N SER C 243 " --> pdb=" O PRO C 70 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLN C 72 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AD3, first strand: chain 'C' and resid 289 through 290 removed outlier: 3.718A pdb=" N THR C 295 " --> pdb=" O HIS C 290 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 102 through 103 Processing sheet with id=AD5, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.941A pdb=" N CYS D 151 " --> pdb=" O HIS D 214 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP D 152 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP D 170 " --> pdb=" O TRP D 152 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 29 through 31 removed outlier: 4.114A pdb=" N PHE D 20 " --> pdb=" O PRO D 257 " (cutoff:3.500A) removed outlier: 10.359A pdb=" N VAL D 22 " --> pdb=" O ARG D 255 " (cutoff:3.500A) removed outlier: 14.029A pdb=" N ARG D 255 " --> pdb=" O VAL D 22 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 35 through 41 Processing sheet with id=AD8, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AD9, first strand: chain 'D' and resid 289 through 290 removed outlier: 3.612A pdb=" N THR D 295 " --> pdb=" O HIS D 290 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AE2, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.502A pdb=" N HIS E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N CYS E 151 " --> pdb=" O HIS E 214 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP E 152 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP E 170 " --> pdb=" O TRP E 152 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 29 through 31 removed outlier: 4.187A pdb=" N PHE E 20 " --> pdb=" O PRO E 257 " (cutoff:3.500A) removed outlier: 10.292A pdb=" N VAL E 22 " --> pdb=" O ARG E 255 " (cutoff:3.500A) removed outlier: 14.005A pdb=" N ARG E 255 " --> pdb=" O VAL E 22 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 35 through 41 Processing sheet with id=AE5, first strand: chain 'E' and resid 270 through 272 Processing sheet with id=AE6, first strand: chain 'E' and resid 289 through 290 removed outlier: 3.665A pdb=" N THR E 295 " --> pdb=" O HIS E 290 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 102 through 103 Processing sheet with id=AE8, first strand: chain 'F' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 23 current: chain 'F' and resid 151 through 158 removed outlier: 6.557A pdb=" N TRP F 152 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP F 170 " --> pdb=" O TRP F 152 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 84 through 93 current: chain 'F' and resid 248 through 251 Processing sheet with id=AF1, first strand: chain 'F' and resid 35 through 38 Processing sheet with id=AF2, first strand: chain 'F' and resid 270 through 272 Processing sheet with id=AF3, first strand: chain 'F' and resid 289 through 290 Processing sheet with id=AF4, first strand: chain 'H' and resid 7 through 9 Processing sheet with id=AF5, first strand: chain 'H' and resid 102 through 103 removed outlier: 3.666A pdb=" N ARG H 102 " --> pdb=" O ARG H 168 " (cutoff:3.500A) 879 hydrogen bonds defined for protein. 2409 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 5.63 Time building geometry restraints manager: 3.21 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: 6795 1.33 - 1.45: 6552 1.45 - 1.57: 15234 1.57 - 1.69: 120 1.69 - 1.81: 219 Bond restraints: 28920 Sorted by residual: bond pdb=" N GLU G 280 " pdb=" CA GLU G 280 " ideal model delta sigma weight residual 1.453 1.489 -0.036 9.20e-03 1.18e+04 1.50e+01 bond pdb=" N VAL J 268 " pdb=" CA VAL J 268 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.11e-02 8.12e+03 1.25e+01 bond pdb=" N VAL H 42 " pdb=" CA VAL H 42 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.14e-02 7.69e+03 1.15e+01 bond pdb=" N GLU G 277 " pdb=" CA GLU G 277 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.03e+01 bond pdb=" N ASP G 273 " pdb=" CA ASP G 273 " ideal model delta sigma weight residual 1.458 1.487 -0.029 9.00e-03 1.23e+04 1.03e+01 ... (remaining 28915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 37504 2.38 - 4.76: 1688 4.76 - 7.14: 234 7.14 - 9.53: 61 9.53 - 11.91: 18 Bond angle restraints: 39505 Sorted by residual: angle pdb=" N ALA E 205 " pdb=" CA ALA E 205 " pdb=" C ALA E 205 " ideal model delta sigma weight residual 111.02 118.93 -7.91 1.25e+00 6.40e-01 4.00e+01 angle pdb=" N ALA C 205 " pdb=" CA ALA C 205 " pdb=" C ALA C 205 " ideal model delta sigma weight residual 111.02 118.66 -7.64 1.25e+00 6.40e-01 3.74e+01 angle pdb=" O5' C K 28 " pdb=" C5' C K 28 " pdb=" C4' C K 28 " ideal model delta sigma weight residual 109.40 114.29 -4.89 8.00e-01 1.56e+00 3.73e+01 angle pdb=" N ALA F 205 " pdb=" CA ALA F 205 " pdb=" C ALA F 205 " ideal model delta sigma weight residual 111.02 118.33 -7.31 1.25e+00 6.40e-01 3.42e+01 angle pdb=" C GLU C 96 " pdb=" N LEU C 97 " pdb=" CA LEU C 97 " ideal model delta sigma weight residual 120.29 128.36 -8.07 1.42e+00 4.96e-01 3.23e+01 ... (remaining 39500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.87: 16882 34.87 - 69.74: 354 69.74 - 104.60: 32 104.60 - 139.47: 1 139.47 - 174.34: 5 Dihedral angle restraints: 17274 sinusoidal: 7497 harmonic: 9777 Sorted by residual: dihedral pdb=" O4' U K 42 " pdb=" C1' U K 42 " pdb=" N1 U K 42 " pdb=" C2 U K 42 " ideal model delta sinusoidal sigma weight residual 200.00 44.90 155.10 1 1.50e+01 4.44e-03 8.14e+01 dihedral pdb=" O4' C K 38 " pdb=" C1' C K 38 " pdb=" N1 C K 38 " pdb=" C2 C K 38 " ideal model delta sinusoidal sigma weight residual 232.00 57.66 174.34 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C K 12 " pdb=" C1' C K 12 " pdb=" N1 C K 12 " pdb=" C2 C K 12 " ideal model delta sinusoidal sigma weight residual 200.00 76.85 123.15 1 1.50e+01 4.44e-03 6.60e+01 ... (remaining 17271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3478 0.079 - 0.159: 774 0.159 - 0.238: 93 0.238 - 0.318: 25 0.318 - 0.397: 4 Chirality restraints: 4374 Sorted by residual: chirality pdb=" CG LEU G 112 " pdb=" CB LEU G 112 " pdb=" CD1 LEU G 112 " pdb=" CD2 LEU G 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C2' U K 20 " pdb=" C3' U K 20 " pdb=" O2' U K 20 " pdb=" C1' U K 20 " both_signs ideal model delta sigma weight residual False -2.60 -2.23 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CB THR D 146 " pdb=" CA THR D 146 " pdb=" OG1 THR D 146 " pdb=" CG2 THR D 146 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.34 2.00e-01 2.50e+01 2.83e+00 ... (remaining 4371 not shown) Planarity restraints: 4822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 11 " -0.055 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO H 12 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO H 12 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO H 12 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 9 " 0.018 2.00e-02 2.50e+03 2.19e-02 9.62e+00 pdb=" CG TYR D 9 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR D 9 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR D 9 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR D 9 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR D 9 " 0.004 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 ALA A 194 " -0.051 5.00e-02 4.00e+02 7.70e-02 9.49e+00 pdb=" N PRO A 195 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 195 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 195 " -0.043 5.00e-02 4.00e+02 ... (remaining 4819 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 283 2.61 - 3.18: 22430 3.18 - 3.76: 42349 3.76 - 4.33: 61001 4.33 - 4.90: 100201 Nonbonded interactions: 226264 Sorted by model distance: nonbonded pdb=" O2' A K 44 " pdb=" O5' A K 45 " model vdw 2.040 3.040 nonbonded pdb=" O2' A K 44 " pdb=" OP1 A K 45 " model vdw 2.102 3.040 nonbonded pdb=" O SER G 95 " pdb=" OG SER G 95 " model vdw 2.132 3.040 nonbonded pdb=" O SER F 95 " pdb=" OG SER F 95 " model vdw 2.134 3.040 nonbonded pdb=" O SER D 95 " pdb=" OG SER D 95 " model vdw 2.149 3.040 ... (remaining 226259 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 1 through 36 or resid 73 through 228 or resid 242 through \ 350)) selection = (chain 'C' and (resid 1 through 36 or resid 73 through 228 or resid 242 through \ 350)) selection = (chain 'D' and (resid 1 through 36 or resid 73 through 228 or resid 242 through \ 350)) selection = (chain 'E' and (resid 1 through 36 or resid 73 through 350)) selection = (chain 'F' and (resid 1 through 36 or resid 73 through 228 or resid 242 through \ 350)) selection = (chain 'G' and (resid 1 through 228 or resid 242 through 350)) } ncs_group { reference = chain 'I' selection = (chain 'J' and (resid 1 through 265 or resid 270 through 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 32.640 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:9.