Starting phenix.real_space_refine on Fri Mar 6 04:05:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v9q_21126/03_2026/6v9q_21126_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v9q_21126/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6v9q_21126/03_2026/6v9q_21126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v9q_21126/03_2026/6v9q_21126.map" model { file = "/net/cci-nas-00/data/ceres_data/6v9q_21126/03_2026/6v9q_21126_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v9q_21126/03_2026/6v9q_21126_neut.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 6.68, per 1000 atoms: 0.24 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: 2.46 Conformation dependent library (CDL) restraints added in 1.0 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: 3.66 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: 6.96 Time building geometry restraints manager: 3.33 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: 37562 2.38 - 4.76: 1630 4.76 - 7.14: 233 7.14 - 9.53: 62 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=" 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 angle pdb=" N MET A 564 " pdb=" CA MET A 564 " pdb=" C MET A 564 " ideal model delta sigma weight residual 110.91 117.55 -6.64 1.17e+00 7.31e-01 3.22e+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: 3521 0.079 - 0.159: 727 0.159 - 0.238: 97 0.238 - 0.318: 26 0.318 - 0.397: 3 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=" 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 chirality pdb=" C3' C K 46 " pdb=" C4' C K 46 " pdb=" O3' C K 46 " pdb=" C2' C K 46 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.71e+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: 2.220 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 34.090 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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= 0.436 Angle : 1.123 11.907 39505 Z= 0.660 Chirality : 0.068 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 covalent geometry : bond 0.00840 (28920) covalent geometry : angle 1.12250 (39505) hydrogen bonds : bond 0.30491 ( 861) hydrogen bonds : angle 10.02253 ( 2431) metal coordination : bond 0.24358 ( 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 : 0.812 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: 0.4836 (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: 0.7772 (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: 0.7413 (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: 0.6793 (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: 0.7798 (mmtt) outliers start: 46 outliers final: 12 residues processed: 778 average time/residue: 0.7269 time to fit residues: 644.2185 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 : 1.002 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 200 GLN A 227 GLN A 235 HIS A 420 HIS A 443 HIS A 486 ASN A 610 ASN J 66 ASN J 143 HIS J 237 HIS J 262 ASN J 313 GLN J 381 GLN I 47 ASN I 66 ASN I 202 ASN I 237 HIS I 296 HIS I 324 ASN G 299 HIS 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 C 349 HIS D 77 HIS D 84 HIS D 110 GLN D 214 HIS D 299 HIS E 42 GLN E 55 GLN E 77 HIS ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 HIS F 99 GLN F 299 HIS F 328 GLN 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: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.166879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114966 restraints weight = 34413.460| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.70 r_work: 0.3072 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28929 Z= 0.130 Angle : 0.638 10.497 39505 Z= 0.331 Chirality : 0.043 0.234 4374 Planarity : 0.006 0.064 4822 Dihedral : 15.144 177.966 4548 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.43 % Allowed : 13.84 % Favored : 81.73 % 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: -2.84 (0.13), residues: 3269 helix: -2.05 (0.13), residues: 1104 sheet: -0.81 (0.24), residues: 460 loop : -2.07 (0.13), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 37 TYR 0.021 0.002 TYR J 219 PHE 0.022 0.002 PHE J 235 TRP 0.018 0.002 TRP G 161 HIS 0.009 0.001 HIS C 315 Details of bonding type rmsd covalent geometry : bond 0.00293 (28920) covalent geometry : angle 0.63768 (39505) hydrogen bonds : bond 0.04247 ( 861) hydrogen bonds : angle 5.48548 ( 2431) metal coordination : bond 0.00534 ( 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 556 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 425 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5893 (tpp) cc_final: 0.4078 (mpt) REVERT: A 210 TYR cc_start: 0.8805 (m-80) cc_final: 0.8471 (m-80) REVERT: A 472 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7981 (t70) REVERT: A 485 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8451 (p) REVERT: A 522 PHE cc_start: 0.8546 (m-80) cc_final: 0.8328 (m-80) REVERT: A 543 TYR cc_start: 0.7404 (t80) cc_final: 0.6873 (t80) REVERT: A 570 TYR cc_start: 0.7898 (m-80) cc_final: 0.7181 (m-80) REVERT: J 169 TYR cc_start: 0.3964 (p90) cc_final: 0.3295 (p90) REVERT: J 228 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7672 (mtt) REVERT: J 238 PHE cc_start: 0.6931 (t80) cc_final: 0.6616 (t80) REVERT: J 272 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7918 (pt0) REVERT: J 331 MET cc_start: 0.8393 (ttt) cc_final: 0.8181 (ttm) REVERT: J 344 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7174 (pp20) REVERT: I 4 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6609 (mm-40) REVERT: I 142 TRP cc_start: 0.8651 (m-10) cc_final: 0.8441 (m-10) REVERT: I 177 ILE cc_start: 0.6847 (mm) cc_final: 0.6423 (pt) REVERT: I 183 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.6123 (mm-30) REVERT: I 258 GLU cc_start: 0.6807 (mm-30) cc_final: 0.5992 (tp30) REVERT: I 342 MET cc_start: 0.5326 (mmt) cc_final: 0.4593 (ttm) REVERT: I 348 LEU cc_start: 0.5669 (OUTLIER) cc_final: 0.4769 (pt) REVERT: G 17 ASP cc_start: 0.9036 (m-30) cc_final: 0.8744 (m-30) REVERT: G 146 THR cc_start: 0.8457 (m) cc_final: 0.7895 (p) REVERT: G 204 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.6374 (tp) REVERT: B 172 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7720 (ttm110) REVERT: B 294 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8356 (m) REVERT: B 329 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8170 (tm-30) REVERT: C 42 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8001 (mt0) REVERT: C 210 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7991 (ttm170) REVERT: D 63 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8046 (tt0) REVERT: D 96 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: E 99 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8706 (pt0) REVERT: E 176 THR cc_start: 0.9055 (m) cc_final: 0.8838 (m) REVERT: E 180 ASP cc_start: 0.9139 (m-30) cc_final: 0.8706 (m-30) REVERT: E 220 MET cc_start: 0.8344 (ttt) cc_final: 0.8004 (ttt) REVERT: E 277 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6816 (mp0) REVERT: E 287 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.5509 (p90) REVERT: E 348 GLN cc_start: 0.8183 (mp10) cc_final: 0.7877 (mp10) REVERT: F 146 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8307 (p) REVERT: H 73 TYR cc_start: 0.7566 (t80) cc_final: 0.7232 (t80) REVERT: H 83 PHE cc_start: 0.6116 (OUTLIER) cc_final: 0.5907 (m-10) REVERT: H 102 ARG cc_start: 0.6139 (pmt100) cc_final: 0.4988 (tpt170) REVERT: H 109 LYS cc_start: 0.8099 (mttt) cc_final: 0.7578 (mmtt) REVERT: H 137 SER cc_start: 0.8817 (p) cc_final: 0.8572 (p) REVERT: H 161 ARG cc_start: 0.7475 (mtt90) cc_final: 0.7178 (mtp85) REVERT: H 162 ASN cc_start: 0.7811 (m-40) cc_final: 0.7331 (m-40) outliers start: 131 outliers final: 39 residues processed: 517 average time/residue: 0.5942 time to fit residues: 358.5483 Evaluate side-chains 387 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 331 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 472 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 344 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 289 VAL 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 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 287 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 63 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 280 GLU 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 121 THR 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 287 PHE Chi-restraints excluded: chain F residue 3 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 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 Chi-restraints excluded: chain H residue 155 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 175 optimal weight: 2.9990 chunk 193 optimal weight: 0.0030 chunk 266 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 258 optimal weight: 4.9990 chunk 195 optimal weight: 0.5980 chunk 286 optimal weight: 0.2980 chunk 223 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 131 optimal weight: 0.0470 chunk 145 optimal weight: 0.2980 overall best weight: 0.2488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 313 GLN J 381 GLN I 42 GLN I 80 GLN G 35 ASN G 290 HIS B 114 GLN C 299 HIS D 110 GLN E 55 GLN E 299 HIS E 349 HIS F 99 GLN H 71 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.169564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119083 restraints weight = 34688.443| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.75 r_work: 0.3117 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28929 Z= 0.099 Angle : 0.544 9.561 39505 Z= 0.281 Chirality : 0.040 0.222 4374 Planarity : 0.005 0.061 4822 Dihedral : 14.819 179.417 4537 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.79 % Allowed : 16.44 % Favored : 79.77 % 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: -1.83 (0.13), residues: 3269 helix: -0.80 (0.14), residues: 1111 sheet: -0.46 (0.23), residues: 475 loop : -1.72 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 20 TYR 0.018 0.001 TYR D 275 PHE 0.025 0.001 PHE H 163 TRP 0.015 0.001 TRP I 247 HIS 0.023 0.001 HIS H 150 Details of bonding type rmsd covalent geometry : bond 0.00210 (28920) covalent geometry : angle 0.54433 (39505) hydrogen bonds : bond 0.03347 ( 861) hydrogen bonds : angle 4.84523 ( 2431) metal coordination : bond 0.00107 ( 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 495 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 383 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6034 (tpp) cc_final: 0.4477 (mpt) REVERT: A 180 GLN cc_start: 0.7240 (mt0) cc_final: 0.6586 (tm-30) REVERT: A 210 TYR cc_start: 0.8761 (m-80) cc_final: 0.8453 (m-80) REVERT: A 247 MET cc_start: 0.8287 (tpt) cc_final: 0.7763 (tpt) REVERT: A 543 TYR cc_start: 0.7574 (t80) cc_final: 0.6875 (t80) REVERT: A 562 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6682 (mt0) REVERT: A 570 TYR cc_start: 0.7906 (m-80) cc_final: 0.7182 (m-80) REVERT: J 105 THR cc_start: 0.3357 (m) cc_final: 0.3084 (p) REVERT: J 169 TYR cc_start: 0.4033 (p90) cc_final: 0.3512 (p90) REVERT: J 208 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6906 (tm-30) REVERT: J 228 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7688 (tmt) REVERT: J 238 PHE cc_start: 0.7024 (t80) cc_final: 0.6819 (t80) REVERT: J 272 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7909 (pt0) REVERT: J 384 GLU cc_start: 0.7019 (pt0) cc_final: 0.6735 (pt0) REVERT: I 3 LEU cc_start: 0.8614 (mt) cc_final: 0.8312 (mp) REVERT: I 4 GLN cc_start: 0.7208 (mm-40) cc_final: 0.6612 (mm-40) REVERT: I 99 MET cc_start: 0.6737 (mtm) cc_final: 0.6240 (ptp) REVERT: I 142 TRP cc_start: 0.8641 (m-10) cc_final: 0.8414 (m-10) REVERT: I 177 ILE cc_start: 0.6752 (mm) cc_final: 0.6275 (pt) REVERT: I 234 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.5981 (pm20) REVERT: I 258 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6154 (tp30) REVERT: I 332 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6637 (mt) REVERT: I 342 MET cc_start: 0.5183 (mmt) cc_final: 0.4678 (mtp) REVERT: I 348 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.4737 (pt) REVERT: G 86 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7922 (tp30) REVERT: G 146 THR cc_start: 0.8436 (m) cc_final: 0.7860 (p) REVERT: G 193 MET cc_start: 0.8940 (mtt) cc_final: 0.8538 (mtt) REVERT: B 294 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8333 (m) REVERT: B 305 ASP cc_start: 0.8686 (p0) cc_final: 0.8485 (p0) REVERT: B 329 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8256 (tm-30) REVERT: C 42 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8269 (mt0) REVERT: C 58 LYS cc_start: 0.8214 (mmmm) cc_final: 0.7802 (mmmm) REVERT: D 96 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: E 176 THR cc_start: 0.9027 (m) cc_final: 0.8785 (m) REVERT: E 180 ASP cc_start: 0.9138 (m-30) cc_final: 0.8696 (m-30) REVERT: E 220 MET cc_start: 0.8368 (ttt) cc_final: 0.7927 (ttm) REVERT: E 277 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6748 (mp0) REVERT: E 287 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.5557 (p90) REVERT: E 314 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7961 (mp0) REVERT: E 348 GLN cc_start: 0.8048 (mp10) cc_final: 0.7806 (mp10) REVERT: F 146 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8086 (p) REVERT: F 293 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7838 (p0) REVERT: H 102 ARG cc_start: 0.6011 (pmt100) cc_final: 0.4986 (tpt170) REVERT: H 109 LYS cc_start: 0.8001 (mttt) cc_final: 0.7479 (mmtt) outliers start: 112 outliers final: 38 residues processed: 462 average time/residue: 0.6343 time to fit residues: 340.4605 Evaluate side-chains 385 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 334 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 562 GLN 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 228 MET 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 G residue 86 GLU Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 146 THR 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 91 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 30 THR 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 280 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 304 LYS 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 91 VAL Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 346 MET 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 289 VAL Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 151 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 105 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 240 optimal weight: 0.0050 chunk 64 optimal weight: 20.0000 chunk 230 optimal weight: 3.9990 chunk 292 optimal weight: 5.9990 chunk 303 optimal weight: 2.9990 chunk 199 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 121 optimal weight: 0.0370 overall best weight: 2.