Starting phenix.real_space_refine on Mon Aug 25 08:51:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eh8_28143/08_2025/8eh8_28143.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eh8_28143/08_2025/8eh8_28143.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 { model { file = "/net/cci-nas-00/data/ceres_data/8eh8_28143/08_2025/8eh8_28143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eh8_28143/08_2025/8eh8_28143.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eh8_28143/08_2025/8eh8_28143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eh8_28143/08_2025/8eh8_28143.map" } 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= 0.000 sd= 0.007 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 63 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16257 2.51 5 N 4640 2.21 5 O 5177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 26246 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 472 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 627 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "R" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "G" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1679 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10375 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 10533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10533 Classifications: {'peptide': 1358} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1302} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15505 SG CYS J 70 103.836 100.483 90.419 1.00 70.37 S ATOM 15519 SG CYS J 72 104.023 104.237 91.029 1.00 75.80 S ATOM 15627 SG CYS J 85 106.007 101.835 93.174 1.00 70.92 S ATOM 15651 SG CYS J 88 102.184 102.000 93.480 1.00 68.44 S ATOM 21331 SG CYS J 814 86.797 35.957 86.865 1.00 40.60 S ATOM 21896 SG CYS J 888 85.189 39.298 87.381 1.00 32.63 S ATOM 21947 SG CYS J 895 85.991 38.080 83.828 1.00 30.88 S ATOM 21968 SG CYS J 898 83.206 36.455 85.725 1.00 30.20 S Time building chain proxies: 5.46, per 1000 atoms: 0.21 Number of scatterers: 26246 At special positions: 0 Unit cell: (137.8, 145.6, 165.1, 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 106 16.00 P 63 15.00 Mg 1 11.99 O 5177 8.00 N 4640 7.00 C 16257 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 805.0 milliseconds 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 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " 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 888 " Number of angles added : 12 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5884 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 49 sheets defined 36.8% alpha, 16.1% beta 28 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.778A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 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 212 through 229 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.717A 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 212 through 228 Processing helix chain 'I' and resid 30 through 40 Processing helix chain 'I' and resid 49 through 54 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 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 294 removed outlier: 3.706A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 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: 4.185A 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 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 480 removed outlier: 4.177A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 528 removed outlier: 3.528A pdb=" N GLU I 523 " --> pdb=" O ASN I 519 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG I 528 " --> pdb=" O ILE I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 544 through 549 removed outlier: 3.756A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP I 549 " --> pdb=" O PHE I 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 544 through 549' Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.723A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 656 through 660 removed outlier: 4.298A pdb=" N VAL I 660 " --> pdb=" O THR I 657 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.791A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 689 Processing helix chain 'I' and resid 704 through 713 removed outlier: 4.447A pdb=" N GLY I 713 " --> pdb=" O ALA I 709 " (cutoff:3.500A) Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 