Starting phenix.real_space_refine on Mon Aug 25 12:25:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pfj_17647/08_2025/8pfj_17647.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pfj_17647/08_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_17647/08_2025/8pfj_17647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pfj_17647/08_2025/8pfj_17647.map" model { file = "/net/cci-nas-00/data/ceres_data/8pfj_17647/08_2025/8pfj_17647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pfj_17647/08_2025/8pfj_17647.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.03, per 1000 atoms: 0.25 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: 2.67 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 3.75 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: 7.76 Time building geometry restraints manager: 3.38 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: 3.740 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: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 35.240 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.500 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.000 ARG G 158 TYR 0.029 0.001 TYR G 185 PHE 0.006 0.001 PHE J1325 TRP 0.023 0.001 TRP J1193 HIS 0.004 0.000 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00229 (28474) covalent geometry : angle 0.54250 (38874) hydrogen bonds : bond 0.12365 ( 1224) hydrogen bonds : angle 4.92477 ( 3369) metal coordination : bond 0.00274 ( 8) metal coordination : angle 1.16210 ( 12) *********************** 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 : 1.119 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: 0.1711 time to fit residues: 82.7691 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 : 1.080 ------------------------------------------------------------------------------- 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 197 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 4.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 70 ASN P 77 HIS I 20 GLN I 490 GLN I 965 GLN I1324 ASN J 294 ASN J 435 GLN J 465 GLN J 712 GLN J 921 GLN K 75 GLN G 23 HIS H 194 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.065034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.043800 restraints weight = 100577.795| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 3.24 r_work: 0.2499 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2501 r_free = 0.2501 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2501 r_free = 0.2501 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.119 28482 Z= 0.548 Angle : 0.842 10.328 38886 Z= 0.437 Chirality : 0.050 0.214 4445 Planarity : 0.006 0.060 4763 Dihedral : 17.134 175.794 4840 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 6.90 % Allowed : 24.67 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.15), residues: 3296 helix: 1.50 (0.15), residues: 1178 sheet: 0.39 (0.23), residues: 509 loop : -0.23 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 933 TYR 0.027 0.002 TYR H 177 PHE 0.029 0.003 PHE J 437 TRP 0.017 0.002 TRP J 409 HIS 0.010 0.002 HIS P 65 Details of bonding type rmsd covalent geometry : bond 0.01233 (28474) covalent geometry : angle 0.83425 (38874) hydrogen bonds : bond 0.06181 ( 1224) hydrogen bonds : angle 4.88422 ( 3369) metal coordination : bond 0.02813 ( 8) metal coordination : angle 6.34681 ( 12) *********************** 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 379 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 184 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 22 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: P 95 GLN cc_start: 0.8914 (mp10) cc_final: 0.8707 (mp10) REVERT: I 175 ARG cc_start: 0.9445 (OUTLIER) cc_final: 0.8090 (mtp-110) REVERT: I 189 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8484 (t0) REVERT: I 284 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8759 (tp) REVERT: I 352 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8494 (mtt90) REVERT: I 461 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8470 (tm-30) REVERT: I 529 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8946 (ttm170) REVERT: I 930 ASP cc_start: 0.9034 (t0) cc_final: 0.8683 (t0) REVERT: I 1047 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9109 (pp) REVERT: J 21 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8070 (ttmm) REVERT: J 224 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9176 (mm) REVERT: J 229 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8949 (mm-40) REVERT: J 497 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8871 (mt-10) REVERT: J 541 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9252 (mm) REVERT: J 747 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8578 (mtp) REVERT: J 1165 PHE cc_start: 0.6795 (m-10) cc_final: 0.6462 (m-10) REVERT: J 1189 MET cc_start: 0.8344 (tpp) cc_final: 0.8014 (tpp) REVERT: J 1253 ILE cc_start: 0.9511 (OUTLIER) cc_final: 0.9310 (mm) REVERT: H 231 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8762 (m-80) outliers start: 195 outliers final: 106 residues processed: 353 average time/residue: 0.1855 time to fit residues: 106.7501 Evaluate side-chains 288 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 166 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 13 GLN 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 46 VAL Chi-restraints excluded: chain P residue 63 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 28 LEU 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 175 ARG 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 352 ARG Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 461 GLU Chi-restraints excluded: chain I residue 473 ARG 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 514 PHE Chi-restraints excluded: chain I residue 529 ARG Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 596 ASP Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1047 LEU 