Starting phenix.real_space_refine on Mon May 26 07:41:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pfj_17647/05_2025/8pfj_17647.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pfj_17647/05_2025/8pfj_17647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pfj_17647/05_2025/8pfj_17647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pfj_17647/05_2025/8pfj_17647.map" model { file = "/net/cci-nas-00/data/ceres_data/8pfj_17647/05_2025/8pfj_17647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pfj_17647/05_2025/8pfj_17647.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 91 5.49 5 Mg 1 5.21 5 S 112 5.16 5 C 17166 2.51 5 N 4933 2.21 5 O 5551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27856 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 7, 'TRANS': 93} Chain: "I" Number of atoms: 10423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1321, 10423 Classifications: {'peptide': 1321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 1 Chain: "J" Number of atoms: 10449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1343, 10449 Classifications: {'peptide': 1343} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1287} Chain breaks: 2 Chain: "K" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 663 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "R" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 355 Classifications: {'RNA': 17} Modifications used: {'5*END': 1, 'rna2p_pyr': 3, 'rna3p_pur': 7, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 13} Chain: "A" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 771 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "B" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 786 Classifications: {'DNA': 38} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 37} Chain: "G" Number of atoms: 1811 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 233, 1803 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 223} Conformer: "B" Number of residues, atoms: 233, 1803 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 223} bond proxies already assigned to first conformer: 1816 Chain: "H" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1784 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11692 SG CYS J 70 24.994 69.348 82.807 1.00166.66 S ATOM 11706 SG CYS J 72 23.731 65.754 82.309 1.00168.46 S ATOM 11814 SG CYS J 85 22.200 67.952 84.957 1.00163.60 S ATOM 11838 SG CYS J 88 25.790 66.701 85.371 1.00159.23 S ATOM 17526 SG CYS J 814 58.663 126.421 91.486 1.00130.98 S ATOM 18091 SG CYS J 888 59.528 122.849 90.696 1.00134.62 S ATOM 18142 SG CYS J 895 59.009 125.383 87.852 1.00128.61 S ATOM 18163 SG CYS J 898 62.097 125.554 90.044 1.00130.26 S Time building chain proxies: 17.03, per 1000 atoms: 0.61 Number of scatterers: 27856 At special positions: 0 Unit cell: (140.608, 169.728, 157.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 112 16.00 P 91 15.00 Mg 1 11.99 O 5551 8.00 N 4933 7.00 C 17166 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: 8.89 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " Number of angles added : 12 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6126 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 48 sheets defined 39.1% alpha, 17.7% beta 38 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 10.09 Creating SS restraints... Processing helix chain 'P' and resid 13 through 24 Processing helix chain 'P' and resid 65 through 71 removed outlier: 3.524A pdb=" N ILE P 69 " --> pdb=" O HIS P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 99 removed outlier: 3.568A pdb=" N ILE P 93 " --> pdb=" O PRO P 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 10 removed outlier: 4.093A pdb=" N ARG I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 29 through 40 removed outlier: 3.834A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE I 35 " --> pdb=" O GLN I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.819A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.629A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 295 removed outlier: 3.935A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS I 295 " --> pdb=" O TYR I 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 295' Processing helix chain 'I' and resid 318 through 329 Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.897A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 482 Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.748A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.799A pdb=" N SER I 509 " --> pdb=" O PHE I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 545 through 549 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.531A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 614 removed outlier: 3.679A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 614' Processing helix chain 'I' and resid 624 through 628 removed outlier: 3.827A pdb=" N HIS I 628 " --> pdb=" O GLU I 625 " (cutoff:3.500A) Processing helix chain 'I' and resid 662 through 667 Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 removed outlier: 4.131A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 826 Processing helix chain 'I' and resid 942 through 983 removed outlier: 3.899A pdb=" N GLU I 963 " --> pdb=" O ASP I 959 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 992 Processing helix chain 'I' and resid 993 through 997 Processing helix chain 'I' and resid 1005 through 1038 Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1107 removed outlier: 4.097A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.596A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 removed outlier: 3.657A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.538A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1282 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.727A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.677A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.512A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.603A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.704A pdb=" N SER J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 336 through 342 removed outlier: 3.701A pdb=" N LEU J 342 " --> pdb=" O PHE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 403 Processing helix chain 'J' and resid 405 through 416 Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.866A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.692A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.642A pdb=" N VAL J 618 " --> pdb=" O LEU J 614 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE J 619 " --> pdb=" O LYS J 615 