942 through 980 removed outlier: 3.520A pdb=" N LEU I 960 " --> pdb=" O ALA I 956 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.938A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS I 991 " --> pdb=" O GLU I 987 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1037 removed outlier: 3.523A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 3.931A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1101 through 1106' Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 4.033A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.745A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.836A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.651A 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 removed outlier: 3.617A pdb=" N TRP I1276 " --> pdb=" O GLU I1272 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA I1277 " --> pdb=" O MET I1273 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU I1278 " --> pdb=" O GLU I1274 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.568A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1298 through 1309 Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.650A 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 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.852A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.682A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) 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 Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.693A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 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 removed outlier: 3.511A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP J 284 " --> pdb=" O LYS J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.711A pdb=" N LEU J 374 " --> pdb=" O LYS J 370 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 removed outlier: 3.754A pdb=" N ALA J 397 " --> pdb=" O THR J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 416 removed outlier: 4.007A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) 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 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 removed outlier: 3.512A pdb=" N ASN J 489 " --> pdb=" O SER J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 505 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 573 through 580 Processing helix chain 'J' and resid 598 through 612 Processing helix chain 'J' and resid 613 through 634 removed outlier: 3.704A pdb=" N THR J 617 " --> pdb=" O GLY J 613 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 671 removed outlier: 3.555A pdb=" N ILE J 653 " --> pdb=" O LYS J 649 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.027A pdb=" N TYR J 679 " --> pdb=" O ALA J 675 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN J 680 " --> pdb=" O GLY J 676 " (cutoff:3.500A) removed outlier: 3.995A 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 770 through 790 removed outlier: 3.793A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR J 786 " --> pdb=" O GLY J 782 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA J 787 " --> pdb=" O LEU J 783 " (cutoff:3.500A) Processing helix chain 'J' and resid 790 through 805 removed outlier: 4.169A pdb=" N LEU J 796 " --> pdb=" O ASN J 792 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL J 803 " --> pdb=" O ARG J 799 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 914 through 932 removed outlier: 3.572A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Proline residue: J 926 - end of helix removed outlier: 4.142A pdb=" N GLN J 929 " --> pdb=" O GLU J 925 " (cutoff:3.500A) Processing helix chain 'J' and resid 1069 through 1074 removed outlier: 4.430A pdb=" N ASP J1073 " --> pdb=" O GLY J1070 " (cutoff:3.500A) Processing helix chain 'J' and resid 1139 through 1147 Processing helix chain 'J' and resid 1218 through 1244 removed outlier: 7.919A pdb=" N VAL J1226 " --> pdb=" O ARG J1222 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N HIS J1227 " --> pdb=" O LEU J1223 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA J1228 " --> pdb=" O ARG J1224 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.402A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.911A pdb=" N ASN J1295 " --> pdb=" O GLU J1291 " (cutoff:3.500A) Processing helix chain 'J' and resid 1310 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.564A 