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 1232 MET Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 17 PHE Chi-restraints excluded: chain J residue 21 LYS 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 152 THR Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 252 LEU 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 303 VAL Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 434 ILE 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 604 MET Chi-restraints excluded: chain J residue 670 SER Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 894 VAL 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 984 LEU Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1134 ILE 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 1199 PHE Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1267 VAL 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 4 VAL Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain G residue 77 ASP 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 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 78 ILE Chi-restraints excluded: chain H residue 80 GLU 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 194 GLN Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 222 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 218 optimal weight: 0.8980 chunk 304 optimal weight: 6.9990 chunk 242 optimal weight: 10.0000 chunk 210 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 251 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 387 ASN J 465 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.068780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.047392 restraints weight = 99581.780| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.29 r_work: 0.2600 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 28482 Z= 0.119 Angle : 0.528 11.120 38886 Z= 0.276 Chirality : 0.041 0.171 4445 Planarity : 0.003 0.053 4763 Dihedral : 16.891 177.872 4786 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.28 % Allowed : 25.95 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.15), residues: 3296 helix: 2.01 (0.15), residues: 1166 sheet: 0.33 (0.24), residues: 485 loop : -0.03 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 33 TYR 0.017 0.001 TYR H 177 PHE 0.015 0.001 PHE I1323 TRP 0.008 0.001 TRP J1193 HIS 0.004 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00268 (28474) covalent geometry : angle 0.52405 (38874) hydrogen bonds : bond 0.03931 ( 1224) hydrogen bonds : angle 4.20347 ( 3369) metal coordination : bond 0.00695 ( 8) metal coordination : angle 3.48028 ( 12) *********************** 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 309 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 188 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 13 GLN cc_start: 0.8100 (pt0) cc_final: 0.7744 (pt0) REVERT: P 22 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: P 58 GLU cc_start: 0.8572 (tt0) cc_final: 0.8371 (tt0) REVERT: P 62 GLU cc_start: 0.9360 (mm-30) cc_final: 0.8849 (mp0) REVERT: I 189 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8347 (t70) REVERT: I 269 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8819 (mp) REVERT: I 546 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8145 (tm-30) REVERT: I 1188 ASP cc_start: 0.8222 (t0) cc_final: 0.7668 (t0) REVERT: J 21 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.7962 (ttmm) REVERT: J 237 MET cc_start: 0.9492 (OUTLIER) cc_final: 0.9256 (mtp) REVERT: J 747 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8447 (mtp) REVERT: J 1189 MET cc_start: 0.8405 (tpp) cc_final: 0.7997 (tpp) REVERT: J 1253 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9173 (mm) REVERT: H 185 TYR cc_start: 0.9071 (p90) cc_final: 0.8843 (p90) REVERT: H 186 ASN cc_start: 0.8646 (t0) cc_final: 0.8419 (t0) REVERT: H 231 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8420 (m-80) outliers start: 121 outliers final: 69 residues processed: 293 average time/residue: 0.1788 time to fit residues: 87.3213 Evaluate side-chains 254 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 177 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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 46 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 55 SER 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 269 ILE Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 332 ARG 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 400 VAL Chi-restraints excluded: chain I residue 403 MET 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 565 GLU Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 805 MET 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 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 21 LYS 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 205 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 434 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 661 VAL 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 891 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 997 VAL 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 1253 ILE Chi-restraints excluded: chain J residue 1344 LEU 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 234 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 137 ASN Chi-restraints excluded: chain H residue 160 HIS Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 127 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 240 optimal weight: 6.9990 chunk 256 optimal weight: 30.0000 chunk 62 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 276 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 241 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.067927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.046402 restraints weight = 110146.500| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.44 r_work: 0.2573 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28482 Z= 0.178 Angle : 0.531 