Starting phenix.real_space_refine (version: dev) on Thu Feb 23 01:50:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ayh_15713/02_2023/8ayh_15713_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ayh_15713/02_2023/8ayh_15713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ayh_15713/02_2023/8ayh_15713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ayh_15713/02_2023/8ayh_15713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ayh_15713/02_2023/8ayh_15713_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ayh_15713/02_2023/8ayh_15713_updated.pdb" } resolution = 3.35 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= 0.001 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 "C TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C ASP 317": "OD1" <-> "OD2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "C TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 515": "NH1" <-> "NH2" Residue "C TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 622": "NH1" <-> "NH2" Residue "C ASP 631": "OD1" <-> "OD2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 792": "OD1" <-> "OD2" Residue "A ASP 813": "OD1" <-> "OD2" Residue "A GLU 937": "OE1" <-> "OE2" Residue "A ASP 945": "OD1" <-> "OD2" Residue "A TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 966": "OD1" <-> "OD2" Residue "A GLU 972": "OE1" <-> "OE2" Residue "A GLU 995": "OE1" <-> "OE2" Residue "A ASP 1037": "OD1" <-> "OD2" Residue "A ASP 1114": "OD1" <-> "OD2" Residue "A PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1177": "OE1" <-> "OE2" Residue "A PHE 1227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1249": "OE1" <-> "OE2" Residue "A TYR 1285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1299": "OE1" <-> "OE2" Residue "A ASP 1314": "OD1" <-> "OD2" Residue "A TYR 1317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1330": "OD1" <-> "OD2" Residue "A ASP 1345": "OD1" <-> "OD2" Residue "A PHE 1352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1457": "OD1" <-> "OD2" Residue "A ASP 1471": "OD1" <-> "OD2" Residue "A PHE 1472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1481": "OE1" <-> "OE2" Residue "A PHE 1487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 393": "OD1" <-> "OD2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 499": "OD1" <-> "OD2" Residue "B PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 553": "OD1" <-> "OD2" Residue "B ASP 589": "OD1" <-> "OD2" Residue "B ASP 742": "OD1" <-> "OD2" Residue "B PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 817": "OD1" <-> "OD2" Residue "B GLU 842": "OE1" <-> "OE2" Residue "B TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1393": "OD1" <-> "OD2" Residue "B PHE 1446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1475": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 19109 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5123 Classifications: {'peptide': 648} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 613} Chain breaks: 1 Chain: "A" Number of atoms: 6454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6454 Classifications: {'peptide': 815} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 783} Chain breaks: 2 Chain: "B" Number of atoms: 7499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 951, 7499 Classifications: {'peptide': 951} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 901} Chain breaks: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'H1H': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.00, per 1000 atoms: 0.58 Number of scatterers: 19109 At special positions: 0 Unit cell: (108.36, 145.34, 138.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 Mg 1 11.99 O 3625 8.00 N 3167 7.00 C 12241 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS C 567 " - pdb=" SG CYS A 810 " distance=2.03 Simple disulfide: pdb=" SG CYS C 634 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 698 " - pdb=" SG CYS A 724 " distance=2.03 Simple disulfide: pdb=" SG CYS A 699 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 711 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A 856 " - pdb=" SG CYS A 883 " distance=2.04 Simple disulfide: pdb=" SG CYS A1101 " - pdb=" SG CYS A1159 " distance=2.03 Simple disulfide: pdb=" SG CYS A1375 " - pdb=" SG CYS A1505 " distance=2.04 Simple disulfide: pdb=" SG CYS A1405 " - pdb=" SG CYS A1474 " distance=2.04 Simple disulfide: pdb=" SG CYS B 544 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS B 609 " - pdb=" SG CYS B 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B1340 " - pdb=" SG CYS B1468 " distance=2.03 Simple disulfide: pdb=" SG CYS B1368 " - pdb=" SG CYS B1437 " distance=2.03 Simple disulfide: pdb=" SG CYS B1485 " - pdb=" SG CYS B1490 " distance=2.04 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: 7.15 Conformation dependent library (CDL) restraints added in 3.0 seconds 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4550 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 48 sheets defined 11.7% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 303 through 306 No H-bonds generated for 'chain 'C' and resid 303 through 306' Processing helix chain 'C' and resid 493 through 495 No H-bonds generated for 'chain 'C' and resid 493 through 495' Processing helix chain 'C' and resid 607 through 609 No H-bonds generated for 'chain 'C' and resid 607 through 609' Processing helix chain 'C' and resid 624 through 630 removed outlier: 5.358A pdb=" N LYS C 629 " --> pdb=" O GLN C 625 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N SER C 630 " --> pdb=" O PHE C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 648 Processing helix chain 'A' and resid 682 through 688 Processing helix chain 'A' and resid 696 through 700 Processing helix chain 'A' and resid 722 through 739 removed outlier: 3.612A pdb=" N CYS A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL A 734 " --> pdb=" O GLU A 730 