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 1347 through 1354 Processing helix chain 'J' and resid 1362 through 1373 removed outlier: 3.658A pdb=" N ARG J1373 " --> pdb=" O ARG J1369 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.713A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 78 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.320A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.320A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 97 through 99 removed outlier: 6.901A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA G 55 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 97 through 99 Processing sheet with id=AA5, first strand: chain 'G' and resid 102 through 105 removed outlier: 3.617A pdb=" N LYS G 104 " --> pdb=" O ILE G 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.553A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 12 through 15 removed outlier: 5.457A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 12 through 15 removed outlier: 5.457A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LYS H 200 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL H 187 " --> pdb=" O LYS H 200 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL H 202 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 97 through 101 removed outlier: 6.477A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AB2, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AB3, first strand: chain 'H' and resid 108 through 111 removed outlier: 6.666A pdb=" N GLY H 108 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N HIS H 132 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB5, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.442A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.809A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB8, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.531A pdb=" N HIS I 150 " --> pdb=" O ARG I 452 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.580A pdb=" N ASN I 173 " --> pdb=" O ASP I 158 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE I 176 " --> pdb=" O LEU I 184 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AC2, first strand: chain 'I' and resid 239 through 240 removed outlier: 3.595A pdb=" N MET I 239 " --> pdb=" O ILE I 285 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 285 " --> pdb=" O MET I 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'I' and resid 255 through 256 Processing sheet with id=AC4, first strand: chain 'I' and resid 296 through 297 removed outlier: 4.151A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.910A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.351A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC8, first strand: chain 'I' and resid 616 through 617 Processing sheet with id=AC9, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.551A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 749 through 752 removed outlier: 3.651A pdb=" N ASP I 749 " --> pdb=" O ILE I 734 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AD3, first strand: chain 'I' and resid 1076 through 1080 removed outlier: 5.997A pdb=" N ILE I 816 " --> pdb=" O ILE I1076 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS I1078 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 830 through 841 removed outlier: 5.927A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.903A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.182A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AD8, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AD9, first strand: chain 'J' and resid 103 through 112 removed outlier: 10.141A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.732A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 144 through 145 Processing sheet with id=AE2, first strand: chain 'J' and resid 548 through 554 removed outlier: 3.710A pdb=" N GLU J 554 " --> pdb=" O LYS J 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AE4, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE5, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE6, first strand: chain 'J' and resid 842 through 843 removed outlier: 4.169A pdb=" N ARG J 842 " --> pdb=" O LEU J 864 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU J 864 " --> pdb=" O ARG J 842 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'J' and resid 949 through 952 removed