9.778 38886 Z= 0.277 Chirality : 0.041 0.166 4445 Planarity : 0.003 0.053 4763 Dihedral : 16.767 177.465 4758 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.00 % Allowed : 26.19 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.15), residues: 3296 helix: 2.03 (0.15), residues: 1178 sheet: 0.30 (0.24), residues: 491 loop : -0.06 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 275 TYR 0.018 0.001 TYR H 177 PHE 0.010 0.001 PHE I 390 TRP 0.006 0.001 TRP J1193 HIS 0.004 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00407 (28474) covalent geometry : angle 0.52806 (38874) hydrogen bonds : bond 0.03903 ( 1224) hydrogen bonds : angle 4.11909 ( 3369) metal coordination : bond 0.01061 ( 8) metal coordination : angle 3.01634 ( 12) *********************** 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 297 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 184 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 13 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7951 (pt0) REVERT: P 22 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: P 58 GLU cc_start: 0.8570 (tt0) cc_final: 0.8296 (tt0) REVERT: I 132 ASP cc_start: 0.9215 (p0) cc_final: 0.8990 (p0) REVERT: I 189 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8350 (t70) REVERT: I 332 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8683 (ttp80) REVERT: I 461 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8386 (tm-30) REVERT: I 1188 ASP cc_start: 0.8296 (t0) cc_final: 0.8048 (p0) REVERT: J 21 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.7938 (ttmm) REVERT: J 747 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8568 (mtp) REVERT: J 1189 MET cc_start: 0.8405 (tpp) cc_final: 0.7936 (tpp) REVERT: J 1253 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9198 (mm) REVERT: J 1355 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8199 (mtp85) REVERT: K 41 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8602 (tm-30) REVERT: H 186 ASN cc_start: 0.8691 (t0) cc_final: 0.8428 (t0) REVERT: H 231 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.8456 (m-80) outliers start: 113 outliers final: 78 residues processed: 283 average time/residue: 0.1937 time to fit residues: 88.4868 Evaluate side-chains 262 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 173 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 13 GLN 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 75 VAL Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 151 ARG 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 332 ARG 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 400 VAL Chi-restraints excluded: chain I residue 403 MET 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 565 GLU Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 596 ASP Chi-restraints excluded: chain I residue 888 THR 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 1238 LEU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 17 PHE Chi-restraints excluded: chain J residue 21 LYS 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 205 LEU Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 285 LEU 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 434 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 661 VAL 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 1169 THR Chi-restraints excluded: chain J residue 1172 LYS 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 1253 ILE Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1355 ARG 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 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 G residue 234 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 85 LEU Chi-restraints excluded: chain H residue 137 ASN 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 260 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 257 optimal weight: 30.0000 chunk 30 optimal weight: 2.9990 chunk 331 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** H 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.066758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.045438 restraints weight = 100032.584| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 3.26 r_work: 0.2543 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 28482 Z= 0.247 Angle : 0.574 9.230 38886 Z= 0.299 Chirality : 0.042 0.172 4445 Planarity : 0.004 0.053 4763 Dihedral : 16.830 177.099 4751 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.03 % Allowed : 25.38 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.15), residues: 3296 helix: 1.96 (0.15), residues: 1180 sheet: 0.25 (0.24), residues: 507 loop : -0.15 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 275 TYR 0.021 0.001 TYR H 177 PHE 0.012 0.001 PHE I 390 TRP 0.006 0.001 TRP J 409 HIS 0.003 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00561 (28474) covalent geometry : angle 0.57084 (38874) hydrogen bonds : bond 0.04212 ( 1224) hydrogen bonds : angle 4.22510 ( 3369) metal coordination : bond 0.01501 ( 8) metal coordination : angle 3.41452 ( 12) *********************** 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 321 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 179 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 13 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8127 (pt0) REVERT: P 22 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: P 58 GLU cc_start: 0.8571 (tt0) cc_final: 0.8325 (tt0) REVERT: I 132 ASP cc_start: 0.9211 (p0) cc_final: 0.9006 (p0) REVERT: I 189 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8406 (t0) REVERT: I 269 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8718 (mp) REVERT: I 284 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8842 (tp) REVERT: I 461 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8389 (tm-30) REVERT: I 1059 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.7669 (mtp85) REVERT: J 21 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.7945 (ttmm) REVERT: J 283 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9263 (mt) REVERT: J 541 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9297 (mm) REVERT: J 747 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8538 (mtp) REVERT: J 964 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8465 (mmtm) REVERT: J 1040 MET cc_start: 0.4141 (ptp) cc_final: 0.3847 (ptp) REVERT: J 1095 MET cc_start: 0.7433 (tpt) cc_final: 0.7058 (tmm) REVERT: J 1189 MET cc_start: 0.8442 (tpp) cc_final: 0.7987 (tpp) REVERT: J 1253 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.9219 (mm) REVERT: J 1355 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8318 (mtp85) REVERT: H 186 ASN cc_start: 0.8709 (t0) cc_final: 0.8424 (t0) REVERT: H 231 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8571 (m-80) outliers start: 142 outliers final: 93 residues processed: 304 average time/residue: 0.1842 time to fit residues: 91.5519 Evaluate side-chains 282 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 174 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 13 GLN 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 63 VAL Chi-restraints excluded: chain P residue 75 VAL 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 151 ARG Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 332 ARG 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 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 488 MET 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 596 ASP Chi-restraints excluded: chain I residue 811 ASN 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 1059 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 17 PHE Chi-restraints excluded: chain J residue 21 LYS Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 285 LEU 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 434 ILE Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 661 VAL 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 839 VAL Chi-restraints excluded: chain J residue 849 LEU 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 964 LYS 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 1172 LYS 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 1253 ILE Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1355 ARG 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 145 LYS 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 19 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 160 HIS Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 291 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 321 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.067697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.046062 restraints weight = 100018.623| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.34 r_work: 0.2566 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28482 Z= 0.162 Angle : 0.536 9.426 38886 Z= 0.279 Chirality : 0.041 0.168 4445 Planarity : 0.003 0.053 4763 Dihedral : 16.783 177.231 4748 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.42 % Allowed : 25.91 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.15), residues: 3296 helix: 2.07 (0.15), residues: 1175 sheet: 0.26 (0.24), residues: 488 loop : -0.07 (0.16), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 322 TYR 0.017 0.001 TYR H 177 PHE 0.017 0.001 PHE I 545 TRP 0.005 0.001 TRP J1193 HIS 0.003 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00371 (28474) covalent geometry : angle 0.53391 (38874) hydrogen bonds : bond 0.03825 ( 1224) hydrogen bonds : angle 4.11037 ( 3369) metal coordination : bond 0.01017 ( 8) metal coordination : angle 2.83218 ( 12) *********************** 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 306 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 181 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 13 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8116 (pt0) REVERT: P 22 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: I 189 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8413 (t0) REVERT: I 269 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8709 (mp) REVERT: I 370 MET cc_start: 0.9535 (tpt) cc_final: 0.9260 (tpt) REVERT: I 951 MET cc_start: 0.9225 (mmm) cc_final: 0.8998 (mmt) REVERT: J 21 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.7937 (ttmm) REVERT: J 175 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: J 541 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9313 (mm) REVERT: J 747 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8541 (mtp) REVERT: J 1040 MET cc_start: 0.4173 (ptp) cc_final: 0.3873 (ptp) REVERT: J 1189 MET cc_start: 0.8444 (tpp) cc_final: 0.8016 (tpp) REVERT: J 1253 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.9175 (mm) REVERT: J 1355 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8293 (mtp85) REVERT: K 69 ARG cc_start: 0.9060 (mmm-85) cc_final: 0.8706 (mmm160) REVERT: H 186 ASN cc_start: 0.8692 (t0) cc_final: 0.8402 (t0) REVERT: H 231 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8432 (m-80) outliers start: 125 outliers final: 91 residues processed: 290 average time/residue: 0.1708 time to fit residues: 81.0482 Evaluate side-chains 273 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 171 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 13 GLN 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 46 VAL Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 151 ARG 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 269 ILE Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 332 ARG 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 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 565 GLU Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 596 ASP 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 978 VAL 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 1238 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 17 PHE Chi-restraints excluded: chain J residue 21 LYS Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 562 GLU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 661 VAL 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 849 LEU 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 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 1172 LYS Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1355 ARG Chi-restraints excluded: chain J residue 1366 HIS 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 145 LYS 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 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 80 GLU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 160 HIS Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 124 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 131 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.067341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.045698 restraints weight = 113941.329| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.51 r_work: 0.2545 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28482 Z= 0.194 Angle : 0.545 12.704 38886 Z= 0.284 Chirality : 0.041 0.163 4445 Planarity : 0.003 0.052 4763 Dihedral : 16.784 176.992 4747 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.74 % Allowed : 25.73 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.15), residues: 3296 helix: 2.07 (0.15), residues: 1175 sheet: 0.24 (0.24), residues: 480 loop : -0.10 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 322 TYR 0.018 0.001 TYR H 177 PHE 0.021 0.001 PHE I 545 TRP 0.006 0.001 TRP J1193 HIS 0.004 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00443 (28474) covalent geometry : angle 0.54324 (38874) hydrogen bonds : bond 0.03895 ( 1224) hydrogen bonds : angle 4.12129 ( 3369) metal coordination : bond 0.01209 ( 8) metal coordination : angle 2.73277 ( 12) *********************** 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 312 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 178 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 13 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8192 (pt0) REVERT: P 22 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: I 189 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8411 (t0) REVERT: I 269 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8730 (mp) REVERT: I 284 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8858 (tp) REVERT: I 370 MET cc_start: 0.9549 (tpt) cc_final: 0.9287 (tpt) REVERT: I 461 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8392 (tm-30) REVERT: I 1059 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.7662 (mtp85) REVERT: I 1135 GLN cc_start: 0.9369 (OUTLIER) cc_final: 0.9071 (mp10) REVERT: J 322 ARG cc_start: 0.8274 (mtm110) cc_final: 0.8065 (mtm110) REVERT: J 541 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9330 (mm) REVERT: J 747 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8569 (mtp) REVERT: J 1059 LEU cc_start: 0.3661 (OUTLIER) cc_final: 0.3421 (tp) REVERT: J 1253 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9109 (mm) REVERT: J 1355 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8348 (mtp85) REVERT: K 69 ARG cc_start: 0.9079 (mmm-85) cc_final: 0.8707 (mmm160) REVERT: H 186 ASN cc_start: 0.8708 (t0) cc_final: 0.8417 (t0) REVERT: H 231 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8425 (m-80) outliers start: 134 outliers final: 97 residues processed: 296 average time/residue: 0.1608 time to fit residues: 77.5440 Evaluate side-chains 285 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 174 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 34 THR 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 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 151 ARG Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 332 ARG 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 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 488 MET 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 576 SER Chi-restraints excluded: chain I residue 596 ASP 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 978 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1059 ARG Chi-restraints excluded: chain I residue 1135 GLN Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 17 PHE Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 562 GLU Chi-restraints excluded: chain J residue 566 LYS Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 661 VAL 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 849 LEU 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 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 1172 LYS Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1355 ARG Chi-restraints excluded: chain K residue 4 VAL 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 145 LYS 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 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 80 GLU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 160 HIS Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 135 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 111 optimal weight: 0.0870 chunk 306 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 chunk 323 optimal weight: 0.2980 chunk 333 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 205 optimal weight: 0.0470 overall best weight: 0.3656 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.069426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.047644 restraints weight = 127237.653| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.74 r_work: 0.2602 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 28482 Z= 0.103 Angle : 0.522 13.170 38886 Z= 0.269 Chirality : 0.040 0.198 4445 Planarity : 0.003 0.052 4763 Dihedral : 16.677 177.228 4747 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.64 % Favored : 97.33 % Rotamer: Outliers : 3.33 % Allowed : 26.97 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.15), residues: 3296 