Starting phenix.real_space_refine (version: dev) on Sun Feb 26 04:50:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p19_20234/02_2023/6p19_20234.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p19_20234/02_2023/6p19_20234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p19_20234/02_2023/6p19_20234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p19_20234/02_2023/6p19_20234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p19_20234/02_2023/6p19_20234.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p19_20234/02_2023/6p19_20234.pdb" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 15": "OD1" <-> "OD2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 222": "OD1" <-> "OD2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C GLU 264": "OE1" <-> "OE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C ASP 340": "OD1" <-> "OD2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 472": "OE1" <-> "OE2" Residue "C GLU 477": "OE1" <-> "OE2" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 549": "OD1" <-> "OD2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C ASP 596": "OD1" <-> "OD2" Residue "C ASP 696": "OD1" <-> "OD2" Residue "C ASP 728": "OD1" <-> "OD2" Residue "C ASP 739": "OD1" <-> "OD2" Residue "C PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 826": "OD1" <-> "OD2" Residue "C TYR 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 930": "OD1" <-> "OD2" Residue "C GLU 940": "OE1" <-> "OE2" Residue "C ASP 959": "OD1" <-> "OD2" Residue "C GLU 1016": "OE1" <-> "OE2" Residue "C ASP 1019": "OD1" <-> "OD2" Residue "C GLU 1026": "OE1" <-> "OE2" Residue "C TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1064": "OD1" <-> "OD2" Residue "C TYR 1087": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1088": "OD1" <-> "OD2" Residue "C ASP 1203": "OD1" <-> "OD2" Residue "C TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1240": "OD1" <-> "OD2" Residue "C TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1297": "OD1" <-> "OD2" Residue "C ASP 1310": "OD1" <-> "OD2" Residue "C GLU 1342": "OE1" <-> "OE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 193": "OD1" <-> "OD2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 413": "OD1" <-> "OD2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 658": "OE1" <-> "OE2" Residue "D GLU 677": "OE1" <-> "OE2" Residue "D ASP 684": "OD1" <-> "OD2" Residue "D GLU 765": "OE1" <-> "OE2" Residue "D ASP 837": "OD1" <-> "OD2" Residue "D ASP 902": "OD1" <-> "OD2" Residue "D PHE 1034": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1037": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1039": "OD1" <-> "OD2" Residue "D ASP 1051": "OD1" <-> "OD2" Residue "D GLU 1052": "OE1" <-> "OE2" Residue "D ASP 1082": "OD1" <-> "OD2" Residue "D ASP 1087": "OD1" <-> "OD2" Residue "D TYR 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1110": "OE1" <-> "OE2" Residue "D ASP 1111": "OD1" <-> "OD2" Residue "D GLU 1168": "OE1" <-> "OE2" Residue "D ASP 1181": "OD1" <-> "OD2" Residue "D TYR 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1188": "OE1" <-> "OE2" Residue "D ASP 1208": "OD1" <-> "OD2" Residue "D ASP 1273": "OD1" <-> "OD2" Residue "D GLU 1291": "OE1" <-> "OE2" Residue "D ASP 1368": "OD1" <-> "OD2" Residue "E GLU 11": "OE1" <-> "OE2" Residue "E ASP 36": "OD1" <-> "OD2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 74": "OE1" <-> "OE2" Residue "Q GLU 14": "OE1" <-> "OE2" Residue "Q ARG 51": "NH1" <-> "NH2" Residue "Q ASP 61": "OD1" <-> "OD2" Residue "Q GLU 129": "OE1" <-> "OE2" Residue "Q GLU 132": "OE1" <-> "OE2" Residue "Q PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 156": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 27416 Number of models: 1 Model: "" Number of chains: 10 Chain: "1" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 478 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "2" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 542 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1324, 10437 Classifications: {'peptide': 1324} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1268} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 10319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10319 Classifications: {'peptide': 1327} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1271} Chain breaks: 2 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "Q" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1129 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 1 Chain: "R" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 355 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 11, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 13} Chain: "D" 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 