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.912A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 805 removed outlier: 3.700A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.760A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 removed outlier: 3.548A pdb=" N ASN J 875 " --> pdb=" O LEU J 871 " (cutoff:3.500A) Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.730A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.778A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.326A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1296 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.849A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 Processing helix chain 'J' and resid 1360 through 1375 removed outlier: 3.701A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP J1368 " --> pdb=" O ALA J1364 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA J1375 " --> pdb=" O ARG J1371 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 17 through 34 removed outlier: 3.634A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.507A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 84 Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.553A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN G 41 " --> pdb=" O HIS G 37 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.647A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.200A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.598A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 154 through 159 Processing helix chain 'H' and resid 160 through 166 removed outlier: 6.086A pdb=" N GLU H 163 " --> pdb=" O HIS H 160 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP H 164 " --> pdb=" O SER H 161 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG H 166 " --> pdb=" O GLU H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 229 Processing sheet with id=AA1, first strand: chain 'P' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'P' and resid 32 through 39 Processing sheet with id=AA3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.505A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.942A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA6, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.266A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.577A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 227 through 231 removed outlier: 4.870A pdb=" N VAL I 296 " --> pdb=" O LEU I 336 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 250 through 251 removed outlier: 3.991A pdb=" N ALA I 251 " --> pdb=" O ARG I 267 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG I 267 " --> pdb=" O ALA I 251 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.644A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.418A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB4, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.651A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.192A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 755 through 758 Processing sheet with id=AB7, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AB8, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.584A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.836A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 849 through 850 removed outlier: 4.058A pdb=" N GLU I 849 " --> pdb=" O VAL I 887 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL I 887 " --> pdb=" O GLU I 849 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.837A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.418A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.968A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU J 449 " --> pdb=" O VAL J 354 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR J 356 " --> pdb=" O LEU J 449 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AC6, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.768A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 103 through 112 removed outlier: 10.010A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.721A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.925A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD1, first strand: chain 'J' and resid 706 through 709 Processing sheet with id=AD2, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AD3, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD4, first strand: chain 'J' and resid 826 through 827 removed outlier: 3.885A pdb=" N GLU J 827 " --> pdb=" O ASP J 830 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 842 through 843 removed outlier: 3.993A pdb=" N ARG J 842 " --> pdb=" O LEU J 864 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.609A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 957 through 961 Processing sheet with id=AD8, first strand: chain 'J' and resid 965 through 967 removed outlier: 4.049A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 1024 through 1026 Processing sheet with id=AE1, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE2, first strand: chain 'J' and resid 1187 through 1190 removed outlier: 3.758A pdb=" N VAL J1204 " --> pdb=" O GLY J1161 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.738A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 12 through 17 removed outlier: 4.870A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.621A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AE7, first strand: chain 'G' and resid 108 through 111 Processing sheet with id=AE8, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AE9, first strand: chain 'H' and resid 13 through 17 removed outlier: 6.409A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU H 206 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 98 through 104 removed outlier: 3.864A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AF3, first strand: chain 'H' and resid 108 through 111 removed outlier: 7.345A pdb=" N GLY H 108 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N HIS H 132 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) 1133 hydrogen bonds defined for protein. 3179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 97 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 15.35 Time building geometry restraints manager: 7.