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN J 25 ASN J 194 HIS I 42 GLN I 80 GLN G 35 ASN G 349 HIS B 114 GLN B 184 ASN C 84 HIS C 110 GLN D 110 GLN E 55 GLN E 84 HIS E 218 ASN E 348 GLN F 99 GLN H 32 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.156990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.104209 restraints weight = 33893.385| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.82 r_work: 0.2882 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 28929 Z= 0.266 Angle : 0.730 11.687 39505 Z= 0.374 Chirality : 0.049 0.271 4374 Planarity : 0.006 0.065 4822 Dihedral : 14.924 176.475 4529 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 5.62 % Allowed : 15.87 % Favored : 78.52 % 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: -1.55 (0.14), residues: 3269 helix: -0.45 (0.15), residues: 1115 sheet: -0.48 (0.23), residues: 500 loop : -1.60 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 37 TYR 0.028 0.003 TYR E 50 PHE 0.031 0.002 PHE F 207 TRP 0.022 0.002 TRP G 161 HIS 0.012 0.002 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00644 (28920) covalent geometry : angle 0.73039 (39505) hydrogen bonds : bond 0.04749 ( 861) hydrogen bonds : angle 4.97249 ( 2431) metal coordination : bond 0.00228 ( 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 490 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 324 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5310 (tpp) cc_final: 0.3678 (mpt) REVERT: A 210 TYR cc_start: 0.8848 (m-80) cc_final: 0.8534 (m-80) REVERT: A 247 MET cc_start: 0.8836 (tpt) cc_final: 0.8106 (tpt) REVERT: A 472 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7979 (t70) REVERT: A 543 TYR cc_start: 0.7541 (t80) cc_final: 0.6905 (t80) REVERT: A 562 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.7053 (mt0) REVERT: A 570 TYR cc_start: 0.8068 (m-80) cc_final: 0.7744 (m-80) REVERT: J 105 THR cc_start: 0.3646 (m) cc_final: 0.3200 (p) REVERT: J 169 TYR cc_start: 0.3767 (p90) cc_final: 0.3309 (p90) REVERT: J 228 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7649 (mtt) REVERT: J 238 PHE cc_start: 0.6648 (t80) cc_final: 0.6177 (t80) REVERT: J 249 ARG cc_start: 0.6895 (tpp-160) cc_final: 0.6593 (tpm170) REVERT: J 272 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7929 (pt0) REVERT: J 384 GLU cc_start: 0.7153 (pt0) cc_final: 0.6658 (pt0) REVERT: I 4 GLN cc_start: 0.7330 (mm-40) cc_final: 0.6708 (mm-40) REVERT: I 45 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7746 (m-30) REVERT: I 99 MET cc_start: 0.6848 (mtm) cc_final: 0.6372 (mtm) REVERT: I 177 ILE cc_start: 0.6800 (mm) cc_final: 0.6400 (pt) REVERT: I 258 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6656 (mm-30) REVERT: I 331 MET cc_start: 0.7363 (tpt) cc_final: 0.6948 (tmm) REVERT: I 332 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6777 (mt) REVERT: I 342 MET cc_start: 0.5550 (mmt) cc_final: 0.4686 (mtp) REVERT: I 348 LEU cc_start: 0.5946 (OUTLIER) cc_final: 0.5028 (pt) REVERT: G 146 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8173 (p) REVERT: G 193 MET cc_start: 0.8974 (mtt) cc_final: 0.8686 (mtt) REVERT: B 39 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9084 (pp) REVERT: B 215 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8892 (mm) REVERT: B 241 GLN cc_start: 0.6509 (mt0) cc_final: 0.6248 (tt0) REVERT: B 314 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8184 (mt-10) REVERT: B 320 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.8025 (mt) REVERT: C 42 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8337 (mt0) REVERT: C 44 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8400 (pt0) REVERT: D 63 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8008 (tt0) REVERT: D 96 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: D 146 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.8902 (p) REVERT: D 225 GLN cc_start: 0.9339 (OUTLIER) cc_final: 0.9102 (mt0) REVERT: D 287 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7355 (p90) REVERT: D 311 GLN cc_start: 0.8802 (mt0) cc_final: 0.8361 (mm-40) REVERT: D 346 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8181 (mmm) REVERT: E 37 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8554 (ptt180) REVERT: E 43 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8513 (mmm) REVERT: E 220 MET cc_start: 0.8883 (ttt) cc_final: 0.8532 (ttt) REVERT: E 222 ARG cc_start: 0.9312 (OUTLIER) cc_final: 0.8446 (mtm-85) REVERT: E 279 THR cc_start: 0.8902 (p) cc_final: 0.8691 (m) REVERT: E 293 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7721 (p0) REVERT: F 43 MET cc_start: 0.8649 (mtp) cc_final: 0.8420 (mmt) REVERT: F 220 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8385 (ttp) REVERT: F 280 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8103 (pt0) REVERT: F 292 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: F 293 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7803 (p0) REVERT: H 102 ARG cc_start: 0.6301 (pmt100) cc_final: 0.4957 (tpt170) REVERT: H 109 LYS cc_start: 0.8154 (mttt) cc_final: 0.7651 (mmtt) REVERT: H 161 ARG cc_start: 0.7958 (mtp85) cc_final: 0.7565 (mtp85) outliers start: 166 outliers final: 71 residues processed: 449 average time/residue: 0.6528 time to fit residues: 339.9659 Evaluate side-chains 385 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 286 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 443 HIS 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 616 LEU Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 272 GLU Chi-restraints excluded: chain I residue 45 ASP 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 198 CYS Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 323 MET 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 97 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 176 THR 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 39 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 320 LEU 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 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 27 ASP 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 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 225 GLN Chi-restraints excluded: chain D residue 282 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 14 ASP Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 37 ARG 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 121 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 291 ARG Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 346 MET Chi-restraints excluded: chain E residue 348 GLN Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 292 GLU 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 168 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 157 optimal weight: 0.2980 chunk 140 optimal weight: 0.9990 chunk 229 optimal weight: 0.9990 chunk 264 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 216 optimal weight: 0.8980 chunk 279 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 204 optimal weight: 0.5980 chunk 214 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 581 ASN A 599 ASN J 313 GLN I 80 GLN B 114 GLN C 110 GLN D 110 GLN E 55 GLN E 348 GLN F 349 HIS H 32 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.161621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109628 restraints weight = 34072.072| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.69 r_work: 0.2972 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28929 Z= 0.113 Angle : 0.559 9.212 39505 Z= 0.289 Chirality : 0.041 0.339 4374 Planarity : 0.005 0.052 4822 Dihedral : 14.667 179.985 4529 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.19 % Allowed : 17.59 % Favored : 78.21 % 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: 0.12 (0.16), residues: 1118 sheet: -0.28 (0.24), residues: 485 loop : -1.44 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 164 TYR 0.017 0.001 TYR D 275 PHE 0.025 0.001 PHE H 163 TRP 0.015 0.001 TRP G 161 HIS 0.010 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00257 (28920) covalent geometry : angle 0.55890 (39505) hydrogen bonds : bond 0.03261 ( 861) hydrogen bonds : angle 4.56803 ( 2431) metal coordination : bond 0.00084 ( 