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 0.009 0.477 28929 Z= 0.453 Angle : 1.130 11.907 39505 Z= 0.683 Chirality : 0.069 0.397 4374 Planarity : 0.008 0.083 4822 Dihedral : 14.169 174.339 10916 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.49 % Favored : 93.39 % Rotamer: Outliers : 1.56 % Allowed : 5.41 % Favored : 93.03 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.27 (0.11), residues: 3269 helix: -3.89 (0.09), residues: 1090 sheet: -1.51 (0.22), residues: 497 loop : -2.47 (0.12), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 259 TYR 0.053 0.004 TYR D 9 PHE 0.037 0.004 PHE G 307 TRP 0.032 0.003 TRP B 274 HIS 0.019 0.002 HIS D 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00841 / 0.43 (28920) covalent geometry : angle 1.13042 / 0.68 (39505) hydrogen bonds : bond 0.30491 / 31.53 ( 861) hydrogen bonds : angle 10.02253 / 12.03 ( 2431) metal coordination : bond 0.24358 / 20.07 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 745 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6215 (tpp) cc_final: 0.4174 (mpt) REVERT: A 522 PHE cc_start: 0.8157 (m-80) cc_final: 0.7938 (m-80) REVERT: A 543 TYR cc_start: 0.7174 (t80) cc_final: 0.6775 (t80) REVERT: A 570 TYR cc_start: 0.7983 (m-80) cc_final: 0.7445 (m-80) REVERT: J 2 PHE cc_start: 0.5111 (t80) cc_final: 0.4837 (t80) REVERT: J 154 ASN cc_start: 0.5804 (m110) cc_final: 0.4613 (p0) REVERT: J 238 PHE cc_start: 0.6493 (t80) cc_final: 0.6002 (t80) REVERT: I 38 LYS cc_start: 0.8334 (tttt) cc_final: 0.7773 (tttt) REVERT: I 86 PRO cc_start: 0.8666 (Cg_exo) cc_final: 0.8338 (Cg_endo) REVERT: I 154 ASN cc_start: 0.6573 (m110) cc_final: 0.6330 (t0) REVERT: I 177 ILE cc_start: 0.7149 (mm) cc_final: 0.6815 (pt) REVERT: G 193 MET cc_start: 0.8677 (mtt) cc_final: 0.8464 (mtp) REVERT: G 331 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7861 (mt) REVERT: B 113 VAL cc_start: 0.7782 (t) cc_final: 0.7412 (m) REVERT: E 180 ASP cc_start: 0.8752 (m-30) cc_final: 0.8508 (m-30) REVERT: E 193 MET cc_start: 0.9059 (mtt) cc_final: 0.8794 (mtm) REVERT: F 204 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6792 (tm) REVERT: H 44 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.6928 (m-80) REVERT: H 102 ARG cc_start: 0.6393 (pmt100) cc_final: 0.5167 (ttm170) REVERT: H 109 LYS cc_start: 0.8186 (mttt) cc_final: 0.7799 (mmtt) outliers start: 46 outliers final: 12 residues processed: 778 average time/residue: 0.7755 time to fit residues: 692.3589 Evaluate side-chains 379 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 364 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 331 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 52 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.0670 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN A 200 GLN A 227 GLN A 235 HIS A 246 ASN A 420 HIS A 486 ASN A 610 ASN J 237 HIS J 313 GLN J 381 GLN I 31 HIS I 47 ASN I 66 ASN I 237 HIS I 296 HIS G 290 HIS G 299 HIS G 315 HIS G 328 GLN B 42 GLN B 77 HIS B 84 HIS B 114 GLN B 299 HIS B 348 GLN C 55 GLN C 77 HIS C 110 GLN C 184 ASN C 241 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 HIS D 110 GLN D 299 HIS E 42 GLN E 55 GLN E 77 HIS E 84 HIS ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 GLN F 99 GLN F 299 HIS F 328 GLN H 16 ASN H 32 ASN H 39 ASN ** H 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.165779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113739 restraints weight = 34049.733| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.78 r_work: 0.3041 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 28929 Z= 0.159 Angle : 0.706 11.506 39505 Z= 0.371 Chirality : 0.046 0.511 4374 Planarity : 0.006 0.084 4822 Dihedral : 15.284 176.643 4548 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.43 % Allowed : 13.90 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.13), residues: 3269 helix: -2.03 (0.13), residues: 1104 sheet: -0.77 (0.24), residues: 451 loop : -2.13 (0.13), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 249 TYR 0.023 0.002 TYR J 219 PHE 0.026 0.002 PHE J 235 TRP 0.020 0.002 TRP E 161 HIS 0.011 0.001 HIS C 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (28920) covalent geometry : angle 0.70566 / 0.37 (39505) hydrogen bonds : bond 0.06090 / 6.38 ( 861) hydrogen bonds : angle 5.90721 / 6.92 ( 2431) metal coordination : bond 0.00626 / 0.57 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 402 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: A 177 MET cc_start: 0.5485 (tpp) cc_final: 0.3561 (mpt) REVERT: A 472 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7984 (t70) REVERT: A 543 TYR cc_start: 0.7469 (t80) cc_final: 0.7027 (t80) REVERT: A 562 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6857 (mt0) REVERT: A 570 TYR cc_start: 0.7946 (m-80) cc_final: 0.7396 (m-80) REVERT: J 1 MET cc_start: 0.2314 (ttp) cc_final: 0.1107 (tmm) REVERT: J 52 PHE cc_start: 0.5400 (t80) cc_final: 0.5196 (t80) REVERT: J 217 LYS cc_start: 0.7467 (mmmm) cc_final: 0.6659 (mmmt) REVERT: J 238 PHE cc_start: 0.6968 (t80) cc_final: 0.6533 (t80) REVERT: J 272 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7588 (pt0) REVERT: J 322 LYS cc_start: 0.8422 (mttm) cc_final: 0.8209 (mttp) REVERT: J 345 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7179 (pm20) REVERT: I 4 GLN cc_start: 0.7193 (mm-40) cc_final: 0.6613 (mm-40) REVERT: I 142 TRP cc_start: 0.8627 (m-10) cc_final: 0.8397 (m-10) REVERT: I 177 ILE cc_start: 0.6922 (mm) cc_final: 0.6498 (pt) REVERT: I 231 LYS cc_start: 0.6647 (mmmt) cc_final: 0.6188 (mptp) REVERT: I 320 ASN cc_start: 0.7146 (m-40) cc_final: 0.6878 (m-40) REVERT: I 342 MET cc_start: 0.5331 (mmt) cc_final: 0.4615 (ttm) REVERT: I 348 LEU cc_start: 0.5662 (OUTLIER) cc_final: 0.4628 (pt) REVERT: G 146 THR cc_start: 0.8400 (m) cc_final: 0.7831 (p) REVERT: G 204 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7058 (tm) REVERT: B 113 VAL cc_start: 0.7648 (t) cc_final: 0.7353 (m) REVERT: B 172 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.6969 (ttm110) REVERT: B 329 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8195 (tm-30) REVERT: C 42 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7994 (mt0) REVERT: C 210 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.7936 (ttm170) REVERT: D 58 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7930 (mmtm) REVERT: D 63 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: D 96 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: D 311 GLN cc_start: 0.8571 (mt0) cc_final: 0.8178 (mm-40) REVERT: E 99 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8771 (pt0) REVERT: E 180 ASP cc_start: 0.9200 (m-30) cc_final: 0.8854 (m-30) REVERT: E 193 MET cc_start: 0.9133 (mtt) cc_final: 0.8880 (mtt) REVERT: E 277 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6885 (mp0) REVERT: E 348 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7928 (mp10) REVERT: F 146 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8184 (p) REVERT: H 73 TYR cc_start: 0.7601 (t80) cc_final: 0.7269 (t80) REVERT: H 83 PHE cc_start: 0.6285 (OUTLIER) cc_final: 0.6079 (m-10) REVERT: H 