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9203 1.34 - 1.46: 5843 1.46 - 1.58: 13053 1.58 - 1.70: 181 1.70 - 1.82: 194 Bond restraints: 28474 Sorted by residual: bond pdb=" CA GLU G 193 " pdb=" CB GLU G 193 " ideal model delta sigma weight residual 1.517 1.556 -0.039 2.41e-02 1.72e+03 2.68e+00 bond pdb=" CB GLN K 70 " pdb=" CG GLN K 70 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 2.01e+00 bond pdb=" C3' DG B 5 " pdb=" O3' DG B 5 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.75e+00 bond pdb=" CB GLU H 229 " pdb=" CG GLU H 229 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" CG ARG J 322 " pdb=" CD ARG J 322 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.61e+00 ... (remaining 28469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 38579 2.57 - 5.14: 240 5.14 - 7.70: 37 7.70 - 10.27: 12 10.27 - 12.84: 6 Bond angle restraints: 38874 Sorted by residual: angle pdb=" CA GLU G 193 " pdb=" CB GLU G 193 " pdb=" CG GLU G 193 " ideal model delta sigma weight residual 114.10 124.00 -9.90 2.00e+00 2.50e-01 2.45e+01 angle pdb=" CB MET P 32 " pdb=" CG MET P 32 " pdb=" SD MET P 32 " ideal model delta sigma weight residual 112.70 125.54 -12.84 3.00e+00 1.11e-01 1.83e+01 angle pdb=" CA GLN P 95 " pdb=" CB GLN P 95 " pdb=" CG GLN P 95 " ideal model delta sigma weight residual 114.10 122.07 -7.97 2.00e+00 2.50e-01 1.59e+01 angle pdb=" CB MET P 1 " pdb=" CG MET P 1 " pdb=" SD MET P 1 " ideal model delta sigma weight residual 112.70 124.62 -11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CB MET J1025 " pdb=" CG MET J1025 " pdb=" SD MET J1025 " ideal model delta sigma weight residual 112.70 124.56 -11.86 3.00e+00 1.11e-01 1.56e+01 ... (remaining 38869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 16290 35.52 - 71.03: 981 71.03 - 106.55: 44 106.55 - 142.06: 1 142.06 - 177.58: 3 Dihedral angle restraints: 17319 sinusoidal: 7798 harmonic: 9521 Sorted by residual: dihedral pdb=" O4' C R 2 " pdb=" C1' C R 2 " pdb=" N1 C R 2 " pdb=" C2 C R 2 " ideal model delta sinusoidal sigma weight residual -128.00 48.49 -176.49 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA ASN I 314 " pdb=" C ASN I 314 " pdb=" N MET I 315 " pdb=" CA MET I 315 " ideal model delta harmonic sigma weight residual 180.00 154.96 25.04 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" C4' DG B 5 " pdb=" C3' DG B 5 " pdb=" O3' DG B 5 " pdb=" P DA B 6 " ideal model delta sinusoidal sigma weight residual 220.00 42.42 177.58 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 17316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3147 0.033 - 0.067: 853 0.067 - 0.100: 287 0.100 - 0.134: 152 0.134 - 0.167: 6 Chirality restraints: 4445 Sorted by residual: chirality pdb=" CA GLU H 193 " pdb=" N GLU H 193 " pdb=" C GLU H 193 " pdb=" CB GLU H 193 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA ILE I 104 " pdb=" N ILE I 104 " pdb=" C ILE I 104 " pdb=" CB ILE I 104 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CB ILE J 291 " pdb=" CA ILE J 291 " pdb=" CG1 ILE J 291 " pdb=" CG2 ILE J 291 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 4442 not shown) Planarity restraints: 4763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU I 541 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" CD GLU I 541 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU I 541 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU I 541 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE J1190 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO J1191 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO J1191 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO J1191 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA J 287 " -0.028 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO J 288 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO J 288 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO J 288 " -0.024 5.00e-02 4.00e+02 ... (remaining 4760 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 256 2.59 - 3.17: 22375 3.17 - 3.74: 45743 3.74 - 4.32: 59283 4.32 - 4.90: 98609 Nonbonded interactions: 226266 Sorted by model distance: nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1503 " model vdw 2.011 2.170 nonbonded pdb=" OD2 ASP J 460 " pdb="MG MG J1503 " model vdw 2.030 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1503 " model vdw 2.043 2.170 nonbonded pdb=" CG ASP J 460 " pdb="MG MG J1503 " model vdw 2.075 2.400 nonbonded pdb=" OD2 ASP J 462 " pdb="MG MG J1503 " model vdw 2.085 2.170 ... (remaining 226261 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 'G' and (resid 3 through 218 or resid 220 through 233)) selection = (chain 'H' and (resid 3 through 218 or resid 220 through 233)) } 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=0.50 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: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 77.770 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.100 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 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 : 0.002 0.043 28482 Z= 0.102 Angle : 0.543 12.838 38886 Z= 0.271 Chirality : 0.039 0.167 4445 Planarity : 0.003 0.057 4763 Dihedral : 19.723 177.578 11193 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.34 % Favored : 97.63 % Rotamer: Outliers : 3.15 % Allowed : 29.52 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.15), residues: 3296 helix: 2.29 (0.16), residues: 1159 sheet: 0.72 (0.24), residues: 503 loop : 0.23 (0.16), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J1193 HIS 0.004 0.000 HIS I 165 PHE 0.006 0.001 PHE J1325 TYR 0.029 0.001 TYR G 185 ARG 0.014 0.000 ARG G 158 Details of bonding type rmsd hydrogen bonds : bond 0.12365 ( 1224) hydrogen bonds : angle 4.92477 ( 3369) metal coordination : bond 0.00274 ( 8) metal coordination : angle 1.16210 ( 12) covalent geometry : bond 0.00229 (28474) covalent geometry : angle 0.54250 (38874) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 201 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 22 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: P 76 SER cc_start: 0.9104 (t) cc_final: 0.8440 (p) REVERT: I 1273 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8258 (mtm) REVERT: H 186 ASN cc_start: 0.8386 (t0) cc_final: 0.8017 (t0) outliers start: 89 outliers final: 85 residues processed: 287 average time/residue: 0.3361 time to fit residues: 162.4188 Evaluate side-chains 278 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 191 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 318 SER Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 529 ARG Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 40 LYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 232 ASN Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 670 SER Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1176 VAL Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 20.0000 chunk 255 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 264 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 196 optimal weight: 5.9990 chunk 306 optimal weight: 0.5980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 