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 443 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 319 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7531 (m-80) cc_final: 0.7318 (m-80) REVERT: A 177 MET cc_start: 0.5588 (tpp) cc_final: 0.3998 (mpt) REVERT: A 247 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8012 (tpt) REVERT: A 393 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8131 (mt) REVERT: A 472 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.8010 (t70) REVERT: A 543 TYR cc_start: 0.7604 (t80) cc_final: 0.6813 (t80) REVERT: A 570 TYR cc_start: 0.8092 (m-80) cc_final: 0.7472 (m-80) REVERT: J 105 THR cc_start: 0.3533 (m) cc_final: 0.3103 (p) REVERT: J 154 ASN cc_start: 0.4634 (m110) cc_final: 0.4376 (p0) REVERT: J 169 TYR cc_start: 0.3940 (p90) cc_final: 0.3587 (p90) REVERT: J 228 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7557 (tmt) REVERT: J 238 PHE cc_start: 0.6672 (t80) cc_final: 0.6230 (t80) REVERT: J 272 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8168 (mt-10) REVERT: J 384 GLU cc_start: 0.7124 (pt0) cc_final: 0.6686 (pt0) REVERT: I 3 LEU cc_start: 0.8650 (mt) cc_final: 0.8361 (mp) REVERT: I 4 GLN cc_start: 0.7354 (mm-40) cc_final: 0.6806 (mm-40) REVERT: I 99 MET cc_start: 0.6732 (mtm) cc_final: 0.6116 (ptp) REVERT: I 158 ILE cc_start: 0.6451 (mp) cc_final: 0.6148 (tp) REVERT: I 177 ILE cc_start: 0.6734 (mm) cc_final: 0.6269 (pt) REVERT: I 234 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.6003 (pm20) REVERT: I 258 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6052 (tp30) REVERT: I 342 MET cc_start: 0.5083 (mmt) cc_final: 0.4803 (mtp) REVERT: I 348 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5241 (pt) REVERT: G 86 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7921 (tp30) REVERT: G 193 MET cc_start: 0.8904 (mtt) cc_final: 0.8585 (mtt) REVERT: B 39 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9009 (pp) REVERT: B 215 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8788 (mm) REVERT: B 241 GLN cc_start: 0.6331 (mt0) cc_final: 0.6023 (tt0) REVERT: B 320 LEU cc_start: 0.8233 (mm) cc_final: 0.7956 (mt) REVERT: C 42 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8299 (mt0) REVERT: D 72 GLN cc_start: 0.9106 (tt0) cc_final: 0.8836 (tt0) REVERT: D 96 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: D 311 GLN cc_start: 0.8805 (mt0) cc_final: 0.8345 (mm-40) REVERT: E 185 LYS cc_start: 0.8833 (ttmt) cc_final: 0.8349 (tttt) REVERT: E 220 MET cc_start: 0.8769 (ttt) cc_final: 0.8319 (ttm) REVERT: E 222 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8327 (mtm-85) REVERT: E 277 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6598 (mp0) REVERT: E 287 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.6155 (p90) REVERT: E 348 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: F 42 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.6786 (mm-40) REVERT: F 146 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8362 (p) REVERT: F 220 MET cc_start: 0.8509 (ttt) cc_final: 0.8228 (ttp) REVERT: F 293 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7632 (p0) REVERT: H 102 ARG cc_start: 0.6202 (pmt100) cc_final: 0.4954 (tpt170) REVERT: H 109 LYS cc_start: 0.8157 (mttt) cc_final: 0.7651 (mmtt) REVERT: H 150 HIS cc_start: 0.7174 (OUTLIER) cc_final: 0.6037 (t-90) outliers start: 124 outliers final: 53 residues processed: 409 average time/residue: 0.6476 time to fit residues: 306.8353 Evaluate side-chains 368 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 297 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 393 ILE 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 228 MET Chi-restraints excluded: chain J residue 277 ASP Chi-restraints excluded: chain J residue 322 LYS Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 307 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 287 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 88 SER 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 328 GLN 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 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 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 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 282 LEU 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 30 THR Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 91 VAL 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 E residue 348 GLN Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 42 GLN 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 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: 10.0000 chunk 121 optimal weight: 5.9990 chunk 317 optimal weight: 0.6980 chunk 265 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 238 optimal weight: 0.1980 chunk 105 optimal weight: 0.8980 chunk 288 optimal weight: 4.9990 chunk 160 optimal weight: 0.0050 chunk 18 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN I 80 GLN B 114 GLN B 348 GLN C 110 GLN D 110 GLN E 55 GLN ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.163200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111770 restraints weight = 33831.532| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.67 r_work: 0.3015 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 28929 Z= 0.106 Angle : 0.538 9.139 39505 Z= 0.277 Chirality : 0.040 0.199 4374 Planarity : 0.004 0.052 4822 Dihedral : 14.379 176.731 4527 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.54 % Favored : 94.43 % Rotamer: Outliers : 3.72 % Allowed : 18.23 % Favored : 78.04 % 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: -0.73 (0.15), residues: 3269 helix: 0.56 (0.16), residues: 1114 sheet: -0.17 (0.24), residues: 493 loop : -1.32 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 164 TYR 0.016 0.001 TYR C 275 PHE 0.024 0.001 PHE H 163 TRP 0.016 0.001 TRP I 142 HIS 0.009 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00241 (28920) covalent geometry : angle 0.53773 (39505) hydrogen bonds : bond 0.03062 ( 861) hydrogen bonds : angle 4.41405 ( 2431) metal coordination : bond 0.00093 ( 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 419 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 309 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7587 (m-80) cc_final: 0.7310 (m-80) REVERT: A 177 MET cc_start: 0.5714 (tpp) cc_final: 0.4280 (mpt) REVERT: A 180 GLN cc_start: 0.6753 (mt0) cc_final: 0.6293 (tm-30) REVERT: A 247 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.7950 (tpt) REVERT: A 393 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8190 (mt) REVERT: A 472 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7909 (t70) REVERT: A 543 TYR cc_start: 0.7600 (t80) cc_final: 0.6820 (t80) REVERT: A 562 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6844 (mt0) REVERT: A 570 TYR cc_start: 0.8090 (m-80) cc_final: 0.7436 (m-80) REVERT: J 154 ASN cc_start: 0.4634 (m110) cc_final: 0.4336 (p0) REVERT: J 169 TYR cc_start: 0.3975 (p90) cc_final: 0.3667 (p90) REVERT: J 228 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7679 (tmt) REVERT: J 238 PHE cc_start: 0.6660 (t80) cc_final: 0.6198 (t80) REVERT: J 384 GLU cc_start: 0.7139 (pt0) cc_final: 0.6698 (pt0) REVERT: I 3 LEU cc_start: 0.8597 (mt) cc_final: 0.8310 (mp) REVERT: I 4 GLN cc_start: 0.7375 (mm-40) cc_final: 0.6934 (mm-40) REVERT: I 99 MET cc_start: 0.6803 (mtm) cc_final: 0.6323 (ptp) REVERT: I 158 ILE cc_start: 0.6671 (mp) cc_final: 0.6382 (tp) REVERT: I 177 ILE cc_start: 0.6733 (mm) cc_final: 0.6256 (pt) REVERT: I 234 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.6067 (pm20) REVERT: I 258 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6183 (tp30) REVERT: I 311 