15468 SG CYS D 70 43.245 119.165 62.351 1.00103.34 S ATOM 15482 SG CYS D 72 44.915 122.455 61.689 1.00 94.59 S ATOM 21302 SG CYS D 814 41.460 52.961 47.558 1.00 74.88 S ATOM 21867 SG CYS D 888 43.473 56.080 48.436 1.00 69.19 S ATOM 21918 SG CYS D 895 41.008 54.351 50.914 1.00 60.42 S ATOM 21939 SG CYS D 898 43.952 51.936 49.962 1.00 58.11 S Time building chain proxies: 16.38, per 1000 atoms: 0.60 Number of scatterers: 27416 At special positions: 0 Unit cell: (141.312, 137.216, 146.432, 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 114 16.00 P 66 15.00 Mg 1 11.99 O 5412 8.00 N 4853 7.00 C 16968 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 - 3.50 Amino acid : False - 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: 12.25 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " Number of angles added : 6 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6140 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 45 sheets defined 40.2% alpha, 15.0% beta 22 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 7.43 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 4.262A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.450A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 212 through 228 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.534A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 292 removed outlier: 3.719A pdb=" N TYR C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 346 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.550A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 480 Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.879A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.797A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 4.086A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.736A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 614 removed outlier: 4.310A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 609 through 614' Processing helix chain 'C' and resid 657 through 661 removed outlier: 4.281A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.506A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 861 through 865 removed outlier: 3.860A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 983 Processing helix chain 'C' and resid 986 through 991 Processing helix chain 'C' and resid 993 through 997 Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.643A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1135 Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.941A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1334 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.671A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.636A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 206 removed outlier: 4.483A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.538A pdb=" N ARG D 250 " --> pdb=" O PRO D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 286 removed outlier: 4.090A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 515 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 583 removed outlier: 3.844A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.709A pdb=" N ILE D 653 " --> pdb=" O LYS D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.006A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.622A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 4.055A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1316 Processing helix chain 'D' and resid 1318 through 1326 Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1361 through 1375 removed outlier: 4.457A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 76 Processing helix chain 'Q' and resid 9 through 28 Processing helix chain 'Q' and resid 39 through 48 Processing helix chain 'Q' and resid 60 through 74 Processing helix chain 'Q' and resid 77 through 89 removed outlier: 3.986A pdb=" N PHE Q 81 " --> pdb=" O ASP Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 103 Processing helix chain 'Q' and resid 123 through 151 Proline residue: Q 143 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 removed outlier: 7.510A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 55 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY A 149 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.627A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 153 removed outlier: 3.509A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.835A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 105 removed outlier: 3.686A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.661A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 122 " --> pdb=" O ARG B 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 111 removed outlier: 