387 ASN I 965 GLN ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 435 GLN J 921 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.071947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.050256 restraints weight = 115388.899| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.64 r_work: 0.2679 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28482 Z= 0.144 Angle : 0.506 8.512 38886 Z= 0.264 Chirality : 0.040 0.165 4445 Planarity : 0.003 0.052 4763 Dihedral : 16.622 177.911 4840 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.47 % Allowed : 26.65 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.15), residues: 3296 helix: 2.27 (0.16), residues: 1177 sheet: 0.67 (0.24), residues: 490 loop : 0.22 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J1193 HIS 0.004 0.001 HIS I 165 PHE 0.010 0.001 PHE I 405 TYR 0.011 0.001 TYR H 177 ARG 0.011 0.000 ARG G 158 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 1224) hydrogen bonds : angle 4.02757 ( 3369) metal coordination : bond 0.00661 ( 8) metal coordination : angle 2.35178 ( 12) covalent geometry : bond 0.00325 (28474) covalent geometry : angle 0.50419 (38874) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 205 time to evaluate : 3.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 22 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: P 32 MET cc_start: 0.8860 (mmm) cc_final: 0.8588 (mmm) REVERT: P 58 GLU cc_start: 0.8629 (tt0) cc_final: 0.8407 (tt0) REVERT: P 95 GLN cc_start: 0.8925 (mp10) cc_final: 0.8656 (mp10) REVERT: I 504 GLU cc_start: 0.9267 (tm-30) cc_final: 0.9066 (tm-30) REVERT: I 584 TYR cc_start: 0.7654 (m-80) cc_final: 0.7316 (m-80) REVERT: I 611 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8461 (tt0) REVERT: I 1273 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8464 (mtm) REVERT: J 747 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8429 (mtp) REVERT: J 821 MET cc_start: 0.9132 (mmm) cc_final: 0.8931 (tpt) REVERT: J 1189 MET cc_start: 0.8250 (tpp) cc_final: 0.7971 (tpp) REVERT: J 1253 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9165 (mm) REVERT: K 1 MET cc_start: 0.4840 (pmm) cc_final: 0.4535 (ppp) REVERT: K 70 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8488 (tm-30) REVERT: H 76 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8516 (mp0) REVERT: H 186 ASN cc_start: 0.8577 (t0) cc_final: 0.8240 (t0) REVERT: H 231 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8553 (m-80) outliers start: 98 outliers final: 51 residues processed: 285 average time/residue: 0.3592 time to fit residues: 170.7141 Evaluate side-chains 250 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 192 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 6 LEU Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 509 SER Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1176 VAL Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 307 optimal weight: 8.9990 chunk 232 optimal weight: 0.6980 chunk 306 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 277 optimal weight: 0.7980 chunk 132 optimal weight: 0.0470 chunk 45 optimal weight: 4.9990 chunk 258 optimal weight: 0.9980 chunk 336 optimal weight: 0.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.072543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.051289 restraints weight = 93724.316| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.26 r_work: 0.2719 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 28482 Z= 0.102 Angle : 0.469 10.304 38886 Z= 0.245 Chirality : 0.039 0.162 4445 Planarity : 0.003 0.052 4763 Dihedral : 16.524 178.063 4766 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.15 % Favored : 97.81 % Rotamer: Outliers : 3.89 % Allowed : 26.05 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.15), residues: 3296 helix: 2.27 (0.16), residues: 1180 sheet: 0.66 (0.24), residues: 489 loop : 0.19 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J1193 HIS 0.003 0.000 HIS I 165 PHE 0.013 0.001 PHE I 545 TYR 0.019 0.001 TYR G 185 ARG 0.006 0.000 ARG I 275 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 1224) hydrogen bonds : angle 3.87427 ( 3369) metal coordination : bond 0.00457 ( 8) metal coordination : angle 1.68477 ( 12) covalent geometry : bond 0.00229 (28474) covalent geometry : angle 0.46796 (38874) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 197 time to evaluate : 3.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 22 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: P 58 GLU cc_start: 0.8583 (tt0) cc_final: 0.8347 (tt0) REVERT: P 76 SER cc_start: 0.9161 (t) cc_final: 0.8405 (p) REVERT: P 95 GLN cc_start: 0.8935 (mp10) cc_final: 0.8590 (mp10) REVERT: I 189 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8089 (t0) REVERT: I 584 TYR cc_start: 0.7605 (m-80) cc_final: 0.7264 (m-80) REVERT: I 1059 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.7547 (mtp85) REVERT: I 1273 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8437 (mtm) REVERT: J 229 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8918 (mm-40) REVERT: J 405 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: J 417 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8687 (mtp85) REVERT: J 747 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8342 (mtp) REVERT: J 821 MET cc_start: 0.9067 (mmm) cc_final: 0.8804 (tpt) REVERT: J 832 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8734 (mtmm) REVERT: J 1189 MET cc_start: 0.8291 (tpp) cc_final: 0.7932 (tpp) REVERT: J 1253 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9131 (mm) REVERT: K 69 ARG cc_start: 0.9197 (mmm-85) cc_final: 0.8994 (mmm-85) REVERT: H 76 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8595 (mp0) REVERT: H 186 ASN cc_start: 0.8595 (t0) cc_final: 0.8198 (t0) REVERT: H 231 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8546 (m-80) outliers start: 110 outliers final: 66 residues processed: 292 average time/residue: 0.3856 time to fit residues: 183.9232 Evaluate side-chains 263 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 185 time to evaluate : 3.