LEU cc_start: 0.6612 (tm) cc_final: 0.6157 (pp) REVERT: I 342 MET cc_start: 0.5058 (mmt) cc_final: 0.4829 (mtp) REVERT: I 348 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5344 (pt) REVERT: G 86 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7879 (tp30) REVERT: G 193 MET cc_start: 0.8890 (mtt) cc_final: 0.8570 (mtt) REVERT: B 39 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9047 (pp) REVERT: B 44 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: B 215 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8735 (mm) REVERT: B 241 GLN cc_start: 0.6275 (mt0) cc_final: 0.5830 (tt0) REVERT: C 42 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8306 (mt0) REVERT: D 72 GLN cc_start: 0.9081 (tt0) cc_final: 0.8808 (tt0) REVERT: D 96 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: D 287 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7344 (p90) REVERT: E 43 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8523 (mmm) REVERT: E 57 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7823 (pt) REVERT: E 185 LYS cc_start: 0.8816 (ttmt) cc_final: 0.8352 (tttt) REVERT: E 220 MET cc_start: 0.8783 (ttt) cc_final: 0.8397 (ttm) REVERT: E 222 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.8354 (mtm-85) REVERT: E 287 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.6059 (p90) REVERT: E 314 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8329 (mp0) REVERT: F 146 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8285 (p) REVERT: F 220 MET cc_start: 0.8500 (ttt) cc_final: 0.8217 (ttp) REVERT: H 102 ARG cc_start: 0.6248 (pmt100) cc_final: 0.4981 (tpt170) REVERT: H 109 LYS cc_start: 0.8188 (mttt) cc_final: 0.7719 (mmtt) REVERT: H 150 HIS cc_start: 0.7236 (OUTLIER) cc_final: 0.6143 (t-90) REVERT: H 161 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7767 (mtp85) outliers start: 110 outliers final: 53 residues processed: 388 average time/residue: 0.6728 time to fit residues: 301.8118 Evaluate side-chains 354 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 280 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 277 ASP Chi-restraints excluded: chain J residue 322 LYS Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 374 CYS Chi-restraints excluded: chain G residue 2 LYS 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 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 289 VAL Chi-restraints excluded: chain B residue 328 GLN 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 226 VAL 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 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 282 LEU 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 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 57 ILE Chi-restraints excluded: chain E residue 91 VAL 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 314 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 224 optimal weight: 0.5980 chunk 81 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 210 optimal weight: 0.4980 chunk 291 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 283 optimal weight: 3.9990 chunk 316 optimal weight: 0.0980 chunk 147 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN I 80 GLN B 114 GLN C 110 GLN D 110 GLN E 55 GLN E 99 GLN H 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.160128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107905 restraints weight = 33501.040| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.67 r_work: 0.2960 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28929 Z= 0.147 Angle : 0.589 10.058 39505 Z= 0.301 Chirality : 0.042 0.206 4374 Planarity : 0.005 0.065 4822 Dihedral : 14.419 178.438 4527 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.63 % Favored : 94.34 % Rotamer: Outliers : 3.99 % Allowed : 18.47 % Favored : 77.54 % 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: -0.66 (0.15), residues: 3269 helix: 0.61 (0.16), residues: 1118 sheet: -0.08 (0.24), residues: 489 loop : -1.29 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 164 TYR 0.015 0.002 TYR B 175 PHE 0.027 0.001 PHE H 163 TRP 0.020 0.001 TRP I 142 HIS 0.011 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00353 (28920) covalent geometry : angle 0.58928 (39505) hydrogen bonds : bond 0.03536 ( 861) hydrogen bonds : angle 4.48381 ( 2431) metal coordination : bond 0.00144 ( 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 402 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 284 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5616 (tpp) cc_final: 0.4128 (mpt) REVERT: A 180 GLN cc_start: 0.6774 (mt0) cc_final: 0.6432 (tm-30) REVERT: A 247 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8003 (tpt) REVERT: A 393 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8225 (mt) REVERT: A 472 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7913 (t70) REVERT: A 541 SER cc_start: 0.8447 (t) cc_final: 0.8225 (p) REVERT: A 543 TYR cc_start: 0.7590 (t80) cc_final: 0.6924 (t80) REVERT: A 570 TYR cc_start: 0.8097 (m-80) cc_final: 0.7506 (m-80) REVERT: J 62 TYR cc_start: 0.4989 (p90) cc_final: 0.4569 (p90) REVERT: J 154 ASN cc_start: 0.4678 (m110) cc_final: 0.4365 (p0) REVERT: J 169 TYR cc_start: 0.3942 (p90) cc_final: 0.3570 (p90) REVERT: J 228 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7665 (tmt) REVERT: J 238 PHE cc_start: 0.6616 (t80) cc_final: 0.6280 (t80) REVERT: J 272 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8128 (mt-10) REVERT: J 384 GLU cc_start: 0.7093 (pt0) cc_final: 0.6643 (pt0) REVERT: I 4 GLN cc_start: 0.7479 (mm-40) cc_final: 0.6780 (mm-40) REVERT: I 99 MET cc_start: 0.6866 (mtm) cc_final: 0.6505 (mtm) REVERT: I 158 ILE cc_start: 0.6711 (mp) cc_final: 0.6422 (tp) REVERT: I 177 ILE cc_start: 0.6708 (mm) cc_final: 0.6230 (pt) REVERT: I 258 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6675 (mm-30) REVERT: I 311 LEU cc_start: 0.6542 (tm) cc_final: 0.6055 (pp) REVERT: I 342 MET cc_start: 0.5393 (mmt) cc_final: 0.4856 (mtp) REVERT: I 348 LEU cc_start: 0.6118 (OUTLIER) cc_final: 0.5317 (pt) REVERT: G 86 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7935 (tp30) REVERT: G 193 MET cc_start: 0.8927 (mtt) cc_final: 0.8635 (mtt) REVERT: B 39 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9045 (pp) REVERT: B 215 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8782 (mm) REVERT: B 241 GLN cc_start: 0.6465 (mt0) cc_final: 0.6161 (tt0) REVERT: C 42 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8287 (mt0) REVERT: C 58 LYS cc_start: 0.8413 (mmmm) cc_final: 0.8120 (mmmm) REVERT: D 63 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: D 72 GLN cc_start: 0.9079 (tt0) cc_final: 0.8826 (tt0) REVERT: D 96 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: D 176 THR cc_start: 0.9142 (m) cc_final: 0.8921 (p) REVERT: D 287 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7342 (p90) REVERT: E 2 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8471 (tmtt) REVERT: E 43 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8551 (mmm) REVERT: E 57 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7859 (pt) REVERT: E 220 MET cc_start: 0.8884 (ttt) cc_final: 0.8537 (ttm) REVERT: E 222 ARG cc_start: 0.9275 (OUTLIER) cc_final: 0.8384 (mtm-85) REVERT: E 277 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6671 (mp0) REVERT: E 287 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.5984 (p90) REVERT: E 293 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7658 (p0) REVERT: E 314 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8238 (mp0) REVERT: F 169 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: F 220 MET cc_start: 0.8594 (ttt) cc_final: 0.8325 (ttp) REVERT: H 102 ARG cc_start: 0.6341 (pmt100) cc_final: 0.5026 (tpt170) REVERT: H 109 LYS cc_start: 0.8218 (mttt) cc_final: 0.7721 (mmtt) REVERT: H 150 HIS cc_start: 0.7346 (OUTLIER) cc_final: 0.6003 (t-90) REVERT: H 161 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7726 (mtp85) outliers start: 118 outliers final: 56 residues processed: 371 average time/residue: 0.6408 time to fit residues: 275.7357 Evaluate side-chains 357 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 280 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 393 ILE 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 228 MET Chi-restraints excluded: chain J residue 322 LYS Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 374 CYS Chi-restraints excluded: chain G residue 2 LYS 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 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 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 204 LEU Chi-restraints excluded: chain B residue 215 LEU 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 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 228 THR 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 91 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 282 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 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 44 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 314 GLU 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 169 GLU Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 289 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 297 optimal weight: 1.9990 chunk 323 optimal weight: 9.9990 chunk 59 optimal weight: 0.0970 chunk 19 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 148 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 296 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN I 80 GLN C 110 GLN D 110 GLN E 55 GLN E 99 GLN H 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.161203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.109231 restraints weight = 33744.049| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.68 r_work: 0.2981 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28929 Z= 0.126 Angle : 0.561 12.024 39505 Z= 0.287 Chirality : 0.041 0.197 4374 Planarity : 0.005 0.067 4822 Dihedral : 14.332 177.691 4527 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.49 % Rotamer: Outliers : 3.65 % Allowed : 18.98 % 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: -0.50 (0.15), residues: 3269 helix: 0.79 (0.16), residues: 1112 sheet: 0.05 (0.24), residues: 484 loop : -1.23 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 164 TYR 0.015 0.001 TYR C 275 PHE 0.027 0.001 PHE H 163 TRP 0.017 0.001 TRP I 142 HIS 0.008 0.001 HIS J 225 Details of bonding type rmsd covalent geometry : bond 0.00296 (28920) covalent geometry : angle 0.56125 (39505) hydrogen bonds : bond 0.03271 ( 861) hydrogen bonds : angle 4.40119 ( 2431) metal coordination : bond 0.00092 ( 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 407 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 299 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5496 (tpp) cc_final: 0.3979 (mpt) REVERT: A 180 GLN cc_start: 0.6741 (mt0) cc_final: 0.6346 (tm-30) REVERT: A 210 TYR cc_start: 0.8653 (m-80) cc_final: 0.8387 (m-80) REVERT: A 247 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.7951 (tpt) REVERT: A 393 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8207 (mt) REVERT: A 405 VAL cc_start: 0.8455 (t) cc_final: 0.8153 (m) REVERT: A 472 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7922 (t70) REVERT: A 538 ARG cc_start: 0.8016 (mmt90) cc_final: 0.7763 (mpt-90) REVERT: A 543 TYR cc_start: 0.7552 (t80) cc_final: 0.6845 (t80) REVERT: A 570 TYR cc_start: 0.8093 (m-80) cc_final: 0.7576 (m-80) REVERT: J 62 TYR cc_start: 0.4924 (p90) cc_final: 0.4570 (p90) REVERT: J 120 LEU cc_start: 0.5474 (tp) cc_final: 0.5266 (tt) REVERT: J 154 ASN cc_start: 0.4643 (m110) cc_final: 0.4343 (p0) REVERT: J 169 TYR cc_start: 0.3902 (p90) cc_final: 0.3499 (p90) REVERT: J 272 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8029 (pt0) REVERT: J 345 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7889 (mm110) REVERT: J 384 GLU cc_start: 0.7162 (pt0) cc_final: 0.6727 (pt0) REVERT: I 99 MET cc_start: 0.6846 (mtm) cc_final: 0.6440 (mtm) REVERT: I 158 ILE cc_start: 0.6721 (mp) cc_final: 0.6460 (tp) REVERT: I 177 ILE cc_start: 0.6702 (mm) cc_final: 0.6208 (pt) REVERT: I 236 ASP cc_start: 0.3351 (OUTLIER) cc_final: 0.3027 (t70) REVERT: I 249 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7435 (tpp-160) REVERT: I 258 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6623 (mm-30) REVERT: I 295 GLN cc_start: 0.7221 (tt0) cc_final: 0.6881 (tm-30) REVERT: I 311 LEU cc_start: 0.6651 (tm) cc_final: 0.6146 (pp) REVERT: I 348 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5094 (pt) REVERT: G 86 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7943 (tp30) REVERT: G 112 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8031 (mm) REVERT: G 193 MET cc_start: 0.8912 (mtt) cc_final: 0.8613 (mtt) REVERT: B 39 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9049 (pp) REVERT: B 113 VAL cc_start: 0.7944 (t) cc_final: 0.7719 (m) REVERT: B 215 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8781 (mm) REVERT: B 221 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8325 (t) REVERT: B 241 GLN cc_start: 0.6473 (mt0) cc_final: 0.6159 (tt0) REVERT: C 42 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8265 (mt0) REVERT: C 58 LYS cc_start: 0.8339 (mmmm) cc_final: 0.8000 (mmmm) REVERT: D 72 GLN cc_start: 0.9050 (tt0) cc_final: 0.8791 (tt0) REVERT: D 96 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: D 176 THR cc_start: 0.9139 (m) cc_final: 0.8934 (p) REVERT: D 287 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7347 (p90) REVERT: E 17 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8432 (m-30) REVERT: E 43 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8489 (mmm) REVERT: E 57 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7849 (pt) REVERT: E 220 MET cc_start: 0.8869 (ttt) cc_final: 0.8523 (ttm) REVERT: E 222 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.8364 (mtm-85) REVERT: E 287 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.6071 (p90) REVERT: E 293 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7631 (p0) REVERT: E 314 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: F 43 MET cc_start: 0.8523 (mtp) cc_final: 0.8136 (mmt) REVERT: F 169 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: F 220 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8289 (ttp) REVERT: F 293 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7659 (p0) REVERT: H 102 ARG cc_start: 0.6350 (pmt100) cc_final: 0.5023 (tpt170) REVERT: H 109 LYS cc_start: 0.8220 (mttt) cc_final: 0.7728 (mmtt) REVERT: H 150 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.5909 (t-90) REVERT: H 161 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7952 (mtp85) outliers start: 108 outliers final: 54 residues processed: 382 average time/residue: 0.6479 time to fit residues: 286.7086 Evaluate side-chains 376 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 297 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 407 VAL 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 278 LEU Chi-restraints excluded: chain I residue 236 ASP Chi-restraints excluded: chain I residue 249 ARG Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 374 CYS Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 112 LEU 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 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 204 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 328 GLN 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 59 SER 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 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 91 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 282 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 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 44 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 121 THR 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 293 ASP Chi-restraints excluded: chain E residue 314 GLU 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 169 GLU Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 293 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 280 optimal weight: 0.9990 chunk 114 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 211 optimal weight: 0.0370 chunk 12 optimal weight: 0.8980 chunk 264 optimal weight: 0.0970 chunk 89 optimal weight: 0.9980 chunk 263 optimal weight: 0.7980 chunk 316 optimal weight: 4.