102 ARG cc_start: 0.6249 (pmt100) cc_final: 0.4985 (tpt170) REVERT: H 109 LYS cc_start: 0.8104 (mttt) cc_final: 0.7724 (mttm) REVERT: H 162 ASN cc_start: 0.7720 (m-40) cc_final: 0.7376 (m110) outliers start: 131 outliers final: 46 residues processed: 492 average time/residue: 0.6689 time to fit residues: 386.4916 Evaluate side-chains 395 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 335 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 345 GLN Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 280 GLU Chi-restraints excluded: chain E residue 348 GLN Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 99 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 175 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 266 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 258 optimal weight: 2.9990 chunk 195 optimal weight: 0.3980 chunk 286 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 HIS A 226 HIS A 443 HIS ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 ASN J 143 HIS J 313 GLN J 381 GLN I 42 GLN I 80 GLN I 154 ASN G 138 ASN G 315 HIS B 114 GLN C 110 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS D 110 GLN E 55 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 HIS F 99 GLN F 242 ASN ** H 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.163853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111782 restraints weight = 34152.688| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.78 r_work: 0.3007 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 28929 Z= 0.152 Angle : 0.645 10.563 39505 Z= 0.335 Chirality : 0.044 0.474 4374 Planarity : 0.005 0.066 4822 Dihedral : 15.175 179.424 4538 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.53 % Allowed : 15.02 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.13), residues: 3269 helix: -0.99 (0.14), residues: 1108 sheet: -0.59 (0.24), residues: 464 loop : -1.88 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 20 TYR 0.018 0.002 TYR C 275 PHE 0.030 0.002 PHE H 163 TRP 0.020 0.002 TRP E 161 HIS 0.010 0.001 HIS G 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (28920) covalent geometry : angle 0.64502 / 0.34 (39505) hydrogen bonds : bond 0.04626 / 4.82 ( 861) hydrogen bonds : angle 5.26046 / 6.19 ( 2431) metal coordination : bond 0.00159 / 0.15 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 341 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5842 (tpp) cc_final: 0.3909 (mpt) REVERT: A 247 MET cc_start: 0.8553 (tpt) cc_final: 0.7879 (tpt) REVERT: A 472 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8057 (t70) REVERT: A 543 TYR cc_start: 0.7447 (t80) cc_final: 0.6945 (t80) REVERT: A 570 TYR cc_start: 0.7944 (m-80) cc_final: 0.7350 (m-80) REVERT: J 33 PHE cc_start: 0.3387 (t80) cc_final: 0.3150 (t80) REVERT: J 169 TYR cc_start: 0.3503 (p90) cc_final: 0.2946 (p90) REVERT: J 208 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6789 (tm-30) REVERT: J 217 LYS cc_start: 0.7469 (mmmm) cc_final: 0.6671 (mmmt) REVERT: J 238 PHE cc_start: 0.7018 (t80) cc_final: 0.6703 (t80) REVERT: J 272 GLU cc_start: 0.8248 (mt-10) cc_final: 0.8035 (mt-10) REVERT: J 344 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7151 (pp20) REVERT: I 3 LEU cc_start: 0.8780 (mt) cc_final: 0.8464 (mp) REVERT: I 4 GLN cc_start: 0.7241 (mm-40) cc_final: 0.6666 (mm-40) REVERT: I 7 LYS cc_start: 0.7994 (tptp) cc_final: 0.7745 (tptp) REVERT: I 142 TRP cc_start: 0.8691 (m-10) cc_final: 0.8444 (m-10) REVERT: I 177 ILE cc_start: 0.6883 (mm) cc_final: 0.6429 (pt) REVERT: I 320 ASN cc_start: 0.6989 (m-40) cc_final: 0.6705 (m-40) REVERT: I 342 MET cc_start: 0.5465 (mmt) cc_final: 0.4773 (ttm) REVERT: I 348 LEU cc_start: 0.5716 (OUTLIER) cc_final: 0.4777 (pt) REVERT: G 86 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7872 (tp30) REVERT: G 146 THR cc_start: 0.8601 (m) cc_final: 0.7993 (p) REVERT: G 193 MET cc_start: 0.8952 (mtt) cc_final: 0.8730 (mtt) REVERT: G 204 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.6466 (tp) REVERT: B 172 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7656 (ttm170) REVERT: B 215 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8872 (mm) REVERT: B 294 VAL cc_start: 0.8810 (OUTLIER) cc_final: 0.8302 (m) REVERT: B 329 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8201 (tm-30) REVERT: C 42 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8236 (mt0) REVERT: C 210 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8004 (ttm170) REVERT: D 58 LYS cc_start: 0.8261 (mmtt) cc_final: 0.8010 (mmtm) REVERT: D 63 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: D 96 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: D 311 GLN cc_start: 0.8632 (mt0) cc_final: 0.8261 (mm-40) REVERT: E 99 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8746 (pt0) REVERT: E 180 ASP cc_start: 0.9143 (m-30) cc_final: 0.8711 (m-30) REVERT: E 193 MET cc_start: 0.9103 (mtt) cc_final: 0.8877 (mtt) REVERT: E 222 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8319 (mtm-85) REVERT: E 277 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7001 (mp0) REVERT: E 287 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.5625 (p90) REVERT: F 146 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8326 (p) REVERT: H 73 TYR cc_start: 0.7568 (t80) cc_final: 0.7253 (t80) REVERT: H 102 ARG cc_start: 0.6126 (pmt100) cc_final: 0.5000 (tpt170) REVERT: H 109 LYS cc_start: 0.8017 (mttt) cc_final: 0.7502 (mmtt) outliers start: 134 outliers final: 59 residues processed: 442 average time/residue: 0.6873 time to fit residues: 354.7221 Evaluate side-chains 381 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 306 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 208 GLU Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 280 GLU Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 150 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 105 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 240 optimal weight: 0.9980 chunk 64 optimal weight: 20.0000 chunk 230 optimal weight: 2.9990 chunk 292 optimal weight: 5.9990 chunk 303 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN A 443 HIS ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 262 ASN J 313 GLN J 381 GLN I 80 GLN G 35 ASN G 315 HIS G 349 HIS B 114 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 HIS D 110 GLN E 55 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN H 71 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.155847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.102442 restraints weight = 33918.854| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.72 r_work: 0.2867 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 28929 Z= 0.320 Angle : 0.823 13.892 39505 Z= 0.422 Chirality : 0.054 0.480 4374 Planarity : 0.007 0.082 4822 Dihedral : 15.264 178.455 4537 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 5.99 % Allowed : 15.36 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.14), residues: 3269 helix: -0.66 (0.15), residues: 1120 sheet: -0.60 (0.23), residues: 512 loop : -1.84 (0.14), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 37 TYR 0.031 0.003 TYR G 9 PHE 0.039 0.003 PHE F 207 TRP 0.025 0.003 TRP G 161 HIS 0.040 0.003 HIS H 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00779 / 0.32 (28920) covalent geometry : angle 0.82333 / 0.42 (39505) hydrogen bonds : bond 0.05431 / 5.63 ( 861) hydrogen bonds : angle 5.14464 / 6.12 ( 2431) metal coordination : bond 0.00347 / 0.32 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 320 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5561 (tpp) cc_final: 0.3564 (mpt) REVERT: A 247 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8335 (tpt) REVERT: A 405 VAL cc_start: 0.8296 (OUTLIER) cc_final: 0.8089 (m) REVERT: A 472 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7934 (t70) REVERT: A 543 TYR cc_start: 0.7589 (t80) cc_final: 0.7023 (t80) REVERT: A 562 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7224 (mt0) REVERT: A 570 TYR cc_start: 0.8198 (m-80) cc_final: 0.7917 (m-80) REVERT: J 1 MET cc_start: 0.2979 (ppp) cc_final: 0.2754 (tmt) REVERT: J 105 THR cc_start: 0.3333 (m) cc_final: 0.3055 (p) REVERT: J 169 TYR cc_start: 0.3601 (p90) cc_final: 0.2924 (p90) REVERT: J 217 LYS cc_start: 0.7508 (mmmm) cc_final: 0.6688 (mmmt) REVERT: J 228 MET cc_start: 0.7679 (mtt) cc_final: 0.7381 (mmt) REVERT: J 238 PHE cc_start: 0.6884 (t80) cc_final: 0.6486 (t80) REVERT: J 272 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.8050 (mt-10) REVERT: J 344 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7217 (pp20) REVERT: J 384 GLU cc_start: 0.6987 (pt0) cc_final: 0.6587 (pt0) REVERT: I 4 GLN cc_start: 0.7332 (mm-40) cc_final: 0.6676 (mm-40) REVERT: I 89 LEU cc_start: 0.8753 (mt) cc_final: 0.8498 (mt) REVERT: I 142 TRP cc_start: 0.8759 (m-10) cc_final: 0.8538 (m-10) REVERT: I 177 ILE cc_start: 0.6837 (mm) cc_final: 0.6419 (pt) REVERT: I 320 ASN cc_start: 0.7097 (m-40) cc_final: 0.6775 (m-40) REVERT: I 342 MET cc_start: 0.5390 (mmt) cc_final: 0.4465 (mtp) REVERT: I 348 LEU cc_start: 0.5753 (OUTLIER) cc_final: 0.4639 (pt) REVERT: G 146 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8186 (p) REVERT: G 185 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8737 (ttpt) REVERT: B 39 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9062 (pp) REVERT: B 172 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7689 (ttm170) REVERT: B 215 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8836 (mm) REVERT: B 241 GLN cc_start: 0.6240 (mt0) cc_final: 0.5885 (tt0) REVERT: C 39 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9037 (pp) REVERT: C 42 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8270 (mt0) REVERT: C 210 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8114 (ttm170) REVERT: D 3 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8569 (mp) REVERT: D 96 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: D 146 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.8877 (p) REVERT: D 277 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: D 287 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7374 (p90) REVERT: D 291 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7950 (mtp180) REVERT: D 346 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8322 (mtm) REVERT: E 99 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8619 (pm20) REVERT: E 193 MET cc_start: 0.9240 (mtt) cc_final: 0.8970 (mtt) REVERT: E 204 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8039 (tp) REVERT: E 222 ARG cc_start: 0.9302 (OUTLIER) cc_final: 0.8408 (mtm-85) REVERT: E 287 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.6052 (p90) REVERT: F 220 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8261 (ttp) REVERT: F 293 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7725 (p0) REVERT: H 102 ARG cc_start: 0.6216 (pmt100) cc_final: 0.4949 (tpt170) REVERT: H 109 LYS cc_start: 0.8099 (mttt) cc_final: 0.7705 (mttm) REVERT: H 137 SER cc_start: 0.8833 (p) cc_final: 0.8533 (p) REVERT: H 150 HIS cc_start: 0.7437 (OUTLIER) cc_final: 0.6980 (m170) outliers start: 177 outliers final: 74 residues processed: 455 average time/residue: 0.6717 time to fit residues: 356.4016 Evaluate side-chains 402 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 299 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 254 ILE Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain J residue 272 GLU Chi-restraints excluded: chain J residue 322 LYS Chi-restraints excluded: chain J residue 344 GLU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 280 GLU Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 167 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 157 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 chunk 229 optimal weight: 1.9990 chunk 264 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 216 optimal weight: 0.5980 chunk 279 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 204 optimal weight: 0.7980 chunk 214 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 25 ASN J 313 GLN I 80 GLN G 35 ASN G 315 HIS B 114 GLN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN C 110 GLN C 299 HIS D 110 GLN E 55 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN H 162 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.159857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.106748 restraints weight = 34032.805| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.76 r_work: 0.2940 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28929 Z= 0.124 Angle : 0.595 9.783 39505 Z= 0.313 Chirality : 0.043 0.446 4374 Planarity : 0.005 0.069 4822 Dihedral : 14.998 179.393 4533 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.20 % Favored : 94.77 % Rotamer: Outliers : 4.16 % Allowed : 17.86 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.14), residues: 3269 helix: -0.14 (0.15), residues: 1113 sheet: -0.48 (0.24), residues: 484 loop : -1.62 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 286 TYR 0.018 0.002 TYR H 149 PHE 0.029 0.001 PHE H 163 TRP 0.018 0.001 TRP A 71 HIS 0.012 0.001 HIS G 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (28920) covalent geometry : angle 0.59456 / 0.31 (39505) hydrogen bonds : bond 0.03793 / 3.90 ( 861) hydrogen bonds : angle 4.83893 / 5.77 ( 2431) metal coordination : bond 0.00087 / 0.08 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 330 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5423 (tpp) cc_final: 0.3769 (mpt) REVERT: A 210 TYR cc_start: 0.8572 (m-80) cc_final: 0.8356 (m-80) REVERT: A 247 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8401 (tpt) REVERT: A 472 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7997 (t70) REVERT: A 543 TYR cc_start: 0.7554 (t80) cc_final: 0.6971 (t80) REVERT: A 570 TYR cc_start: 0.8117 (m-80) cc_final: 0.7627 (m-80) REVERT: A 574 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8242 (pt0) REVERT: J 105 THR cc_start: 0.3284 (m) cc_final: 0.3009 (p) REVERT: J 169 TYR cc_start: 0.3692 (p90) cc_final: 0.2995 (p90) REVERT: J 217 LYS cc_start: 0.7436 (mmmm) cc_final: 0.6657 (mmmt) REVERT: J 238 PHE cc_start: 0.6915 (t80) cc_final: 0.6669 (t80) REVERT: J 249 ARG cc_start: 0.6785 (tpp-160) cc_final: 0.6371 (tpp-160) REVERT: J 272 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8050 (mt-10) REVERT: J 315 LYS cc_start: 0.8231 (mttt) cc_final: 0.7952 (pptt) REVERT: J 344 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7269 (pp20) REVERT: J 384 GLU cc_start: 0.7045 (pt0) cc_final: 0.6612 (pt0) REVERT: I 3 LEU cc_start: 0.8849 (mt) cc_final: 0.8553 (mp) REVERT: I 4 GLN cc_start: 0.7295 (mm-40) cc_final: 0.6687 (mm-40) REVERT: I 89 LEU cc_start: 0.8697 (mt) cc_final: 0.8434 (mt) REVERT: I 99 MET cc_start: 0.6715 (mtm) cc_final: 0.6490 (ptp) REVERT: I 177 ILE cc_start: 0.6780 (mm) cc_final: 0.6334 (pt) REVERT: I 234 GLU cc_start: 0.6221 (pp20) cc_final: 0.5948 (pm20) REVERT: I 320 ASN cc_start: 0.7222 (m-40) cc_final: 0.6958 (m-40) REVERT: I 342 MET cc_start: 0.5629 (mmt) cc_final: 0.4792 (mtp) REVERT: I 348 LEU cc_start: 0.5927 (OUTLIER) cc_final: 0.4849 (pt) REVERT: G 86 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7916 (tp30) REVERT: G 146 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8063 (p) REVERT: G 193 MET cc_start: 0.8912 (mtt) cc_final: 0.8634 (mtt) REVERT: G 222 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8611 (mtt180) REVERT: B 39 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9086 (pp) REVERT: B 215 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8802 (mm) REVERT: B 241 GLN cc_start: 0.6202 (mt0) cc_final: 0.5794 (tt0) REVERT: B 294 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8409 (m) REVERT: C 42 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8298 (mt0) REVERT: D 63 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: D 96 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: D 287 