outlier: 6.600A pdb=" N ILE J 950 " --> pdb=" O VAL J1017 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU J1015 " --> pdb=" O VAL J 952 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 957 through 961 Processing sheet with id=AE9, first strand: chain 'J' and resid 1025 through 1026 Processing sheet with id=AF1, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 3.575A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR J1038 " --> pdb=" O ALA J1077 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 1046 through 1051 removed outlier: 3.810A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU J1056 " --> pdb=" O ASP J1051 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 1186 through 1190 removed outlier: 4.541A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE J1177 " --> pdb=" O TYR J1186 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL J1204 " --> pdb=" O GLY J1161 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 3.778A pdb=" N VAL J1280 " --> pdb=" O ALA J1264 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) 970 hydrogen bonds defined for protein. 2709 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 2.42 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: 8688 1.34 - 1.46: 4857 1.46 - 1.58: 12911 1.58 - 1.70: 126 1.70 - 1.82: 187 Bond restraints: 26769 Sorted by residual: bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.824 -0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.729 -0.197 2.00e-02 2.50e+03 9.74e+01 bond pdb=" C7 1N7 I1401 " pdb=" C8 1N7 I1401 " ideal model delta sigma weight residual 1.542 1.705 -0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" C19 1N7 I1401 " pdb=" C2 1N7 I1401 " ideal model delta sigma weight residual 1.551 1.403 0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" C4 1N7 I1401 " pdb=" C5 1N7 I1401 " ideal model delta sigma weight residual 1.534 1.396 0.138 2.00e-02 2.50e+03 4.76e+01 ... (remaining 26764 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 36019 2.22 - 4.44: 373 4.44 - 6.66: 37 6.66 - 8.88: 7 8.88 - 11.10: 1 Bond angle restraints: 36437 Sorted by residual: angle pdb=" N ILE J 331 " pdb=" CA ILE J 331 " pdb=" C ILE J 331 " ideal model delta sigma weight residual 113.53 108.67 4.86 9.80e-01 1.04e+00 2.46e+01 angle pdb=" N VAL J 769 " pdb=" CA VAL J 769 " pdb=" C VAL J 769 " ideal model delta sigma weight residual 113.00 108.09 4.91 1.30e+00 5.92e-01 1.43e+01 angle pdb=" C GLY J 924 " pdb=" N GLU J 925 " pdb=" CA GLU J 925 " ideal model delta sigma weight residual 121.80 113.14 8.66 2.44e+00 1.68e-01 1.26e+01 angle pdb=" C ARG J 709 " pdb=" N ASP J 710 " pdb=" CA ASP J 710 " ideal model delta sigma weight residual 126.45 132.56 -6.11 1.77e+00 3.19e-01 1.19e+01 angle pdb=" N GLU J 925 " pdb=" CA GLU J 925 " pdb=" C GLU J 925 " ideal model delta sigma weight residual 109.81 117.05 -7.24 2.21e+00 2.05e-01 1.07e+01 ... (remaining 36432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 15863 35.83 - 71.65: 507 71.65 - 107.48: 27 107.48 - 143.30: 1 143.30 - 179.13: 1 Dihedral angle restraints: 16399 sinusoidal: 7248 harmonic: 9151 Sorted by residual: dihedral pdb=" CA LEU J1138 " pdb=" C LEU J1138 " pdb=" N PRO J1139 " pdb=" CA PRO J1139 " ideal model delta harmonic sigma weight residual 180.00 145.39 34.61 0 5.00e+00 4.00e-02 4.79e+01 dihedral pdb=" CA GLU J 925 " pdb=" C GLU J 925 " pdb=" N PRO J 926 " pdb=" CA PRO J 926 " ideal model delta harmonic sigma weight residual 180.00 147.14 32.86 0 5.00e+00 4.00e-02 4.32e+01 dihedral pdb=" CA GLY J 852 " pdb=" C GLY J 852 " pdb=" N THR J 853 " pdb=" CA THR J 853 " ideal model delta harmonic sigma weight residual -180.00 -155.47 -24.53 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 16396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3875 0.082 - 0.164: 295 0.164 - 0.247: 3 0.247 - 0.329: 2 0.329 - 0.411: 1 Chirality restraints: 4176 Sorted by residual: chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.94 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C15 1N7 I1401 " pdb=" C14 1N7 I1401 " pdb=" C16 1N7 I1401 " pdb=" C2 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.47 -2.75 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C5 1N7 I1401 " pdb=" C4 1N7 I1401 " pdb=" C6 1N7 I1401 " pdb=" C9 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.85 -2.60 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 