helix: 2.14 (0.15), residues: 1183 sheet: 0.35 (0.25), residues: 473 loop : -0.03 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 275 TYR 0.013 0.001 TYR G 185 PHE 0.021 0.001 PHE I 545 TRP 0.008 0.001 TRP J1193 HIS 0.003 0.000 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00231 (28474) covalent geometry : angle 0.52134 (38874) hydrogen bonds : bond 0.03312 ( 1224) hydrogen bonds : angle 3.95732 ( 3369) metal coordination : bond 0.00442 ( 8) metal coordination : angle 1.79281 ( 12) *********************** 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 290 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 196 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 22 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: P 76 SER cc_start: 0.9270 (t) cc_final: 0.8553 (p) REVERT: I 189 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8282 (t70) REVERT: I 269 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8749 (mp) REVERT: I 332 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8720 (ttp80) REVERT: I 349 GLU cc_start: 0.9325 (OUTLIER) cc_final: 0.8780 (mm-30) REVERT: I 461 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8339 (tm-30) REVERT: I 1059 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.7650 (mtp85) REVERT: I 1135 GLN cc_start: 0.9297 (OUTLIER) cc_final: 0.9049 (mp10) REVERT: J 175 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7349 (pm20) REVERT: J 747 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8636 (mtp) REVERT: J 857 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8264 (tm) REVERT: J 1040 MET cc_start: 0.3849 (ptp) cc_final: 0.3509 (pmm) REVERT: J 1095 MET cc_start: 0.7751 (tpt) cc_final: 0.7318 (tmm) REVERT: J 1189 MET cc_start: 0.8458 (tpp) cc_final: 0.8048 (tpp) REVERT: J 1253 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9103 (mm) REVERT: J 1355 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8296 (mtp85) REVERT: K 1 MET cc_start: 0.5512 (ppp) cc_final: 0.5164 (ppp) REVERT: K 3 ARG cc_start: 0.8128 (mmp80) cc_final: 0.7758 (mmp80) REVERT: K 69 ARG cc_start: 0.9076 (mmm-85) cc_final: 0.8707 (mmm160) REVERT: H 185 TYR cc_start: 0.9042 (p90) cc_final: 0.8841 (p90) REVERT: H 231 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8194 (m-80) outliers start: 94 outliers final: 68 residues processed: 280 average time/residue: 0.1900 time to fit residues: 86.2086 Evaluate side-chains 267 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 185 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 39 VAL 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 269 ILE Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 332 ARG 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 400 VAL 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 576 SER Chi-restraints excluded: chain I residue 768 MET 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 1101 LEU Chi-restraints excluded: chain I residue 1135 GLN Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 218 THR 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 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 562 GLU Chi-restraints excluded: chain J residue 661 VAL 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 849 LEU 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 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 1172 LYS Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1239 ASP 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 J residue 1355 ARG Chi-restraints excluded: chain J residue 1366 HIS 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 145 LYS 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 19 VAL 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 160 HIS Chi-restraints excluded: chain H residue 183 ILE 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.9081 > 50: distance: 28 - 51: 5.248 distance: 37 - 59: 6.472 distance: 42 - 68: 7.909 distance: 45 - 51: 4.402 distance: 46 - 73: 19.644 distance: 51 - 52: 4.610 distance: 52 - 53: 5.112 distance: 52 - 55: 3.766 distance: 53 - 54: 6.760 distance: 53 - 59: 3.611 distance: 54 - 84: 6.775 distance: 55 - 56: 5.576 distance: 56 - 57: 4.119 distance: 56 - 58: 4.364 distance: 60 - 61: 5.617 distance: 61 - 62: 8.290 distance: 61 - 68: 7.282 distance: 62 - 91: 10.603 distance: 63 - 64: 4.311 distance: 65 - 66: 4.143 distance: 65 - 67: 3.396 distance: 68 - 69: 8.326 distance: 69 - 70: 22.311 distance: 69 - 72: 21.306 distance: 70 - 71: 7.662 distance: 70 - 73: 33.575 distance: 73 - 74: 14.268 distance: 74 - 75: 8.736 distance: 74 - 77: 5.192 distance: 75 - 76: 22.158 distance: 75 - 84: 3.900 distance: 77 - 78: 3.520 distance: 78 - 80: 7.527 distance: 79 - 81: 6.804 distance: 80 - 82: 5.922 distance: 81 - 83: 6.718 distance: 82 - 83: 7.432 distance: 84 - 85: 6.200 distance: 85 - 86: 5.638 distance: 85 - 88: 4.225 distance: 86 - 87: 5.031 distance: 86 - 91: 3.688 distance: 88 - 90: 12.286 distance: 91 - 92: 9.069 distance: 92 - 93: 16.322 distance: 92 - 95: 8.490 distance: 93 - 94: 14.683 distance: 93 - 100: 18.819 distance: 95 - 96: 5.323 distance: 96 - 97: 6.880 distance: 97 - 98: 4.443 distance: 97 - 99: 4.374 distance: 100 - 101: 28.665 distance: 101 - 102: 26.126 distance: 101 - 104: 10.606 distance: 102 - 103: 34.267 distance: 102 - 106: 28.517 distance: 104 - 105: 17.632 distance: 106 - 107: 33.790 distance: 107 - 108: 26.701 distance: 108 - 109: 37.150 distance: 108 - 110: 15.688 distance: 110 - 111: 16.346 distance: 111 - 112: 28.146 distance: 111 - 114: 20.016 distance: 112 - 113: 26.377 distance: 112 - 118: 34.559 distance: 114 - 115: 15.604 distance: 115 - 116: 15.760 distance: 115 - 117: 30.270 distance: 118 - 119: 24.417 distance: 119 - 120: 29.083 distance: 119 - 122: 39.381 distance: 120 - 121: 16.044 distance: 120 - 127: 4.123 distance: 121 - 141: 18.435 distance: 122 - 123: 33.122 distance: 123 - 124: 38.027 distance: 124 - 125: 30.744 distance: 125 - 126: 27.757