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7430 (p90) REVERT: D 346 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8212 (mmm) REVERT: E 43 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8518 (mtp) REVERT: E 99 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8671 (pt0) REVERT: E 193 MET cc_start: 0.9204 (mtt) cc_final: 0.8915 (mtt) REVERT: E 222 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.8376 (mtm-85) REVERT: E 277 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6962 (mp0) REVERT: E 287 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.6023 (p90) REVERT: E 293 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7678 (p0) REVERT: E 318 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7845 (mm-30) REVERT: F 146 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8589 (p) REVERT: F 164 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: F 220 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8005 (ttp) REVERT: F 292 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: F 293 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7677 (p0) REVERT: H 102 ARG cc_start: 0.6196 (pmt100) cc_final: 0.4942 (tpt170) REVERT: H 109 LYS cc_start: 0.8043 (mttt) cc_final: 0.7564 (mmtt) REVERT: H 149 TYR cc_start: 0.7426 (p90) cc_final: 0.7116 (p90) REVERT: H 150 HIS cc_start: 0.7239 (OUTLIER) cc_final: 0.6316 (t-90) REVERT: H 162 ASN cc_start: 0.7745 (m110) cc_final: 0.7209 (m110) outliers start: 123 outliers final: 55 residues processed: 421 average time/residue: 0.7006 time to fit residues: 342.5952 Evaluate side-chains 380 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 298 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain J residue 344 GLU Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 374 CYS Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 43 MET Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 346 MET Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 150 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 100 optimal weight: 0.0870 chunk 121 optimal weight: 6.9990 chunk 317 optimal weight: 0.0000 chunk 265 optimal weight: 0.9990 chunk 224 optimal weight: 0.4980 chunk 238 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 288 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 overall best weight: 0.7166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 HIS J 313 GLN J 345 GLN I 31 HIS I 80 GLN G 35 ASN G 315 HIS B 114 GLN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN D 110 GLN E 55 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.161044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108859 restraints weight = 33983.615| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.80 r_work: 0.2954 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28929 Z= 0.123 Angle : 0.574 8.575 39505 Z= 0.300 Chirality : 0.042 0.424 4374 Planarity : 0.005 0.070 4822 Dihedral : 14.858 179.555 4533 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.54 % Favored : 94.43 % Rotamer: Outliers : 3.79 % Allowed : 18.64 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3269 helix: 0.24 (0.16), residues: 1108 sheet: -0.31 (0.24), residues: 487 loop : -1.53 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 286 TYR 0.016 0.001 TYR C 275 PHE 0.029 0.001 PHE H 163 TRP 0.019 0.001 TRP I 142 HIS 0.012 0.001 HIS G 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (28920) covalent geometry : angle 0.57360 / 0.30 (39505) hydrogen bonds : bond 0.03547 / 3.65 ( 861) hydrogen bonds : angle 4.66311 / 5.56 ( 2431) metal coordination : bond 0.00090 / 0.08 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 316 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5604 (tpp) cc_final: 0.4146 (mpt) REVERT: A 180 GLN cc_start: 0.7397 (mt0) cc_final: 0.6606 (tm-30) REVERT: A 210 TYR cc_start: 0.8613 (m-80) cc_final: 0.8322 (m-80) REVERT: A 247 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.7886 (tpt) REVERT: A 472 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7974 (t70) REVERT: A 543 TYR cc_start: 0.7580 (t80) cc_final: 0.6885 (t80) REVERT: A 570 TYR cc_start: 0.8113 (m-80) cc_final: 0.7619 (m-80) REVERT: J 105 THR cc_start: 0.3207 (m) cc_final: 0.2956 (p) REVERT: J 169 TYR cc_start: 0.3711 (p90) cc_final: 0.3090 (p90) REVERT: J 217 LYS cc_start: 0.7444 (mmmm) cc_final: 0.6675 (mmmt) REVERT: J 238 PHE cc_start: 0.7016 (t80) cc_final: 0.6757 (t80) REVERT: J 249 ARG cc_start: 0.6804 (tpp-160) cc_final: 0.6534 (tpp-160) REVERT: J 272 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8096 (mt-10) REVERT: J 315 LYS cc_start: 0.8207 (mttt) cc_final: 0.7953 (pptt) REVERT: J 344 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7259 (pp20) REVERT: J 384 GLU cc_start: 0.7039 (pt0) cc_final: 0.6586 (pt0) REVERT: I 3 LEU cc_start: 0.8739 (mt) cc_final: 0.8466 (mp) REVERT: I 4 GLN cc_start: 0.7365 (mm-40) cc_final: 0.6807 (mm-40) REVERT: I 89 LEU cc_start: 0.8696 (mt) cc_final: 0.8453 (mt) REVERT: I 99 MET cc_start: 0.6772 (mtm) cc_final: 0.6471 (ptp) REVERT: I 177 ILE cc_start: 0.6753 (mm) cc_final: 0.6285 (pt) REVERT: I 234 GLU cc_start: 0.6127 (pp20) cc_final: 0.5877 (pm20) REVERT: I 311 LEU cc_start: 0.6488 (tm) cc_final: 0.6184 (pt) REVERT: I 320 ASN cc_start: 0.7124 (m-40) cc_final: 0.6851 (m-40) REVERT: I 342 MET cc_start: 0.5607 (mmt) cc_final: 0.4795 (mtp) REVERT: I 348 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.4918 (pt) REVERT: G 86 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7974 (tp30) REVERT: G 193 MET cc_start: 0.8948 (mtt) cc_final: 0.8677 (mtt) REVERT: G 222 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8589 (mtt180) REVERT: G 349 HIS cc_start: 0.6651 (OUTLIER) cc_final: 0.6427 (t70) REVERT: B 39 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9120 (pp) REVERT: B 215 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8783 (mm) REVERT: B 241 GLN cc_start: 0.6187 (mt0) cc_final: 0.5768 (tt0) REVERT: B 294 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8393 (m) REVERT: C 42 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8372 (mt0) REVERT: D 96 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: D 287 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7456 (p90) REVERT: E 99 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8709 (pt0) REVERT: E 193 MET cc_start: 0.9200 (mtt) cc_final: 0.8979 (mtt) REVERT: E 222 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8346 (mtm-85) REVERT: E 277 GLU cc_start: 0.7382 (mm-30) cc_final: 0.6957 (mp0) REVERT: E 287 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.6082 (p90) REVERT: F 146 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8493 (p) REVERT: F 220 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8011 (ttp) REVERT: F 292 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: H 83 PHE cc_start: 0.6653 (OUTLIER) cc_final: 0.6446 (m-10) REVERT: H 102 ARG cc_start: 0.6225 (pmt100) cc_final: 0.4953 (tpt170) REVERT: H 109 LYS cc_start: 0.8068 (mttt) cc_final: 0.7589 (mmtt) REVERT: H 149 TYR cc_start: 0.7347 (p90) cc_final: 0.7121 (p90) REVERT: H 150 HIS cc_start: 0.7255 (OUTLIER) cc_final: 0.6377 (t-90) REVERT: H 164 ARG cc_start: 0.7354 (mmm160) cc_final: 0.7095 (mtp85) outliers start: 112 outliers final: 58 residues processed: 404 average time/residue: 0.6812 time to fit residues: 320.7677 Evaluate side-chains 368 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 288 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 272 GLU Chi-restraints excluded: chain J residue 277 ASP Chi-restraints excluded: chain J residue 344 GLU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 374 CYS Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 349 HIS Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 346 MET Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 224 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 122 optimal weight: 0.3980 chunk 210 optimal weight: 0.5980 chunk 291 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 