4173 not shown) Planarity restraints: 4544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU J 925 " -0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO J 926 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO J 926 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO J 926 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J1138 " 0.052 5.00e-02 4.00e+02 7.96e-02 1.02e+01 pdb=" N PRO J1139 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO J1139 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO J1139 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 850 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO J 851 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO J 851 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 851 " 0.027 5.00e-02 4.00e+02 ... (remaining 4541 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 345 2.63 - 3.20: 22614 3.20 - 3.77: 40855 3.77 - 4.33: 56010 4.33 - 4.90: 93272 Nonbonded interactions: 213096 Sorted by model distance: nonbonded pdb=" O3' C R 18 " pdb="MG MG R 101 " model vdw 2.066 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG R 101 " model vdw 2.164 2.170 nonbonded pdb=" O ILE I 11 " pdb=" OH TYR I1149 " model vdw 2.197 3.040 nonbonded pdb=" OG SER J1318 " pdb=" OD2 ASP J1342 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR J 795 " pdb=" OE1 GLN J1326 " model vdw 2.221 3.040 ... (remaining 213091 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 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 231)) selection = (chain 'H' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 231)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.050 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.005 0.292 26778 Z= 0.252 Angle : 0.594 11.095 36449 Z= 0.334 Chirality : 0.043 0.411 4176 Planarity : 0.004 0.084 4544 Dihedral : 15.425 179.130 10515 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.77 % Allowed : 8.65 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.56 (0.14), residues: 3174 helix: 0.12 (0.15), residues: 1094 sheet: -1.45 (0.25), residues: 410 loop : -1.74 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 28 TYR 0.011 0.001 TYR I1018 PHE 0.009 0.001 PHE I1025 TRP 0.005 0.001 TRP J 580 HIS 0.005 0.001 HIS J 430 Details of bonding type rmsd covalent geometry : bond 0.00429 (26769) covalent geometry : angle 0.59325 (36437) hydrogen bonds : bond 0.18102 ( 1033) hydrogen bonds : angle 6.72312 ( 2851) metal coordination : bond 0.00629 ( 8) metal coordination : angle 1.40163 ( 12) Misc. bond : bond 0.22679 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 462 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: I 70 TYR cc_start: 0.8481 (t80) cc_final: 0.8206 (t80) REVERT: I 207 THR cc_start: 0.8596 (p) cc_final: 0.8304 (p) REVERT: I 573 ASN cc_start: 0.7851 (m110) cc_final: 0.7594 (m110) REVERT: I 686 GLN cc_start: 0.8475 (tt0) cc_final: 0.8246 (tt0) REVERT: I 814 ASP cc_start: 0.8319 (m-30) cc_final: 0.8063 (m-30) REVERT: I 1027 LYS cc_start: 0.8042 (ptpt) cc_final: 0.7608 (ptpt) REVERT: I 1180 MET cc_start: 0.8741 (ttm) cc_final: 0.8413 (ttm) REVERT: I 1243 MET cc_start: 0.8089 (ttp) cc_final: 0.7857 (ttt) REVERT: J 48 THR cc_start: 0.7019 (OUTLIER) cc_final: 0.6815 (t) REVERT: J 56 LEU cc_start: 0.8995 (mt) cc_final: 0.8748 (mt) REVERT: J 135 ILE cc_start: 0.8611 (pt) cc_final: 0.8395 (mm) REVERT: J 324 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8883 (pp) REVERT: J 626 TYR cc_start: 0.8327 (m-10) cc_final: 0.8091 (m-10) REVERT: J 864 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8579 (pp) REVERT: J 892 PHE cc_start: 0.8390 (m-80) cc_final: 0.7995 (m-10) REVERT: J 1107 VAL cc_start: 0.7639 (OUTLIER) cc_final: 0.7438 (p) REVERT: J 1349 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6972 (mt-10) outliers start: 102 outliers final: 48 residues processed: 540 average time/residue: 0.1486 time to fit residues: 125.9563 Evaluate side-chains 415 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 363 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1366 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 490 GLN I 688 GLN I 965 GLN I1010 GLN J 545 HIS J 951 GLN J1326 GLN K 15 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.153560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.117073 restraints weight = 32836.751| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.77 