7.259A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.556A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.847A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.708A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 104 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU C 106 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL C 114 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB6, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.234A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB8, first strand: chain 'C' and resid 158 through 160 removed outlier: 3.830A pdb=" N ASP C 160 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AC1, first strand: chain 'C' and resid 284 through 287 removed outlier: 3.843A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 240 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.589A pdb=" N CYS C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.510A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.510A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 615 through 617 Processing sheet with id=AC6, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.940A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC8, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC9, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AD1, first strand: chain 'C' and resid 1065 through 1067 removed outlier: 7.675A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.668A pdb=" N GLY C 846 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 849 through 850 removed outlier: 3.987A pdb=" N LYS C 914 " --> pdb=" O THR C 888 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1269 through 1270 removed outlier: 3.591A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1341 Processing sheet with id=AD6, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.319A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 159 through 160 removed outlier: 7.132A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 253 through 254 removed outlier: 4.238A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA D 261 " --> pdb=" O VAL D 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 350 through 357 removed outlier: 7.612A pdb=" N ALA D 446 " --> pdb=" O PRO D 369 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.555A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'D' and resid 958 through 961 removed outlier: 3.551A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 965 through 966 removed outlier: 4.302A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1025 through 1026 removed outlier: 3.615A pdb=" N ILE D1124 " --> pdb=" O MET D1025 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1034 through 1036 removed outlier: 3.756A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1046 through 1050 removed outlier: 3.950A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1174 through 1178 removed outlier: 6.520A pdb=" N ARG D1174 " --> pdb=" O GLY D1166 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1280 through 1281 removed outlier: 3.575A pdb=" N VAL D1280 " --> pdb=" O ALA D1264 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL D1267 " --> pdb=" O THR D1301 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 1113 hydrogen bonds defined for protein. 3177 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 12.27 Time building geometry restraints manager: 12.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7017 1.33 - 1.45: 5218 1.45 - 1.57: 15411 1.57 - 1.69: 127 1.69 - 1.82: 198 Bond restraints: 27971 Sorted by residual: bond pdb=" N ILE B 211 " pdb=" CA ILE B 211 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.07e-02 8.73e+03 1.35e+01 bond pdb=" C PHE D 49 " pdb=" N LYS D 50 " ideal model delta sigma weight residual 1.333 1.253 0.080 2.74e-02 1.33e+03 8.48e+00 bond pdb=" CA MET D 644 " pdb=" CB MET D 644 " ideal model delta sigma weight residual 1.526 1.481 0.046 1.76e-02 3.23e+03 6.71e+00 bond pdb=" N LYS C 991 " pdb=" CA LYS C 991 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.31e-02 5.83e+03 5.80e+00 bond pdb=" CG LEU C 817 " pdb=" CD1 LEU C 817 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.69e+00 ... (remaining 27966 not shown) Histogram of bond angle deviations from ideal: 96.48 - 103.99: 601 103.99 - 111.50: 11995 111.50 - 119.01: 11034 119.01 - 126.52: 13993 126.52 - 134.03: 443 Bond angle restraints: 38066 Sorted by residual: angle pdb=" C SER D 503 " pdb=" N GLN D 504 " pdb=" CA GLN D 504 " ideal model delta sigma weight residual 121.54 131.24 -9.70 1.91e+00 2.74e-01 2.58e+01 angle pdb=" N ILE B 130 " pdb=" CA ILE B 130 " pdb=" C ILE B 130 " ideal model delta sigma weight residual 111.48 106.92 4.56 9.40e-01 1.13e+00 2.35e+01 angle pdb=" C SER D 122 " pdb=" N ARG D 123 " pdb=" CA ARG D 123 " ideal model delta sigma weight residual 121.54 130.61 -9.07 1.91e+00 2.74e-01 2.26e+01 angle pdb=" C ARG D 709 " pdb=" N ASP D 710 " pdb=" CA ASP D 710 " ideal model delta sigma weight residual 121.54 129.83 -8.29 1.91e+00 2.74e-01 1.88e+01 angle pdb=" N LYS C 991 " pdb=" CA LYS C 991 " pdb=" C LYS C 991 " ideal model delta sigma weight residual 113.18 108.53 4.65 1.21e+00 6.83e-01 1.48e+01 ... (remaining 38061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.92: 16114 29.92 - 59.84: 780 59.84 - 89.76: 69 89.76 - 119.68: 1 119.68 - 149.60: 1 Dihedral angle restraints: 16965 sinusoidal: 7420 harmonic: 9545 Sorted by residual: dihedral pdb=" O4' U R 58 " pdb=" C1' U R 58 " pdb=" N1 U R 58 " pdb=" C2 U R 58 " ideal model delta sinusoidal sigma weight residual 200.00 50.40 149.60 1 1.50e+01 4.44e-03 7.95e+01 dihedral pdb=" CA ASP D 710 " pdb=" C ASP D 710 " pdb=" N GLY D 711 " pdb=" CA GLY D 711 " ideal model delta harmonic sigma weight residual 180.00 150.91 29.09 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA VAL B 192 " pdb=" C VAL B 192 " pdb=" N GLU B 193 " pdb=" CA GLU B 193 " ideal model delta harmonic sigma weight residual 180.00 -153.81 -26.19 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 16962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3246 0.060 - 0.120: 910 0.120 - 0.180: 151 0.180 - 0.240: 26 0.240 - 0.300: 4 Chirality restraints: 4337 Sorted by residual: chirality pdb=" CB ILE D1177 " pdb=" CA ILE D1177 " pdb=" CG1 ILE D1177 " pdb=" CG2 ILE D1177 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB VAL C1094 " pdb=" CA VAL C1094 " pdb=" CG1 VAL C1094 " pdb=" CG2 VAL C1094 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE C1060 " pdb=" CA ILE C1060 " pdb=" CG1 ILE C1060 " pdb=" CG2 ILE C1060 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 4334 not shown) Planarity restraints: 4749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 504 " -0.025 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C GLN D 504 " 0.085 2.00e-02 2.50e+03 pdb=" O GLN D 504 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP D 505 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 450 " 0.048 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO D 451 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO D 451 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 451 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 209 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" C GLY B 209 " -0.046 2.00e-02 2.50e+03 pdb=" O GLY B 209 " 0.017 2.00e-02 2.50e+03 pdb=" N THR B 210 " 0.015 2.00e-02 2.50e+03 ... (remaining 4746 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 452 2.63 - 3.20: 23145 3.20 - 3.76: 44219 3.76 - 4.33: 57163 4.33 - 4.90: 93319 Nonbonded interactions: 218298 Sorted by model distance: nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.061 2.170 nonbonded pdb=" O3' A R 70 " pdb="MG MG D1503 " model vdw 2.075 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 2.108 2.170 nonbonded pdb=" OD2 ASP D 460 " pdb="MG MG D1503 " model vdw 2.217 2.170 nonbonded pdb=" N CYS D 72 " pdb="ZN ZN D1501 " model vdw 2.222 2.310 ... (remaining 218293 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 233) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 66 5.49 5 Mg 1 5.21 5 S 114 5.16 5 C 16968 2.51 5 N 4853 2.21 5 O 5412 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 0.710 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: 5.920 Check model and map are aligned: 0.390 Process input model: 81.950 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.280 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 : 0.008 0.091 27971 Z= 0.523 Angle : 0.920 10.665 38066 Z= 0.507 Chirality : 0.056 0.300 4337 Planarity : 0.007 0.073 4749 Dihedral : 16.494 149.597 10825 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.11), residues: 3303 helix: -2.40 (0.10), residues: 1223 sheet: -2.64 (0.24), residues: 352 loop : -2.78 (0.12), residues: 1728 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 401 time to evaluate : 3.136 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 414 average time/residue: 0.4607 time to fit residues: 287.5925 Evaluate side-chains 282 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 274 time to evaluate : 3.259 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2553 time to fit residues: 8.4135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 282 optimal weight: 0.0470 chunk 253 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 170 optimal weight: 0.7980 chunk 135 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 194 optimal weight: 20.0000 chunk 303 optimal weight: 10.0000 