283 optimal weight: 0.9980 chunk 316 optimal weight: 0.0370 chunk 147 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN I 80 GLN G 315 HIS B 114 GLN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN D 110 GLN E 55 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.162362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111740 restraints weight = 33940.384| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.10 r_work: 0.2986 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28929 Z= 0.110 Angle : 0.553 8.976 39505 Z= 0.291 Chirality : 0.041 0.405 4374 Planarity : 0.005 0.073 4822 Dihedral : 14.668 178.735 4531 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.62 % Rotamer: Outliers : 3.82 % Allowed : 18.81 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.15), residues: 3269 helix: 0.47 (0.16), residues: 1120 sheet: -0.05 (0.25), residues: 455 loop : -1.42 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 37 TYR 0.016 0.001 TYR C 275 PHE 0.030 0.001 PHE H 163 TRP 0.022 0.001 TRP I 142 HIS 0.012 0.001 HIS G 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (28920) covalent geometry : angle 0.55273 / 0.29 (39505) hydrogen bonds : bond 0.03255 / 3.34 ( 861) hydrogen bonds : angle 4.53604 / 5.40 ( 2431) metal coordination : bond 0.00085 / 0.08 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 310 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5675 (tpp) cc_final: 0.3881 (mpt) REVERT: A 179 LYS cc_start: 0.6465 (mttt) cc_final: 0.6215 (mtpp) REVERT: A 210 TYR cc_start: 0.8625 (m-80) cc_final: 0.8297 (m-80) REVERT: A 247 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.7861 (tpt) REVERT: A 472 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7943 (t70) REVERT: A 543 TYR cc_start: 0.7598 (t80) cc_final: 0.6888 (t80) REVERT: A 570 TYR cc_start: 0.8083 (m-80) cc_final: 0.7540 (m-80) REVERT: A 574 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8237 (pt0) REVERT: J 105 THR cc_start: 0.3145 (m) cc_final: 0.2920 (p) REVERT: J 169 TYR cc_start: 0.3736 (p90) cc_final: 0.3130 (p90) REVERT: J 217 LYS cc_start: 0.7433 (mmmm) cc_final: 0.6667 (mmmt) REVERT: J 232 ASP cc_start: 0.7468 (m-30) cc_final: 0.7053 (m-30) REVERT: J 238 PHE cc_start: 0.7007 (t80) cc_final: 0.6680 (t80) REVERT: J 272 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8091 (mt-10) REVERT: J 344 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7261 (pp20) REVERT: J 384 GLU cc_start: 0.6999 (pt0) cc_final: 0.6547 (pt0) REVERT: I 3 LEU cc_start: 0.8679 (mt) cc_final: 0.8420 (mp) REVERT: I 4 GLN cc_start: 0.7330 (mm-40) cc_final: 0.6791 (mm-40) REVERT: I 89 LEU cc_start: 0.8664 (mt) cc_final: 0.8417 (mt) REVERT: I 177 ILE cc_start: 0.6781 (mm) cc_final: 0.6292 (pt) REVERT: I 234 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.6106 (pm20) REVERT: I 320 ASN cc_start: 0.7214 (m-40) cc_final: 0.6920 (m-40) REVERT: I 323 MET cc_start: 0.3545 (mpt) cc_final: 0.2861 (mpt) REVERT: I 342 MET cc_start: 0.5194 (mmt) cc_final: 0.4648 (mtp) REVERT: I 348 LEU cc_start: 0.5957 (OUTLIER) cc_final: 0.5062 (pt) REVERT: G 193 MET cc_start: 0.8915 (mtt) cc_final: 0.8647 (mtt) REVERT: G 222 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8697 (mtt180) REVERT: G 293 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7534 (p0) REVERT: G 349 HIS cc_start: 0.6665 (OUTLIER) cc_final: 0.6402 (t70) REVERT: B 39 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9120 (pp) REVERT: B 241 GLN cc_start: 0.6173 (mt0) cc_final: 0.5783 (tt0) REVERT: B 294 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8254 (m) REVERT: C 42 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: D 96 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: D 176 THR cc_start: 0.9118 (m) cc_final: 0.8890 (p) REVERT: D 287 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7467 (p90) REVERT: E 17 ASP cc_start: 0.8959 (OUTLIER) cc_final: 0.8472 (m-30) REVERT: E 43 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8487 (mmm) REVERT: E 99 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8717 (pt0) REVERT: E 193 MET cc_start: 0.9124 (mtt) cc_final: 0.8853 (mtt) REVERT: E 222 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8325 (mtm-85) REVERT: E 277 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6945 (mp0) REVERT: E 287 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.5958 (p90) REVERT: F 146 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8331 (p) REVERT: F 292 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: H 55 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6733 (mmpt) REVERT: H 83 PHE cc_start: 0.6428 (OUTLIER) cc_final: 0.6218 (m-10) REVERT: H 102 ARG cc_start: 0.6212 (pmt100) cc_final: 0.4931 (tpt170) REVERT: H 109 LYS cc_start: 0.8048 (mttt) cc_final: 0.7584 (mmtt) REVERT: H 149 TYR cc_start: 0.7297 (p90) cc_final: 0.7056 (p90) outliers start: 113 outliers final: 53 residues processed: 394 average time/residue: 0.6632 time to fit residues: 304.5628 Evaluate side-chains 368 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 292 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 288 ARG Chi-restraints excluded: chain J residue 322 LYS Chi-restraints excluded: chain J residue 344 GLU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 374 CYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 293 ASP Chi-restraints excluded: chain G residue 349 HIS Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 43 MET Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 346 MET Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 104 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 297 optimal weight: 0.0170 chunk 323 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 215 optimal weight: 0.0980 chunk 166 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 123 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 218 optimal weight: 0.6980 chunk 296 optimal weight: 0.0980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 581 ASN A 599 ASN J 345 GLN I 80 GLN G 315 HIS ** B 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN D 110 GLN E 55 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN H 162 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.163820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112487 restraints weight = 34225.748| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.72 r_work: 0.3017 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28929 Z= 0.101 Angle : 0.546 11.455 39505 Z= 0.283 Chirality : 0.040 0.396 4374 Planarity : 0.005 0.063 4822 Dihedral : 14.525 177.921 4531 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.45 % Favored : 94.52 % Rotamer: Outliers : 3.18 % Allowed : 19.49 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.15), residues: 3269 helix: 0.73 (0.16), residues: 1120 sheet: 0.06 (0.24), residues: 473 loop : -1.32 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 164 TYR 0.018 0.001 TYR D 275 PHE 0.035 0.001 PHE H 163 TRP 0.024 0.001 TRP I 142 HIS 0.012 0.001 HIS G 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (28920) covalent geometry : angle 0.54603 / 0.28 (39505) hydrogen bonds : bond 0.03081 / 3.16 ( 861) hydrogen bonds : angle 4.43219 / 5.27 ( 2431) metal coordination : bond 0.00096 / 0.09 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 305 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5829 (tpp) cc_final: 0.4007 (mpt) REVERT: A 210 TYR cc_start: 0.8696 (m-80) cc_final: 0.8371 (m-80) REVERT: A 247 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.7953 (tpt) REVERT: A 472 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.8002 (t70) REVERT: A 543 TYR cc_start: 0.7658 (t80) cc_final: 0.6902 (t80) REVERT: A 570 TYR cc_start: 0.8066 (m-80) cc_final: 0.7527 (m-80) REVERT: J 105 THR cc_start: 0.3347 (m) cc_final: 0.3025 (p) REVERT: J 169 TYR cc_start: 0.3770 (p90) cc_final: 0.3189 (p90) REVERT: J 217 LYS cc_start: 0.7460 (mmmm) cc_final: 0.6698 (mmmt) REVERT: J 238 PHE cc_start: 0.6997 (t80) cc_final: 0.6639 (t80) REVERT: J 315 LYS cc_start: 0.8117 (mttt) cc_final: 0.7807 (pptt) REVERT: J 344 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7233 (pp20) REVERT: J 384 GLU cc_start: 0.7023 (pt0) cc_final: 0.6513 (pt0) REVERT: I 3 LEU cc_start: 0.8674 (mt) cc_final: 0.8392 (mp) REVERT: I 4 GLN cc_start: 0.7366 (mm-40) cc_final: 0.6817 (mm-40) REVERT: I 89 LEU cc_start: 0.8692 (mt) cc_final: 0.8437 (mt) REVERT: I 155 VAL cc_start: 0.7671 (t) cc_final: 0.7083 (m) REVERT: I 177 ILE cc_start: 0.6729 (mm) cc_final: 0.6215 (pt) REVERT: I 234 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.6022 (pm20) REVERT: I 258 GLU cc_start: 0.6626 (mm-30) cc_final: 0.5768 (tp30) REVERT: I 311 LEU cc_start: 0.6473 (tm) cc_final: 0.6150 (pt) REVERT: I 320 ASN cc_start: 0.7313 (m-40) cc_final: 0.7036 (m-40) REVERT: I 342 MET cc_start: 0.5196 (mmt) cc_final: 0.4666 (mtp) REVERT: I 348 LEU cc_start: 0.6150 (OUTLIER) cc_final: 0.5185 (pt) REVERT: G 193 MET cc_start: 0.8949 (mtt) cc_final: 0.8646 (mtt) REVERT: G 222 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8707 (mtt180) REVERT: G 349 HIS cc_start: 0.6693 (OUTLIER) cc_final: 0.6457 (t70) REVERT: B 39 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9088 (pp) REVERT: B 215 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8727 (mm) REVERT: B 241 GLN cc_start: 0.6218 (mt0) cc_final: 0.5838 (tt0) REVERT: B 294 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8274 (m) REVERT: B 314 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8178 (mt-10) REVERT: C 42 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8248 (mt0) REVERT: D 96 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: E 2 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8508 (tmtt) REVERT: E 99 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8831 (pt0) REVERT: E 193 MET cc_start: 0.9115 (mtt) cc_final: 0.8901 (mtt) REVERT: E 277 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6909 (mp0) REVERT: E 287 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.5949 (p90) REVERT: F 146 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8197 (p) REVERT: F 292 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: F 293 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7742 (p0) REVERT: H 102 ARG cc_start: 0.6329 (pmt100) cc_final: 0.4956 (tpt170) REVERT: H 109 LYS cc_start: 0.8087 (mttt) cc_final: 0.7632 (mmtt) outliers start: 94 outliers final: 47 residues processed: 377 average time/residue: 0.6666 time to fit residues: 294.0722 Evaluate side-chains 354 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 288 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 344 GLU Chi-restraints excluded: chain J residue 345 GLN Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 374 CYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 349 HIS Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 104 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 280 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 120 optimal weight: 0.0370 chunk 91 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 264 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 263 optimal weight: 1.9990 chunk 316 optimal weight: 4.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 599 ASN J 313 GLN I 80 GLN G 315 HIS B 114 GLN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN D 110 GLN E 55 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 HIS H 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.161486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.108857 restraints weight = 34138.041| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.72 r_work: 0.2959 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28929 Z= 0.137 Angle : 0.578 11.177 39505 Z= 0.298 Chirality : 0.042 0.400 4374 Planarity : 0.005 0.059 4822 Dihedral : 14.505 178.987 4529 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.45 % Favored : 94.52 % Rotamer: Outliers : 3.01 % Allowed : 20.26 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.15), residues: 3269 helix: 0.76 (0.16), residues: 1116 sheet: 0.13 (0.25), residues: 466 loop : -1.32 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 164 TYR 0.016 0.001 TYR C 275 PHE 0.043 0.001 PHE J 40 TRP 0.022 0.001 TRP I 142 HIS 0.013 0.001 HIS G 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (28920) covalent geometry : angle 0.57772 / 0.30 (39505) hydrogen bonds : bond 0.03389 / 3.49 ( 861) hydrogen bonds : angle 4.45277 / 5.30 ( 2431) metal coordination : bond 0.00119 / 0.11 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 285 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5656 (tpp) cc_final: 0.3855 (mpt) REVERT: A 210 TYR cc_start: 0.8695 (m-80) cc_final: 0.8366 (m-80) REVERT: A 472 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7967 (t70) REVERT: A 543 TYR cc_start: 0.7635 (t80) cc_final: 0.6887 (t80) REVERT: A 570 TYR cc_start: 0.8041 (m-80) cc_final: 0.7584 (m-80) REVERT: J 105 THR cc_start: 0.3423 (m) cc_final: 0.3129 (p) REVERT: J 169 TYR cc_start: 0.3790 (p90) cc_final: 0.3144 (p90) REVERT: J 217 LYS cc_start: 0.7449 (mmmm) cc_final: 0.6685 (mmmt) REVERT: J 228 MET cc_start: 0.7866 (mtt) cc_final: 0.7289 (tmt) REVERT: J 232 ASP cc_start: 0.7463 (m-30) cc_final: 0.7186 (m-30) REVERT: J 238 PHE cc_start: 0.6924 (t80) cc_final: 0.6569 (t80) REVERT: J 272 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8138 (mt-10) REVERT: J 322 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7983 (tppp) REVERT: J 344 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7287 (pp20) REVERT: J 345 GLN cc_start: 0.8172 (pt0) cc_final: 0.7933 (pt0) REVERT: J 384 GLU cc_start: 0.6936 (pt0) cc_final: 0.6472 (pt0) REVERT: I 3 LEU cc_start: 0.8647 (mt) cc_final: 0.8382 (mp) REVERT: I 4 GLN cc_start: 0.7379 (mm-40) cc_final: 0.6850 (mm-40) REVERT: I 89 LEU cc_start: 0.8626 (mt) cc_final: 0.8385 (mt) REVERT: I 155 VAL cc_start: 0.7627 (t) cc_final: 0.7023 (m) REVERT: I 177 ILE cc_start: 0.6717 (mm) cc_final: 0.6211 (pt) REVERT: I 234 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.6084 (pm20) REVERT: I 258 GLU cc_start: 0.6642 (mm-30) cc_final: 0.5764 (tp30) REVERT: I 311 LEU cc_start: 0.6532 (tm) cc_final: 0.6174 (pt) REVERT: I 320 ASN cc_start: 0.7316 (m-40) cc_final: 0.7021 (m-40) REVERT: I 342 MET cc_start: 0.5201 (mmt) cc_final: 0.4729 (mtp) REVERT: I 348 LEU cc_start: 0.6165 (OUTLIER) cc_final: 0.5269 (pt) REVERT: G 86 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7869 (tp30) REVERT: G 193 MET cc_start: 0.8969 (mtt) cc_final: 0.8695 (mtt) REVERT: G 222 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8668 (mtt180) REVERT: G 293 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7401 (p0) REVERT: G 349 HIS cc_start: 0.6630 (OUTLIER) cc_final: 0.6430 (t70) REVERT: B 39 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9116 (pp) REVERT: B 215 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8714 (mm) REVERT: B 241 GLN cc_start: 0.6222 (mt0) cc_final: 0.5812 (tt0) REVERT: B 314 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8160 (mt-10) REVERT: B 346 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8260 (mpp) REVERT: C 42 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8341 (mt0) REVERT: D 96 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: D 287 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7317 (p90) REVERT: E 43 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8378 (mtp) REVERT: E 99 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8730 (pt0) REVERT: E 193 MET cc_start: 0.9136 (mtt) cc_final: 0.8860 (mtt) REVERT: E 277 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6977 (mp0) REVERT: E 287 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.5998 (p90) REVERT: F 292 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: F 293 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7725 (p0) REVERT: H 102 ARG cc_start: 0.6068 (pmt100) cc_final: 0.4849 (tpt170) REVERT: H 109 LYS cc_start: 0.8062 (mttt) cc_final: 0.7617 (mmtt) outliers start: 89 outliers final: 55 residues processed: 350 average time/residue: 0.6703 time to fit residues: 275.3207 Evaluate side-chains 356 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 280 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 322 LYS Chi-restraints excluded: chain J residue 344 GLU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 374 CYS Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 293 ASP Chi-restraints excluded: chain G residue 349 HIS Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 43 MET Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 346 MET Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 57 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 309 optimal weight: 0.9980 chunk 276 optimal weight: 0.7980 chunk 143 optimal weight: 0.0870 chunk 146 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 210 optimal weight: 0.9980 chunk 165 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 599 ASN J 345 GLN I 80 GLN G 315 HIS B 114 GLN B 138 ASN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN C 218 ASN D 110 GLN E 55 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.162207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110407 restraints weight = 33887.350| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.66 r_work: 0.2980 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28929 Z= 0.114 Angle : 0.554 12.249 39505 Z= 0.286 Chirality : 0.041 0.384 4374 Planarity : 0.005 0.055 4822 Dihedral : 14.426 178.047 4529 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.17 % Favored : 94.80 % Rotamer: Outliers : 2.77 % Allowed : 20.40 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.15), residues: 3269 helix: 0.88 (0.16), residues: 1116 sheet: 0.14 (0.25), residues: 461 loop : -1.28 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 103 TYR 0.015 0.001 TYR C 275 PHE 0.035 0.001 PHE J 40 TRP 0.021 0.001 TRP I 142 HIS 0.014 0.001 HIS G 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (28920) covalent geometry : angle 0.55370 / 0.29 (39505) hydrogen bonds : bond 0.03203 / 3.30 ( 861) hydrogen bonds : angle 4.42486 / 5.26 ( 2431) metal coordination : bond 0.00089 / 0.08 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 291 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5640 (tpp) cc_final: 0.3825 (mpt) REVERT: A 210 TYR cc_start: 0.8683 (m-80) cc_final: 0.8327 (m-80) REVERT: A 247 MET cc_start: 0.8523 (tpt) cc_final: 0.7812 (tpt) REVERT: A 472 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7948 (t70) REVERT: A 543 TYR cc_start: 0.7617 (t80) cc_final: 0.6909 (t80) REVERT: A 570 TYR cc_start: 0.8047 (m-80) cc_final: 0.7645 (m-80) REVERT: J 62 TYR cc_start: 0.4805 (p90) cc_final: 0.4372 (p90) REVERT: J 169 TYR cc_start: 0.3736 (p90) cc_final: 0.3115 (p90) REVERT: J 217 LYS cc_start: 0.7386 (mmmm) cc_final: 0.6617 (mmmt) REVERT: J 228 MET cc_start: 0.7932 (mtt) cc_final: 0.7318 (tmt) REVERT: J 238 PHE cc_start: 0.6885 (t80) cc_final: 0.6523 (t80) REVERT: J 272 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8143 (mt-10) REVERT: J 322 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7929 (tppp) REVERT: J 344 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7222 (pp20) REVERT: I 3 LEU cc_start: 0.8627 (mt) cc_final: 0.8365 (mp) REVERT: I 4 GLN cc_start: 0.7366 (mm-40) cc_final: 0.6836 (mm-40) REVERT: I 89 LEU cc_start: 0.8624 (mt) cc_final: 0.8366 (mt) REVERT: I 155 VAL cc_start: 0.7611 (t) cc_final: 0.6999 (m) REVERT: I 177 ILE cc_start: 0.6781 (mm) cc_final: 0.6245 (pt) REVERT: I 234 GLU cc_start: 0.6323 (OUTLIER) cc_final: 0.6007 (pm20) REVERT: I 236 ASP cc_start: 0.3502 (t70) cc_final: 0.3208 (m-30) REVERT: I 258 GLU cc_start: 0.6683 (mm-30) cc_final: 0.5785 (tp30) REVERT: I 311 LEU cc_start: 0.6459 (tm) cc_final: 0.6073 (pt) REVERT: I 320 ASN cc_start: 0.7434 (m-40) cc_final: 0.7161 (m-40) REVERT: I 342 MET cc_start: 0.5178 (mmt) cc_final: 0.4730 (mtp) REVERT: I 348 LEU cc_start: 0.6171 (OUTLIER) cc_final: 0.5278 (pt) REVERT: G 86 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7850 (tp30) REVERT: G 193 MET cc_start: 0.8936 (mtt) cc_final: 0.8652 (mtt) REVERT: G 222 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8613 (mtt180) REVERT: G 293 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7384 (p0) REVERT: G 349 HIS cc_start: 0.6671 (OUTLIER) cc_final: 0.6453 (t70) REVERT: B 39 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9115 (pp) REVERT: B 215 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8730 (mm) REVERT: B 241 GLN cc_start: 0.6270 (mt0) cc_final: 0.5852 (tt0) REVERT: B 314 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8139 (mt-10) REVERT: B 346 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8241 (mpp) REVERT: C 42 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8295 (mt0) REVERT: D 72 GLN cc_start: 0.9094 (tt0) cc_final: 0.8832 (tt0) REVERT: D 96 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: E 43 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8528 (mmm) REVERT: E 99 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8734 (pt0) REVERT: E 193 MET cc_start: 0.9129 (mtt) cc_final: 0.8868 (mtt) REVERT: E 222 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8338 (mtm-85) REVERT: E 277 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6937 (mp0) REVERT: E 287 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.5967 (p90) REVERT: F 292 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: F 293 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7588 (p0) REVERT: H 102 ARG cc_start: 0.6118 (pmt100) cc_final: 0.4832 (tpt170) REVERT: H 109 LYS cc_start: 0.8145 (mttt) cc_final: 0.7691 (mmtt) outliers start: 82 outliers final: 48 residues processed: 349 average time/residue: 0.6866 time to fit residues: 280.6980 Evaluate side-chains 356 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 287 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 322 LYS Chi-restraints excluded: chain J residue 344 GLU Chi-restraints excluded: chain J residue 345 GLN Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 374 CYS Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 293 ASP Chi-restraints excluded: chain G residue 349 HIS Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 43 MET Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 83 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 291 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 42 optimal weight: 0.1980 chunk 292 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 599 ASN J 313 GLN J 345 GLN I 80 GLN G 315 HIS B 114 GLN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN D 110 GLN E 55 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.161045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.108962 restraints weight = 34071.605| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.65 r_work: 0.2966 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28929 Z= 0.139 Angle : 0.579 12.198 39505 Z= 0.298 Chirality : 0.042 0.378 4374 Planarity : 0.005 0.052 4822 Dihedral : 14.437 178.771 4529 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.59 % Rotamer: Outliers : 2.94 % Allowed : 20.43 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 3269 helix: 0.83 (0.16), residues: 1121 sheet: 0.11 (0.25), residues: 471 loop : -1.30 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG J 346 TYR 0.015 0.001 TYR C 275 PHE 0.037 0.001 PHE J 18 TRP 0.022 0.001 TRP I 142 HIS 0.014 0.001 HIS G 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (28920) covalent geometry : angle 0.57850 / 0.30 (39505) hydrogen bonds : bond 0.03388 / 3.51 ( 861) hydrogen bonds : angle 4.43503 / 5.27 ( 2431) metal coordination : bond 0.00115 / 0.11 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11924.64 seconds wall clock time: 203 minutes 32.14 seconds (12212.14 seconds total)