r_work: 0.2908 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26778 Z= 0.139 Angle : 0.557 9.903 36449 Z= 0.292 Chirality : 0.042 0.207 4176 Planarity : 0.004 0.076 4544 Dihedral : 14.427 179.668 4379 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.59 % Allowed : 12.28 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.12 (0.15), residues: 3174 helix: 0.71 (0.16), residues: 1122 sheet: -1.53 (0.24), residues: 431 loop : -1.59 (0.14), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 352 TYR 0.015 0.001 TYR H 177 PHE 0.009 0.001 PHE I 405 TRP 0.007 0.001 TRP J 409 HIS 0.008 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00315 (26769) covalent geometry : angle 0.55471 (36437) hydrogen bonds : bond 0.04100 ( 1033) hydrogen bonds : angle 4.83223 ( 2851) metal coordination : bond 0.01022 ( 8) metal coordination : angle 2.57220 ( 12) Misc. bond : bond 0.00121 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 396 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.9472 (mtmm) cc_final: 0.8717 (pttt) REVERT: H 28 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8702 (pt) REVERT: I 60 GLN cc_start: 0.7715 (pm20) cc_final: 0.7488 (pm20) REVERT: I 207 THR cc_start: 0.8702 (p) cc_final: 0.8446 (p) REVERT: I 341 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8111 (pt) REVERT: I 490 GLN cc_start: 0.7976 (tp40) cc_final: 0.7628 (tp-100) REVERT: I 516 ASP cc_start: 0.8242 (t70) cc_final: 0.7986 (t70) REVERT: I 965 GLN cc_start: 0.8110 (mt0) cc_final: 0.7836 (mt0) REVERT: I 968 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6608 (mm-30) REVERT: I 1180 MET cc_start: 0.9091 (ttm) cc_final: 0.8757 (ttm) REVERT: I 1243 MET cc_start: 0.8884 (ttp) cc_final: 0.8630 (ttt) REVERT: J 48 THR cc_start: 0.7320 (OUTLIER) cc_final: 0.7081 (t) REVERT: J 56 LEU cc_start: 0.9182 (mt) cc_final: 0.8943 (mt) REVERT: J 304 ASP cc_start: 0.8234 (m-30) cc_final: 0.7838 (m-30) REVERT: J 324 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8955 (pp) REVERT: J 532 GLU cc_start: 0.8584 (tp30) cc_final: 0.8211 (tt0) REVERT: J 697 MET cc_start: 0.8750 (ttp) cc_final: 0.8538 (ttp) REVERT: J 738 ARG cc_start: 0.8811 (ttp80) cc_final: 0.8506 (ptt90) REVERT: J 821 MET cc_start: 0.9029 (tpp) cc_final: 0.8783 (mmm) REVERT: J 1254 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8536 (mt-10) REVERT: J 1260 MET cc_start: 0.9185 (mtp) cc_final: 0.8918 (mtm) REVERT: J 1349 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7778 (mt-10) REVERT: K 53 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8382 (mt-10) REVERT: K 55 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8066 (pt0) outliers start: 97 outliers final: 57 residues processed: 464 average time/residue: 0.1473 time to fit residues: 108.1949 Evaluate side-chains 410 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 347 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 778 GLU Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1140 LYS Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 55 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 89 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 203 optimal weight: 0.0970 chunk 56 optimal weight: 3.9990 chunk 288 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 chunk 268 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN J 489 ASN J 951 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.155482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.116610 restraints weight = 33232.810| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.81 r_work: 0.2993 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 26778 Z= 0.242 Angle : 0.617 9.431 36449 Z= 0.321 Chirality : 0.045 0.167 4176 Planarity : 0.005 0.083 4544 Dihedral : 14.412 178.619 4364 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.77 % Allowed : 13.54 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.08 (0.15), residues: 3174 helix: 0.72 (0.16), residues: 1123 sheet: -1.54 (0.25), residues: 419 loop : -1.54 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J1123 TYR 0.016 0.002 TYR J 723 PHE 0.014 0.002 PHE J 116 TRP 0.006 0.001 TRP J 686 HIS 0.009 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00568 (26769) covalent geometry : angle 0.61520 (36437) hydrogen bonds : bond 0.04197 ( 1033) hydrogen bonds : angle 4.66048 ( 2851) metal coordination : bond 0.01331 ( 