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 509 SER Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1059 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 405 GLU Chi-restraints excluded: chain J residue 417 ARG Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1176 VAL Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 43 ASN Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 14 optimal weight: 9.9990 chunk 257 optimal weight: 0.9980 chunk 211 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 319 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.068917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.046988 restraints weight = 116762.986| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.62 r_work: 0.2585 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 28482 Z= 0.247 Angle : 0.559 9.290 38886 Z= 0.292 Chirality : 0.042 0.303 4445 Planarity : 0.004 0.050 4763 Dihedral : 16.639 177.436 4764 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.85 % Favored : 97.12 % Rotamer: Outliers : 4.00 % Allowed : 25.84 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.15), residues: 3296 helix: 2.17 (0.16), residues: 1189 sheet: 0.49 (0.24), residues: 488 loop : 0.09 (0.16), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 409 HIS 0.005 0.001 HIS P 65 PHE 0.015 0.001 PHE I 390 TYR 0.019 0.001 TYR I 62 ARG 0.008 0.000 ARG G 45 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 1224) hydrogen bonds : angle 4.04933 ( 3369) metal coordination : bond 0.01364 ( 8) metal coordination : angle 3.01566 ( 12) covalent geometry : bond 0.00560 (28474) covalent geometry : angle 0.55645 (38874) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 189 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 22 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: P 32 MET cc_start: 0.8877 (mmm) cc_final: 0.8586 (mmm) REVERT: P 58 GLU cc_start: 0.8668 (tt0) cc_final: 0.8343 (tt0) REVERT: P 84 SER cc_start: 0.8723 (OUTLIER) cc_final: 0.8158 (p) REVERT: P 95 GLN cc_start: 0.8976 (mp10) cc_final: 0.8666 (mp10) REVERT: I 189 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8299 (t70) REVERT: I 349 GLU cc_start: 0.9411 (OUTLIER) cc_final: 0.8935 (mm-30) REVERT: I 461 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: I 1059 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.7649 (mtp85) REVERT: I 1188 ASP cc_start: 0.8266 (t0) cc_final: 0.7652 (t0) REVERT: J 237 MET cc_start: 0.9551 (OUTLIER) cc_final: 0.9201 (mtp) REVERT: J 417 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8757 (mmm160) REVERT: J 497 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8920 (mt-10) REVERT: J 541 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9245 (mm) REVERT: J 747 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8519 (mtp) REVERT: J 1189 MET cc_start: 0.8361 (tpp) cc_final: 0.7942 (tpp) REVERT: J 1253 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9234 (mm) REVERT: K 41 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8535 (tm-30) REVERT: G 194 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8851 (mm-40) REVERT: H 186 ASN cc_start: 0.8671 (t0) cc_final: 0.8264 (t0) REVERT: H 231 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.8564 (m-80) outliers start: 113 outliers final: 70 residues processed: 289 average time/residue: 0.3840 time to fit residues: 180.2456 Evaluate side-chains 259 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 175 time to evaluate : 3.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 461 GLU Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 509 SER Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1059 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 417 ARG Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 497 GLU Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1176 VAL Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 289 optimal weight: 5.9990 chunk 276 optimal weight: 7.9990 chunk 249 optimal weight: 0.8980 chunk 315 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 188 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 285 optimal weight: 10.0000 chunk 265 optimal weight: 8.9990 chunk 311 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.069994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.048569 restraints weight = 99522.349| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 3.32 r_work: 0.2634 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28482 Z= 0.134 Angle : 0.497 8.911 38886 Z= 0.260 Chirality : 0.040 0.163 4445 Planarity : 0.003 0.050 4763 Dihedral : 16.597 177.699 4763 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.11 % Allowed : 25.49 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.15), residues: 3296 helix: 2.26 (0.16), residues: 1177 sheet: 0.56 (0.24), residues: 497 loop : 0.08 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J1193 HIS 0.003 0.001 HIS I 165 PHE 0.015 0.001 PHE I 545 TYR 0.018 0.001 TYR G 185 ARG 0.009 0.000 ARG I 275 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 1224) hydrogen bonds : angle 3.91381 ( 3369) metal coordination : bond 0.00778 ( 8) metal coordination : angle 2.58465 ( 12) covalent geometry : bond 0.00308 (28474) covalent geometry : angle 0.49547 (38874) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 183 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 22 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: P 58 GLU cc_start: 0.8591 (tt0) cc_final: 0.8289 (tt0) REVERT: P 84 SER cc_start: 0.8714 (OUTLIER) cc_final: 0.8159 (p) REVERT: I 189 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8242 (t70) REVERT: I 284 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8757 (tp) REVERT: I 349 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.8896 (mm-30) REVERT: I 1059 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.7655 (mtp85) REVERT: I 1273 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8595 (mtm) REVERT: J 417 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8665 (mmm-85) REVERT: J 541 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9221 (mm) REVERT: J 747 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8462 (mtp) REVERT: J 1095 MET cc_start: 0.7423 (tpt) cc_final: 0.6985 (tmm) REVERT: J 1253 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9175 (mm) REVERT: K 41 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8590 (tm-30) REVERT: H 186 ASN cc_start: 0.8648 (t0) cc_final: 0.8379 (t0) REVERT: H 231 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8502 (m-80) outliers start: 116 outliers final: 75 residues processed: 283 average time/residue: 0.3728 time to fit residues: 172.4970 Evaluate side-chains 261 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 173 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 509 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1059 ARG Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 417 ARG Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1176 VAL Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 43 ASN Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 44 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 41 optimal weight: 0.0470 chunk 300 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 