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN I 80 GLN C 110 GLN D 110 GLN E 55 GLN E 99 GLN H 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.163443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112007 restraints weight = 33723.236| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.67 r_work: 0.3019 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 28929 Z= 0.104 Angle : 0.540 13.289 39505 Z= 0.275 Chirality : 0.040 0.191 4374 Planarity : 0.004 0.067 4822 Dihedral : 14.177 176.150 4526 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.45 % Favored : 94.52 % Rotamer: Outliers : 3.21 % Allowed : 19.49 % Favored : 77.30 % 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: -0.32 (0.15), residues: 3269 helix: 1.01 (0.16), residues: 1111 sheet: 0.13 (0.25), residues: 473 loop : -1.17 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 164 TYR 0.016 0.001 TYR C 275 PHE 0.029 0.001 PHE H 163 TRP 0.015 0.001 TRP I 142 HIS 0.009 0.001 HIS J 225 Details of bonding type rmsd covalent geometry : bond 0.00239 (28920) covalent geometry : angle 0.53987 (39505) hydrogen bonds : bond 0.02979 ( 861) hydrogen bonds : angle 4.29329 ( 2431) metal coordination : bond 0.00065 ( 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 411 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 316 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5752 (tpp) cc_final: 0.4299 (mpt) REVERT: A 180 GLN cc_start: 0.6596 (mt0) cc_final: 0.6314 (tm-30) REVERT: A 247 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8042 (tpt) REVERT: A 393 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8248 (mt) REVERT: A 405 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8256 (m) REVERT: A 472 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7911 (t70) REVERT: A 526 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7273 (mp0) REVERT: A 538 ARG cc_start: 0.8082 (mmt90) cc_final: 0.7818 (mpt-90) REVERT: A 543 TYR cc_start: 0.7569 (t80) cc_final: 0.6933 (t80) REVERT: A 562 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6889 (mt0) REVERT: A 570 TYR cc_start: 0.8033 (m-80) cc_final: 0.7519 (m-80) REVERT: A 574 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7280 (pp20) REVERT: J 154 ASN cc_start: 0.4476 (m110) cc_final: 0.4214 (p0) REVERT: J 169 TYR cc_start: 0.3956 (p90) cc_final: 0.3581 (p90) REVERT: J 238 PHE cc_start: 0.6504 (t80) cc_final: 0.6171 (t80) REVERT: J 272 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8050 (pt0) REVERT: J 331 MET cc_start: 0.8284 (ttm) cc_final: 0.7872 (ptm) REVERT: J 345 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7696 (mm110) REVERT: J 384 GLU cc_start: 0.7186 (pt0) cc_final: 0.6745 (pt0) REVERT: I 4 GLN cc_start: 0.7556 (mm110) cc_final: 0.6646 (mm-40) REVERT: I 66 ASN cc_start: 0.8376 (m-40) cc_final: 0.8061 (m110) REVERT: I 99 MET cc_start: 0.6758 (mtm) cc_final: 0.6379 (ptp) REVERT: I 158 ILE cc_start: 0.6785 (mp) cc_final: 0.6570 (tp) REVERT: I 177 ILE cc_start: 0.6772 (mm) cc_final: 0.6282 (pt) REVERT: I 236 ASP cc_start: 0.3400 (OUTLIER) cc_final: 0.3072 (t70) REVERT: I 258 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6101 (tp30) REVERT: I 295 GLN cc_start: 0.7255 (tt0) cc_final: 0.6918 (tm-30) REVERT: I 311 LEU cc_start: 0.6717 (tm) cc_final: 0.6186 (pp) REVERT: I 348 LEU cc_start: 0.5421 (OUTLIER) cc_final: 0.5131 (pt) REVERT: G 86 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7944 (tp30) REVERT: G 193 MET cc_start: 0.8899 (mtt) cc_final: 0.8679 (mtt) REVERT: G 222 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8718 (mtt180) REVERT: G 329 GLU cc_start: 0.7960 (tt0) cc_final: 0.7646 (mt-10) REVERT: B 1 MET cc_start: 0.6266 (ttm) cc_final: 0.5963 (mtp) REVERT: B 39 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9046 (pp) REVERT: B 113 VAL cc_start: 0.7985 (t) cc_final: 0.7765 (m) REVERT: B 210 ARG cc_start: 0.8439 (ttm-80) cc_final: 0.8069 (ttp-170) REVERT: B 215 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8741 (mm) REVERT: B 241 GLN cc_start: 0.6305 (mt0) cc_final: 0.5891 (tt0) REVERT: C 42 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8304 (mt0) REVERT: C 58 LYS cc_start: 0.8350 (mmmm) cc_final: 0.8054 (mmmm) REVERT: D 72 GLN cc_start: 0.9082 (tt0) cc_final: 0.8827 (tt0) REVERT: D 287 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7412 (p90) REVERT: E 43 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8514 (mmm) REVERT: E 57 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7765 (pt) REVERT: E 220 MET cc_start: 0.8830 (ttt) cc_final: 0.8472 (ttm) REVERT: E 222 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.8347 (mtm-85) REVERT: E 277 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6486 (mp0) REVERT: E 287 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.5974 (p90) REVERT: E 314 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8298 (mp0) REVERT: F 287 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7693 (p90) REVERT: F 293 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7648 (p0) REVERT: H 102 ARG cc_start: 0.6417 (pmt100) cc_final: 0.5075 (tpt170) REVERT: H 109 LYS cc_start: 0.8265 (mttt) cc_final: 0.7787 (mmtt) REVERT: H 161 ARG cc_start: 0.8174 (mtp85) cc_final: 0.7878 (mtp85) outliers start: 95 outliers final: 50 residues processed: 388 average time/residue: 0.6446 time to fit residues: 290.2374 Evaluate side-chains 374 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 303 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 236 ASP Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 374 CYS Chi-restraints excluded: chain G residue 2 LYS 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 222 ARG Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 287 PHE Chi-restraints excluded: chain G residue 289 VAL 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 204 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 328 GLN 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 226 VAL 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 91 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 282 LEU 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 44 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 287 PHE Chi-restraints excluded: chain F residue 293 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 57 optimal weight: 0.9980 chunk 59 optimal weight: 0.0470 chunk 309 optimal weight: 0.6980 chunk 276 optimal weight: 0.7980 chunk 143 optimal weight: 0.5980 chunk 146 optimal weight: 0.7980 chunk 228 optimal weight: 0.6980 chunk 210 optimal weight: 0.4980 chunk 165 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN I 80 GLN C 110 GLN D 110 GLN E 55 GLN H 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.163900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.113763 restraints weight = 33657.607| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.94 r_work: 0.3027 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 28929 Z= 0.101 Angle : 0.536 13.367 39505 Z= 0.273 Chirality : 0.040 0.198 4374 Planarity : 0.004 0.069 4822 Dihedral : 14.073 175.509 4526 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.45 % Favored : 94.52 % Rotamer: Outliers : 2.54 % Allowed : 20.47 % Favored : 77.00 % 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: -0.20 (0.15), residues: 3269 helix: 1.17 (0.16), residues: 1106 sheet: 0.12 (0.24), residues: 487 loop : -1.12 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 164 TYR 0.015 0.001 TYR F 275 PHE 0.029 0.001 PHE H 163 TRP 0.015 0.001 TRP I 142 HIS 0.010 0.001 HIS J 225 Details of bonding type rmsd covalent geometry : bond 0.00231 (28920) covalent geometry : angle 0.53584 (39505) hydrogen bonds : bond 0.02952 ( 861) hydrogen bonds : angle 4.24429 ( 2431) metal coordination : bond 0.00056 ( 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 377 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 302 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5713 (tpp) cc_final: 0.4299 (mpt) REVERT: A 180 GLN cc_start: 0.6696 (mt0) cc_final: 0.6372 (tm-30) REVERT: A 247 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.7963 (tpt) REVERT: A 393 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8224 (mt) REVERT: A 405 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8266 (m) REVERT: A 472 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7917 (t70) REVERT: A 485 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8075 (p) REVERT: A 526 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7231 (mp0) REVERT: A 538 ARG cc_start: 0.8001 (mmt90) cc_final: 0.7736 (mpt-90) REVERT: A 543 TYR cc_start: 0.7587 (t80) cc_final: 0.6899 (t80) REVERT: A 570 TYR cc_start: 0.7952 (m-80) cc_final: 0.7466 (m-80) REVERT: A 574 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7249 (pp20) REVERT: J 169 TYR cc_start: 0.3965 (p90) cc_final: 0.3428 (p90) REVERT: J 272 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8067 (pt0) REVERT: J 331 MET cc_start: 0.8259 (ttm) cc_final: 0.7853 (ptm) REVERT: J 345 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7806 (mm-40) REVERT: J 384 GLU cc_start: 0.7152 (pt0) cc_final: 0.6790 (pt0) REVERT: I 66 ASN cc_start: 0.8358 (m-40) cc_final: 0.8029 (m-40) REVERT: I 99 MET cc_start: 0.6706 (mtm) cc_final: 0.6345 (ptp) REVERT: I 158 ILE cc_start: 0.6739 (mp) cc_final: 0.6529 (tp) REVERT: I 177 ILE cc_start: 0.6740 (mm) cc_final: 0.6241 (pt) REVERT: I 236 ASP cc_start: 0.3453 (OUTLIER) cc_final: 0.3114 (t70) REVERT: I 258 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6132 (tp30) REVERT: I 295 GLN cc_start: 0.7203 (tt0) cc_final: 0.6879 (tm-30) REVERT: I 311 LEU cc_start: 0.6684 (tm) cc_final: 0.6162 (pp) REVERT: I 348 LEU cc_start: 0.6124 (mt) cc_final: 0.5778 (pp) REVERT: G 86 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7940 (tp30) REVERT: G 96 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7844 (mp0) REVERT: G 193 MET cc_start: 0.8877 (mtt) cc_final: 0.8661 (mtt) REVERT: G 222 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8703 (mtt180) REVERT: G 293 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7251 (p0) REVERT: G 329 GLU cc_start: 0.7940 (tt0) cc_final: 0.7655 (mt-10) REVERT: B 1 MET cc_start: 0.6159 (ttm) cc_final: 0.5863 (mtp) REVERT: B 39 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9062 (pp) REVERT: B 215 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8711 (mm) REVERT: B 241 GLN cc_start: 0.6242 (mt0) cc_final: 0.5816 (tt0) REVERT: C 42 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8191 (mt0) REVERT: C 58 LYS cc_start: 0.8340 (mmmm) cc_final: 0.8049 (mmmm) REVERT: D 72 GLN cc_start: 0.9060 (tt0) cc_final: 0.8796 (tt0) REVERT: D 287 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7358 (p90) REVERT: E 43 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8464 (mmm) REVERT: E 96 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8057 (mp0) REVERT: E 220 MET cc_start: 0.8841 (ttt) cc_final: 0.8490 (ttm) REVERT: E 222 ARG cc_start: 0.9240 (OUTLIER) cc_final: 0.8366 (mtm-85) REVERT: E 287 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.5873 (p90) REVERT: E 314 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8259 (mp0) REVERT: F 287 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7616 (p90) REVERT: F 293 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7575 (p0) REVERT: H 102 ARG cc_start: 0.6473 (pmt100) cc_final: 0.5069 (tpt170) REVERT: H 109 LYS cc_start: 0.8220 (mttt) cc_final: 0.7706 (mmtt) REVERT: H 161 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7761 (mtp85) outliers start: 75 outliers final: 48 residues processed: 359 average time/residue: 0.6188 time to fit residues: 258.0158 Evaluate side-chains 362 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 294 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 236 ASP Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 374 CYS Chi-restraints excluded: chain G residue 2 LYS 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 222 ARG Chi-restraints excluded: chain G residue 271 ILE 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 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 289 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 328 GLN 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 59 SER Chi-restraints excluded: chain C residue 91 VAL 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 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 91 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 282 LEU 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 43 MET Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 287 PHE Chi-restraints excluded: chain E residue 314 GLU 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 287 PHE Chi-restraints excluded: chain F residue 293 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 291 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 292 optimal weight: 5.9990 chunk 250 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 249 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN C 110 GLN D 110 GLN E 55 GLN H 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.157685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.105243 restraints weight = 33472.392| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.71 r_work: 0.2916 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 28929 Z= 0.205 Angle : 0.651 13.414 39505 Z= 0.332 Chirality : 0.045 0.224 4374 Planarity : 0.005 0.066 4822 Dihedral : 14.387 179.836 4524 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.06 % Favored : 93.91 % Rotamer: Outliers : 3.04 % Allowed : 20.13 % 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: -0.41 (0.15), residues: 3269 helix: 0.88 (0.16), residues: 1109 sheet: 0.00 (0.24), residues: 503 loop : -1.17 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 164 TYR 0.019 0.002 TYR B 175 PHE 0.033 0.002 PHE H 163 TRP 0.022 0.002 TRP I 142 HIS 0.010 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00496 (28920) covalent geometry : angle 0.65074 (39505) hydrogen bonds : bond 0.03965 ( 861) hydrogen bonds : angle 4.53178 ( 2431) metal coordination : bond 0.00170 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10870.89 seconds wall clock time: 185 minutes 22.13 seconds (11122.13 seconds total)