8) metal coordination : angle 2.48687 ( 12) Misc. bond : bond 0.00124 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 382 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: H 28 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8785 (pt) REVERT: H 142 MET cc_start: 0.8243 (ptp) cc_final: 0.7829 (ptp) REVERT: I 5 TYR cc_start: 0.7423 (OUTLIER) cc_final: 0.6833 (m-80) REVERT: I 47 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.7043 (p90) REVERT: I 60 GLN cc_start: 0.7778 (pm20) cc_final: 0.7503 (pm20) REVERT: I 207 THR cc_start: 0.8821 (p) cc_final: 0.8572 (p) REVERT: I 341 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8103 (pt) REVERT: I 370 MET cc_start: 0.8558 (mmm) cc_final: 0.8343 (mmm) REVERT: I 427 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8374 (m-30) REVERT: I 490 GLN cc_start: 0.8063 (tp40) cc_final: 0.7624 (tp-100) REVERT: I 516 ASP cc_start: 0.8288 (t70) cc_final: 0.8069 (t70) REVERT: I 580 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8314 (mt0) REVERT: I 867 GLU cc_start: 0.8344 (pm20) cc_final: 0.7999 (pt0) REVERT: I 965 GLN cc_start: 0.8215 (mt0) cc_final: 0.7877 (mm-40) REVERT: I 1010 GLN cc_start: 0.7166 (mt0) cc_final: 0.6945 (mt0) REVERT: I 1151 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8655 (tt) REVERT: I 1180 MET cc_start: 0.9118 (ttm) cc_final: 0.8790 (ttm) REVERT: I 1243 MET cc_start: 0.8985 (ttp) cc_final: 0.8688 (ttt) REVERT: J 48 THR cc_start: 0.7510 (OUTLIER) cc_final: 0.7186 (t) REVERT: J 500 ILE cc_start: 0.9591 (OUTLIER) cc_final: 0.9323 (pp) REVERT: J 532 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: J 678 ARG cc_start: 0.7896 (tmm-80) cc_final: 0.7665 (tmm-80) REVERT: J 738 ARG cc_start: 0.8841 (ttp80) cc_final: 0.8551 (ptt90) REVERT: J 821 MET cc_start: 0.8913 (tpp) cc_final: 0.8663 (mmm) REVERT: J 1208 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8630 (t0) REVERT: J 1260 MET cc_start: 0.9038 (mtp) cc_final: 0.8747 (mtm) REVERT: J 1349 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7915 (mt-10) REVERT: K 15 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7958 (t0) REVERT: K 55 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8274 (pt0) outliers start: 129 outliers final: 80 residues processed: 476 average time/residue: 0.1490 time to fit residues: 112.6696 Evaluate side-chains 439 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 346 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 5 TYR Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 580 GLN Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 778 GLU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1140 LYS Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1208 ASP Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 55 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 208 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 227 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 204 optimal weight: 0.8980 chunk 283 optimal weight: 20.0000 chunk 249 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 153 optimal weight: 0.7980 chunk 266 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN I 387 ASN J1218 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.153756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.117239 restraints weight = 32508.799| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.84 r_work: 0.2907 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26778 Z= 0.117 Angle : 0.537 12.148 36449 Z= 0.280 Chirality : 0.041 0.146 4176 Planarity : 0.004 0.078 4544 Dihedral : 14.132 179.748 4355 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.03 % Allowed : 14.87 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -0.87 (0.15), residues: 3174 helix: 0.97 (0.16), residues: 1132 sheet: -1.47 (0.24), residues: 432 loop : -1.47 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J1123 TYR 0.015 0.001 TYR J 75 PHE 0.021 0.001 PHE J 172 TRP 0.007 0.001 TRP I 807 HIS 0.010 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00263 (26769) covalent geometry : angle 0.53526 (36437) hydrogen bonds : bond 0.03427 ( 1033) hydrogen bonds : angle 4.40507 ( 2851) metal coordination : bond 0.00731 ( 8) metal coordination : angle 2.12870 ( 12) Misc. bond : bond 0.00073 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 385 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: G 95 LYS