327 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 320 optimal weight: 0.5980 chunk 223 optimal weight: 1.9990 chunk 250 optimal weight: 0.0050 overall best weight: 0.7294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 77 HIS ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.070713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.049207 restraints weight = 99685.163| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.34 r_work: 0.2653 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 28482 Z= 0.106 Angle : 0.489 11.598 38886 Z= 0.254 Chirality : 0.040 0.167 4445 Planarity : 0.003 0.051 4763 Dihedral : 16.549 177.649 4760 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.65 % Allowed : 25.98 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.15), residues: 3296 helix: 2.26 (0.16), residues: 1181 sheet: 0.58 (0.24), residues: 481 loop : 0.09 (0.16), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J1193 HIS 0.003 0.000 HIS I 165 PHE 0.017 0.001 PHE I 545 TYR 0.018 0.001 TYR G 185 ARG 0.011 0.000 ARG J 322 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 1224) hydrogen bonds : angle 3.84772 ( 3369) metal coordination : bond 0.00553 ( 8) metal coordination : angle 1.99272 ( 12) covalent geometry : bond 0.00242 (28474) covalent geometry : angle 0.48796 (38874) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 183 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 22 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: P 58 GLU cc_start: 0.8535 (tt0) cc_final: 0.8252 (tt0) REVERT: P 76 SER cc_start: 0.9236 (t) cc_final: 0.8486 (p) REVERT: P 84 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8175 (p) REVERT: I 132 ASP cc_start: 0.9181 (p0) cc_final: 0.8957 (p0) REVERT: I 189 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8203 (t70) REVERT: I 349 GLU cc_start: 0.9382 (OUTLIER) cc_final: 0.8913 (mm-30) REVERT: I 565 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8399 (mt-10) REVERT: I 1059 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.7628 (mtp85) REVERT: I 1273 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8515 (mtm) REVERT: J 417 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8773 (mtp85) REVERT: J 747 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8432 (mtp) REVERT: J 1189 MET cc_start: 0.8393 (tpp) cc_final: 0.7984 (tpp) REVERT: J 1253 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9160 (mm) REVERT: G 194 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8790 (mm-40) REVERT: H 76 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8595 (mp0) REVERT: H 186 ASN cc_start: 0.8623 (t0) cc_final: 0.8358 (t0) REVERT: H 231 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8426 (m-80) outliers start: 103 outliers final: 71 residues processed: 270 average time/residue: 0.3678 time to fit residues: 164.6648 Evaluate side-chains 259 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 176 time to evaluate : 3.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 509 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1059 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 417 ARG Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1176 VAL Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 270 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 197 optimal weight: 0.0670 chunk 113 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 92 optimal weight: 0.0040 chunk 148 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 294 optimal weight: 6.9990 overall best weight: 0.6934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.071055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.049892 restraints weight = 87925.850| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.12 r_work: 0.2680 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 28482 Z= 0.103 Angle : 0.492 10.508 38886 Z= 0.254 Chirality : 0.040 0.163 4445 Planarity : 0.003 0.050 4763 Dihedral : 16.474 177.509 4753 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.36 % Allowed : 25.91 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.15), residues: 3296 helix: 2.26 (0.16), residues: 1186 sheet: 0.64 (0.24), residues: 487 loop : 0.09 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J1193 HIS 0.003 0.000 HIS I 165 PHE 0.020 0.001 PHE I 545 TYR 0.018 0.001 TYR G 185 ARG 0.012 0.000 ARG J 322 Details of bonding type rmsd hydrogen bonds : bond 0.03049 ( 1224) hydrogen bonds : angle 3.81079 ( 3369) metal coordination : bond 0.00531 ( 8) metal coordination : angle 1.62275 ( 12) covalent geometry : bond 0.00237 (28474) covalent geometry : angle 0.49167 (38874) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 189 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 22 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: P 58 GLU cc_start: 0.8514 (tt0) cc_final: 0.8260 (tt0) REVERT: P 76 SER cc_start: 0.9198 (t) cc_final: 0.8465 (p) REVERT: P 95 GLN cc_start: 0.8934 (mp10) cc_final: 0.8668 (mp10) REVERT: I 189 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8148 (t70) REVERT: I 284 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8748 (tp) REVERT: I 1273 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8503 (mtm) REVERT: J 172 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.6730 (p90) REVERT: J 175 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7252 (pm20) REVERT: J 298 MET cc_start: 0.9015 (ttp) cc_final: 0.8812 (ttp) REVERT: J 417 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8611 (mmm-85) REVERT: J 541 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9212 (mm) REVERT: J 747 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8389 (mtp) REVERT: J 1189 MET cc_start: 0.8431 (tpp) cc_final: 0.8018 (tpp) REVERT: J 1253 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9136 (mm) REVERT: K 43 ASN cc_start: 0.8581 (p0) cc_final: 0.8121 (p0) REVERT: G 194 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8772 (mm-40) REVERT: H 76 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8609 (mp0) REVERT: H 142 MET cc_start: 0.9176 (pmm) cc_final: 0.8542 (pmm) REVERT: H 185 TYR cc_start: 0.9002 (p90) cc_final: 0.8800 (p90) REVERT: H 186 ASN cc_start: 0.8593 (t0) cc_final: 0.8353 (t0) REVERT: H 231 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8315 (m-80) outliers start: 95 outliers final: 62 residues processed: 274 average time/residue: 0.3816 time to fit residues: 172.9167 Evaluate side-chains 251 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 177 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 509 SER Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 417 ARG Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1176 VAL Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 170 optimal weight: 0.8980 chunk 264 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 201 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 325 optimal weight: 0.0570 chunk 249 optimal weight: 0.6980 overall best weight: 1.