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 23 HIS A 117 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 208 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN C 314 ASN C 343 HIS C 517 GLN C 580 GLN C 618 GLN C 659 GLN C 766 ASN C 767 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1009 ASN C1256 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 ASN D 667 GLN D 680 ASN D 875 ASN D 962 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1114 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1259 GLN E 29 GLN Q 17 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 27971 Z= 0.177 Angle : 0.584 11.179 38066 Z= 0.304 Chirality : 0.042 0.192 4337 Planarity : 0.005 0.058 4749 Dihedral : 13.114 146.446 4323 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.13), residues: 3303 helix: -0.44 (0.14), residues: 1232 sheet: -2.04 (0.26), residues: 331 loop : -2.35 (0.13), residues: 1740 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 317 time to evaluate : 3.036 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 20 residues processed: 357 average time/residue: 0.4015 time to fit residues: 228.4062 Evaluate side-chains 286 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 266 time to evaluate : 3.189 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2843 time to fit residues: 14.5931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 168 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 252 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 303 optimal weight: 0.4980 chunk 328 optimal weight: 20.0000 chunk 270 optimal weight: 0.0370 chunk 301 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 243 optimal weight: 4.9990 overall best weight: 1.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS C 856 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS D 875 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 27971 Z= 0.213 Angle : 0.582 12.378 38066 Z= 0.299 Chirality : 0.042 0.220 4337 Planarity : 0.004 0.053 4749 Dihedral : 13.002 146.930 4323 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 3303 helix: 0.19 (0.14), residues: 1239 sheet: -1.75 (0.27), residues: 337 loop : -2.17 (0.13), residues: 1727 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 284 time to evaluate : 3.332 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 22 residues processed: 312 average time/residue: 0.3951 time to fit residues: 199.1256 Evaluate side-chains 287 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 265 time to evaluate : 3.106 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2607 time to fit residues: 14.8106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.546 > 50: distance: 24 - 81: 16.683 distance: 76 - 81: 16.831 distance: 81 - 82: 21.595 distance: 82 - 83: 18.275 distance: 82 - 85: 15.417 distance: 83 - 84: 7.595 distance: 85 - 86: 17.399 distance: 86 - 87: 19.248 distance: 86 - 88: 11.562 distance: 89 - 90: 18.821 distance: 90 - 91: 13.838 distance: 90 - 93: 27.535 distance: 91 - 92: 20.125 distance: 91 - 97: 13.898 distance: 93 - 94: 19.967 distance: 94 - 95: 20.385 distance: 94 - 96: 9.498 distance: 97 - 98: 19.818 distance: 97 - 103: 26.958 distance: 98 - 99: 16.888 distance: 98 - 101: 17.039 distance: 99 - 100: 22.884 distance: 99 - 104: 14.040 distance: 101 - 102: 37.709 distance: 102 - 103: 19.753 distance: 104 - 105: 25.514 distance: 105 - 106: 17.845 distance: 105 - 108: 41.416 distance: 106 - 107: 40.784 distance: 106 - 112: 18.132 distance: 108 - 109: 22.527 distance: 109 - 110: 52.705 distance: 109 - 111: 33.546 distance: 112 - 113: 45.553 distance: 113 - 114: 51.397 distance: 114 - 115: 25.644 distance: 114 - 116: 46.949 distance: 116 - 117: 18.964 distance: 117 - 118: 8.341 distance: 117 - 120: 36.053 distance: 118 - 119: 38.863 distance: 118 - 123: 18.812 distance: 119 - 147: 44.410 distance: 120 - 121: 35.162 distance: 120 - 122: 32.458 distance: 123 - 124: 29.740 distance: 123 - 129: 25.704 distance: 124 - 125: 34.929 distance: 124 - 127: 29.041 distance: 125 - 126: 40.050 distance: 125 - 130: 8.854 distance: 127 - 128: 50.065 distance: 128 - 129: 14.157 distance: 130 - 131: 9.764 distance: 131 - 132: 25.361 distance: 131 - 134: 13.182 distance: 132 - 133: 31.526 distance: 132 - 136: 10.841 distance: 134 - 135: 43.324 distance: 136 - 137: 8.773 distance: 137 - 138: 15.500 distance: 137 - 140: 9.775 distance: 138 - 139: 29.336 distance: 138 - 147: 11.140 distance: 140 - 141: 7.962 distance: 141 - 142: 5.778 distance: 143 - 144: 4.323 distance: 144 - 145: 5.064 distance: 144 - 146: 13.028 distance: 147 - 148: 21.457 distance: 148 - 151: 30.347 distance: 149 - 150: 27.584 distance: 149 - 155: 7.720 distance: 151 - 152: 12.619 distance: 152 - 153: 9.187 distance: 153 - 154: 3.192