cc_start: 0.9441 (mtmm) cc_final: 0.8679 (pttt) REVERT: H 28 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8653 (pt) REVERT: I 207 THR cc_start: 0.8578 (p) cc_final: 0.8321 (p) REVERT: I 341 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8106 (pt) REVERT: I 427 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8235 (m-30) REVERT: I 490 GLN cc_start: 0.8046 (tp40) cc_final: 0.7691 (tp-100) REVERT: I 778 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: I 867 GLU cc_start: 0.8331 (pm20) cc_final: 0.8066 (pt0) REVERT: I 965 GLN cc_start: 0.8191 (mt0) cc_final: 0.7841 (mm-40) REVERT: I 1180 MET cc_start: 0.9145 (ttm) cc_final: 0.8736 (ttm) REVERT: I 1243 MET cc_start: 0.8982 (ttp) cc_final: 0.8693 (ttt) REVERT: J 48 THR cc_start: 0.7308 (OUTLIER) cc_final: 0.7046 (t) REVERT: J 56 LEU cc_start: 0.9155 (mt) cc_final: 0.8924 (mt) REVERT: J 180 MET cc_start: 0.7825 (ptp) cc_final: 0.7562 (ptm) REVERT: J 304 ASP cc_start: 0.8186 (m-30) cc_final: 0.7791 (m-30) REVERT: J 500 ILE cc_start: 0.9522 (OUTLIER) cc_final: 0.9287 (pp) REVERT: J 532 GLU cc_start: 0.8619 (tp30) cc_final: 0.8325 (tt0) REVERT: J 697 MET cc_start: 0.8537 (ttp) cc_final: 0.8256 (ttp) REVERT: J 821 MET cc_start: 0.8941 (tpp) cc_final: 0.8709 (mmm) REVERT: J 1158 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: J 1254 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8508 (mt-10) REVERT: J 1260 MET cc_start: 0.9025 (mtp) cc_final: 0.8674 (mtm) REVERT: J 1342 ASP cc_start: 0.8538 (t70) cc_final: 0.8334 (t0) REVERT: K 15 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.8052 (t0) REVERT: K 56 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6681 (mp0) outliers start: 109 outliers final: 73 residues processed: 469 average time/residue: 0.1462 time to fit residues: 110.1225 Evaluate side-chains 440 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 358 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 5 TYR Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 778 GLU Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1140 LYS Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1158 GLU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 56 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 57.2859 > 50: distance: 62 - 69: 11.380 distance: 69 - 70: 9.090 distance: 70 - 71: 3.733 distance: 70 - 73: 9.466 distance: 71 - 72: 26.320 distance: 71 - 77: 25.077 distance: 73 - 74: 37.303 distance: 74 - 75: 15.041 distance: 75 - 76: 30.338 distance: 77 - 78: 11.108 distance: 78 - 79: 13.830 distance: 78 - 81: 6.954 distance: 79 - 80: 39.727 distance: 79 - 86: 41.567 distance: 81 - 82: 24.440 distance: 82 - 83: 3.418 distance: 83 - 84: 26.348 distance: 83 - 85: 26.372 distance: 86 - 87: 20.374 distance: 86 - 92: 15.678 distance: 87 - 88: 28.753 distance: 87 - 90: 32.193 distance: 88 - 89: 13.006 distance: 88 - 93: 21.510 distance: 90 - 91: 11.259 distance: 91 - 92: 36.366 distance: 93 - 94: 7.364 distance: 94 - 95: 32.680 distance: 95 - 96: 10.716 distance: 95 - 97: 8.829 distance: 97 - 98: 5.998 distance: 98 - 99: 19.672 distance: 98 - 101: 17.131 distance: 99 - 100: 25.925 distance: 99 - 105: 10.741 distance: 101 - 102: 41.105 distance: 102 - 103: 4.888 distance: 103 - 104: 25.197 distance: 105 - 106: 15.550 distance: 105 - 111: 14.170 distance: 106 - 107: 13.444 distance: 106 - 109: 19.842 distance: 107 - 108: 9.267 distance: 107 - 112: 5.997 distance: 109 - 110: 14.449 distance: 110 - 111: 12.235 distance: 112 - 113: 10.107 distance: 113 - 114: 8.118 distance: 113 - 116: 4.593 distance: 114 - 115: 5.468 distance: 114 - 121: 7.425 distance: 116 - 117: 13.072 distance: 117 - 118: 12.803 distance: 118 - 119: 11.606 distance: 118 - 120: 5.368 distance: 121 - 122: 5.194 distance: 122 - 125: 8.609 distance: 123 - 124: 17.480 distance: 124 - 153: 11.438 distance: 125 - 126: 24.050 distance: 127 - 128: 8.175 distance: 128 - 129: 8.482 distance: 128 - 131: 3.710 distance: 129 - 130: 8.678 distance: 129 - 138: 5.009 distance: 130 - 160: 18.926 distance: 131 - 132: 4.376 distance: 132 - 134: 5.908 distance: 133 - 135: 8.757 distance: 134 - 136: 9.115 distance: 135 - 137: 7.791 distance: 136 - 137: 8.719 distance: 138 - 139: 10.341 distance: 139 - 142: 16.970 distance: 140 - 141: 5.408 distance: 140 - 146: 6.109 distance: 141 - 168: 9.932 distance: 142 - 143: 6.911 distance: 143 - 144: 5.624 distance: 143 - 145: 7.828