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.070685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.048889 restraints weight = 114780.505| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 3.60 r_work: 0.2636 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28482 Z= 0.121 Angle : 0.502 10.412 38886 Z= 0.260 Chirality : 0.040 0.161 4445 Planarity : 0.003 0.059 4763 Dihedral : 16.476 177.437 4750 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.47 % Allowed : 26.05 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.15), residues: 3296 helix: 2.26 (0.16), residues: 1186 sheet: 0.61 (0.24), residues: 482 loop : 0.09 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J1193 HIS 0.003 0.000 HIS I 165 PHE 0.020 0.001 PHE I 545 TYR 0.022 0.001 TYR G 185 ARG 0.013 0.000 ARG J 322 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 1224) hydrogen bonds : angle 3.82159 ( 3369) metal coordination : bond 0.00659 ( 8) metal coordination : angle 1.65502 ( 12) covalent geometry : bond 0.00280 (28474) covalent geometry : angle 0.50096 (38874) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 177 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 22 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: P 58 GLU cc_start: 0.8554 (tt0) cc_final: 0.8295 (tt0) REVERT: P 76 SER cc_start: 0.9224 (t) cc_final: 0.8491 (p) REVERT: P 84 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.8146 (p) REVERT: P 95 GLN cc_start: 0.8937 (mp10) cc_final: 0.8659 (mp10) REVERT: I 189 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8170 (t70) REVERT: I 284 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8752 (tp) REVERT: I 349 GLU cc_start: 0.9397 (OUTLIER) cc_final: 0.8929 (mm-30) REVERT: I 1059 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.7657 (mtp85) REVERT: I 1273 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8482 (mtm) REVERT: J 172 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.6712 (p90) REVERT: J 175 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7296 (pm20) REVERT: J 405 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: J 417 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8507 (mmm-85) REVERT: J 541 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9213 (mm) REVERT: J 747 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8465 (mtp) REVERT: J 1095 MET cc_start: 0.7490 (tpt) cc_final: 0.7121 (tmm) REVERT: J 1253 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.9161 (mm) REVERT: G 194 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8794 (mm-40) REVERT: H 76 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8614 (mp0) REVERT: H 186 ASN cc_start: 0.8646 (t0) cc_final: 0.8378 (t0) REVERT: H 231 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8336 (m-80) outliers start: 98 outliers final: 70 residues processed: 266 average time/residue: 0.3686 time to fit residues: 163.1146 Evaluate side-chains 260 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 174 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 509 SER Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1059 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 405 GLU Chi-restraints excluded: chain J residue 417 ARG Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1176 VAL Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 43 ASN Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 165 optimal weight: 0.0010 chunk 285 optimal weight: 10.0000 chunk 246 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 147 optimal weight: 0.2980 chunk 148 optimal weight: 0.8980 chunk 161 optimal weight: 10.0000 chunk 221 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 167 optimal weight: 0.7980 chunk 283 optimal weight: 6.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.071328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.050023 restraints weight = 92937.084| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.22 r_work: 0.2682 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 28482 Z= 0.101 Angle : 0.500 11.636 38886 Z= 0.258 Chirality : 0.040 0.163 4445 Planarity : 0.003 0.050 4763 Dihedral : 16.449 177.478 4748 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.22 % Allowed : 26.41 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.15), residues: 3296 helix: 2.27 (0.16), residues: 1186 sheet: 0.64 (0.24), residues: 474 loop : 0.10 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J1193 HIS 0.003 0.000 HIS I 165 PHE 0.023 0.001 PHE I 545 TYR 0.024 0.001 TYR G 185 ARG 0.012 0.000 ARG I 275 Details of bonding type rmsd hydrogen bonds : bond 0.02992 ( 1224) hydrogen bonds : angle 3.78408 ( 3369) metal coordination : bond 0.00439 ( 8) metal coordination : angle 1.40666 ( 12) covalent geometry : bond 0.00232 (28474) covalent geometry : angle 0.49974 (38874) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 182 time to evaluate : 3.114 Fit side-chains revert: symmetry clash REVERT: P 22 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: P 37 LYS cc_start: 0.8698 (pmtt) cc_final: 0.8319 (ptmm) REVERT: P 48 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8309 (mp0) REVERT: P 58 GLU cc_start: 0.8505 (tt0) cc_final: 0.8262 (tt0) REVERT: P 76 SER cc_start: 0.9184 (t) cc_final: 0.8440 (p) REVERT: P 84 SER cc_start: 0.8673 (OUTLIER) cc_final: 0.8114 (p) REVERT: P 95 GLN cc_start: 0.8954 (mp10) cc_final: 0.8646 (mp10) REVERT: I 124 MET cc_start: 0.9211 (mtp) cc_final: 0.8923 (mtm) REVERT: I 189 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8148 (t70) REVERT: I 284 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8728 (tp) REVERT: I 349 GLU cc_start: 0.9379 (OUTLIER) cc_final: 0.8909 (mm-30) REVERT: I 1059 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7624 (mtp85) REVERT: I 1273 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8497 (mtm) REVERT: J 172 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.6516 (p90) REVERT: J 175 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7185 (pm20) REVERT: J 405 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: J 417 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8356 (mmm-85) REVERT: J 541 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9216 (mm) REVERT: J 677 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8755 (mt-10) REVERT: J 747 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8402 (mtp) REVERT: J 1095 MET cc_start: 0.7335 (tpt) cc_final: 0.6964 (tmm) REVERT: J 1253 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9135 (mm) REVERT: G 194 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8763 (mm-40) REVERT: H 76 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8615 (mp0) REVERT: H 142 MET cc_start: 0.9205 (pmm) cc_final: 0.8600 (pmm) REVERT: H 186 ASN cc_start: 0.8597 (t0) cc_final: 0.8358 (t0) REVERT: H 231 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8273 (m-80) outliers start: 91 outliers final: 66 residues processed: 267 average time/residue: 0.3646 time to fit residues: 160.3042 Evaluate side-chains 258 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 175 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 509 SER Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1059 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 405 GLU Chi-restraints excluded: chain J residue 417 ARG Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 677 GLU Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1176 VAL Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 43 ASN Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 37 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 139 optimal weight: 0.0980 chunk 273 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 297 optimal weight: 0.0570 chunk 98 optimal weight: 1.9990 chunk 269 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.071552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.050296 restraints weight = 87781.560| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.12 r_work: 0.2694 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 28482 Z= 0.102 Angle : 0.506 13.230 38886 Z= 0.261 Chirality : 0.040 0.172 4445 Planarity : 0.003 0.054 4763 Dihedral : 16.432 177.445 4748 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.22 % Allowed : 26.41 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.15), residues: 3296 helix: 2.27 (0.16), residues: 1186 sheet: 0.57 (0.25), residues: 462 loop : 0.11 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J1193 HIS 0.003 0.000 HIS I 165 PHE 0.023 0.001 PHE I 545 TYR 0.023 0.001 TYR G 185 ARG 0.016 0.000 ARG J 322 Details of bonding type rmsd hydrogen bonds : bond 0.02963 ( 1224) hydrogen bonds : angle 3.77428 ( 3369) metal coordination : bond 0.00430 ( 8) metal coordination : angle 1.29229 ( 12) covalent geometry : bond 0.00235 (28474) covalent geometry : angle 0.50584 (38874) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 182 time to evaluate : 2.920 Fit side-chains revert: symmetry clash REVERT: P 22 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: P 48 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8321 (mp0) REVERT: P 58 GLU cc_start: 0.8514 (tt0) cc_final: 0.8263 (tt0) REVERT: P 76 SER cc_start: 0.9174 (t) cc_final: 0.8442 (p) REVERT: P 84 SER cc_start: 0.8665 (OUTLIER) cc_final: 0.8102 (p) REVERT: P 95 GLN cc_start: 0.8953 (mp10) cc_final: 0.8660 (mp10) REVERT: I 189 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8143 (t70) REVERT: I 284 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8727 (tp) REVERT: I 461 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: I 1040 ASP cc_start: 0.7940 (m-30) cc_final: 0.7708 (m-30) REVERT: I 1059 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7612 (mtp85) REVERT: I 1273 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8537 (mtm) REVERT: J 172 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.6518 (p90) REVERT: J 175 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7141 (pm20) REVERT: J 405 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: J 417 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8363 (mmm-85) REVERT: J 541 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9217 (mm) REVERT: J 677 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8758 (mt-10) REVERT: J 747 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8377 (mtp) REVERT: J 1253 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9135 (mm) REVERT: K 41 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: G 194 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8550 (pp30) REVERT: H 76 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8623 (mp0) REVERT: H 142 MET cc_start: 0.9207 (pmm) cc_final: 0.8584 (pmm) REVERT: H 186 ASN cc_start: 0.8597 (t0) cc_final: 0.8336 (t0) REVERT: H 231 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8223 (m-80) outliers start: 91 outliers final: 69 residues processed: 267 average time/residue: 0.3676 time to fit residues: 161.0639 Evaluate side-chains 267 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 180 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 461 GLU Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 509 SER Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1059 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 405 GLU Chi-restraints excluded: chain J residue 417 ARG Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 677 GLU Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1176 VAL Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 19 optimal weight: 0.5980 chunk 147 optimal weight: 0.0060 chunk 98 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 300 optimal weight: 3.9990 chunk 303 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 265 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 276 ASN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.071528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.049529 restraints weight = 115959.412| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 3.66 r_work: 0.2658 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 28482 Z= 0.105 Angle : 0.507 13.553 38886 Z= 0.261 Chirality : 0.040 0.162 4445 Planarity : 0.003 0.055 4763 Dihedral : 16.420 177.394 4748 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.22 % Allowed : 26.44 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.15), residues: 3296 helix: 2.27 (0.16), residues: 1187 sheet: 0.58 (0.24), residues: 487 loop : 0.14 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J1193 HIS 0.002 0.000 HIS J 430 PHE 0.023 0.001 PHE I 545 TYR 0.023 0.001 TYR G 185 ARG 0.015 0.000 ARG J 322 Details of bonding type rmsd hydrogen bonds : bond 0.02955 ( 1224) hydrogen bonds : angle 3.76939 ( 3369) metal coordination : bond 0.00466 ( 8) metal coordination : angle 1.26819 ( 12) covalent geometry : bond 0.00242 (28474) covalent geometry : angle 0.50626 (38874) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13406.84 seconds wall clock time: 233 minutes 4.34 seconds (13984.34 seconds total)