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 738 " --> pdb=" O VAL A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 757 removed outlier: 3.770A pdb=" N LEU A 749 " --> pdb=" O LYS A 745 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 752 " --> pdb=" O GLN A 748 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS A 755 " --> pdb=" O ARG A 751 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU A 757 " --> pdb=" O HIS A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 991 removed outlier: 3.580A pdb=" N ALA A 990 " --> pdb=" O GLU A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1012 No H-bonds generated for 'chain 'A' and resid 1009 through 1012' Processing helix chain 'A' and resid 1016 through 1027 removed outlier: 3.534A pdb=" N VAL A1021 " --> pdb=" O PRO A1017 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR A1024 " --> pdb=" O TYR A1020 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A1026 " --> pdb=" O PHE A1022 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A1027 " --> pdb=" O HIS A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1051 removed outlier: 3.574A pdb=" N GLN A1043 " --> pdb=" O LEU A1039 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A1048 " --> pdb=" O LYS A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1091 removed outlier: 3.549A pdb=" N GLN A1088 " --> pdb=" O ARG A1084 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LYS A1091 " --> pdb=" O GLY A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1110 removed outlier: 3.731A pdb=" N LEU A1107 " --> pdb=" O SER A1103 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A1108 " --> pdb=" O LEU A1104 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A1109 " --> pdb=" O LEU A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1153 removed outlier: 3.973A pdb=" N ARG A1138 " --> pdb=" O PRO A1134 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A1148 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A1150 " --> pdb=" O ALA A1146 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A1151 " --> pdb=" O PHE A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1177 removed outlier: 3.542A pdb=" N ILE A1169 " --> pdb=" O ASP A1165 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS A1170 " --> pdb=" O THR A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1197 removed outlier: 3.984A pdb=" N LEU A1197 " --> pdb=" O TYR A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1214 Processing helix chain 'A' and resid 1245 through 1260 Processing helix chain 'A' and resid 1268 through 1277 removed outlier: 3.704A pdb=" N LYS A1272 " --> pdb=" O ASN A1268 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A1276 " --> pdb=" O LYS A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1294 removed outlier: 3.759A pdb=" N ASN A1292 " --> pdb=" O GLN A1288 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA A1293 " --> pdb=" O ASP A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1299 No H-bonds generated for 'chain 'A' and resid 1296 through 1299' Processing helix chain 'A' and resid 1436 through 1442 removed outlier: 3.652A pdb=" N ALA A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A1442 " --> pdb=" O ASP A1438 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 300 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 512 through 514 No H-bonds generated for 'chain 'B' and resid 512 through 514' Processing helix chain 'B' and resid 582 through 585 No H-bonds generated for 'chain 'B' and resid 582 through 585' Processing helix chain 'B' and resid 595 through 602 removed outlier: 3.682A pdb=" N THR B 601 " --> pdb=" O LYS B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 623 removed outlier: 3.976A pdb=" N PHE B 621 " --> pdb=" O ASN B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 1397 through 1400 No H-bonds generated for 'chain 'B' and resid 1397 through 1400' Processing sheet with id= A, first strand: chain 'C' and resid 651 through 655 removed outlier: 3.511A pdb=" N LEU C 654 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 25 " --> pdb=" O LEU C 654 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ASN C 38 " --> pdb=" O PRO C 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 71 through 73 Processing sheet with id= C, first strand: chain 'C' and resid 125 through 130 Processing sheet with id= D, first strand: chain 'C' and resid 212 through 219 removed outlier: 3.593A pdb=" N PHE C 217 " --> pdb=" O TRP C 199 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS C 204 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP C 172 " --> pdb=" O PHE C 163 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 228 through 233 Processing sheet with id= F, first strand: chain 'C' and resid 288 through 293 removed outlier: 3.586A pdb=" N ILE C 267 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 263 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS C 321 " --> pdb=" O TYR C 347 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 270 through 272 Processing sheet with id= H, first strand: chain 'C' and resid 325 through 330 removed outlier: 3.550A pdb=" N ILE C 325 " --> pdb=" O ILE C 342 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 352 through 356 Processing sheet with id= J, first strand: chain 'C' and resid 407 through 410 Processing sheet with id= K, first strand: chain 'C' and resid 401 through 403 Processing sheet with id= L, first strand: chain 'C' and resid 465 through 469 Processing sheet with id= M, first strand: chain 'C' and resid 553 through 561 removed outlier: 3.523A pdb=" N GLU C 553 " --> pdb=" O VAL C 546 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER C 538 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE C 545 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N HIS C 498 " --> pdb=" O ILE C 545 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER C 505 " --> pdb=" O ILE C 509 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ILE C 509 " --> pdb=" O SER C 505 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 572 through 576 Processing sheet with id= O, first strand: chain 'C' and resid 55 through 57 removed outlier: 3.745A pdb=" N SER C 67 " --> pdb=" O ILE C 56 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 796 through 799 removed outlier: 3.921A pdb=" N TRP A 797 " --> pdb=" O ALA A 817 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 802 through 804 Processing sheet with id= R, first strand: chain 'A' and resid 823 through 827 Processing sheet with id= S, first strand: chain 'A' and resid 853 through 855 Processing sheet with id= T, first strand: chain 'A' and resid 857 through 859 removed outlier: 3.725A pdb=" N LYS A 858 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 919 " --> pdb=" O THR A 916 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 935 through 944 removed outlier: 3.559A pdb=" N LYS A 974 " --> pdb=" O VAL A1364 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG A 975 " --> pdb=" O VAL A1340 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 956 through 959 removed outlier: 3.860A pdb=" N LYS A 957 " --> pdb=" O VAL A1348 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 1217 through 1219 removed outlier: 3.665A pdb=" N TYR A1225 " --> pdb=" O LYS A1219 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 1377 through 1386 removed outlier: 3.569A pdb=" N LYS A1380 " --> pdb=" O CYS A1405 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR A1399 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A1477 " --> pdb=" O ILE A1402 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 1504 through 1509 removed outlier: 4.246A pdb=" N THR A1492 " --> pdb=" O SER A1427 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A1452 " --> pdb=" O GLN A1463 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 1432 through 1434 Processing sheet with id= AA, first strand: chain 'B' and resid 24 through 28 Processing sheet with id= AB, first strand: chain 'B' and resid 38 through 40 Processing sheet with id= AC, first strand: chain 'B' and resid 69 through 75 removed outlier: 3.600A pdb=" N PHE B 69 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 113 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 128 through 130 Processing sheet with id= AE, first strand: chain 'B' and resid 210 through 216 removed outlier: 3.588A pdb=" N PHE B 214 " --> pdb=" O TRP B 197 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL B 161 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 165 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 174 " --> pdb=" O PHE B 165 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'B' and resid 224 through 230 Processing sheet with id= AG, first strand: chain 'B' and resid 234 through 236 removed outlier: 6.049A pdb=" N HIS B 337 " --> pdb=" O PHE B 235 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.553A pdb=" N GLY B 266 " --> pdb=" O TYR B 315 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'B' and resid 266 through 268 Processing sheet with id= AJ, first strand: chain 'B' and resid 344 through 346 Processing sheet with id= AK, first strand: chain 'B' and resid 408 through 414 Processing sheet with id= AL, first strand: chain 'B' and resid 444 through 449 removed outlier: 3.814A pdb=" N LYS B 467 " --> pdb=" O TYR B 444 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'B' and resid 530 through 534 removed outlier: 5.222A pdb=" N GLN B 525 " --> pdb=" O TYR B 478 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR B 478 " --> pdb=" O GLN B 525 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR B 481 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 491 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN B 485 " --> pdb=" O ILE B 489 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE B 489 " --> pdb=" O ASN B 485 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'B' and resid 548 through 551 Processing sheet with id= AO, first strand: chain 'B' and resid 574 through 577 Processing sheet with id= AP, first strand: chain 'B' and resid 579 through 581 Processing sheet with id= AQ, first strand: chain 'B' and resid 792 through 795 removed outlier: 3.647A pdb=" N CYS B 801 " --> pdb=" O SER B 793 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'B' and resid 814 through 817 removed outlier: 3.560A pdb=" N SER B 876 " --> pdb=" O ASN B 838 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'B' and resid 866 through 872 removed outlier: 3.850A pdb=" N TYR B 866 " --> pdb=" O LEU B 850 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B 911 " --> pdb=" O VAL B 894 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'B' and resid 1343 through 1350 removed outlier: 3.697A pdb=" N ASN B1346 " --> pdb=" O CYS B1368 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N CYS B1368 " --> pdb=" O ASN B1346 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B1363 " --> pdb=" O ILE B1442 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B1442 " --> pdb=" O LEU B1363 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'B' and resid 1422 through 1427 removed outlier: 4.249A pdb=" N CYS B1468 " --> pdb=" O VAL B1458 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'B' and resid 1483 through 1486 removed outlier: 3.553A pdb=" N ARG B1491 " --> pdb=" O ILE B1484 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B1489 " --> pdb=" O ILE B1486 " (cutoff:3.500A) 559 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.29 Time building geometry restraints manager: 7.78 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: 6062 1.34 - 1.46: 4325 1.46 - 1.58: 9022 1.58 - 1.70: 0 1.70 - 1.82: 118 Bond restraints: 19527 Sorted by residual: bond pdb=" C30 H1H A1701 " pdb=" O32 H1H A1701 " ideal model delta sigma weight residual 1.240 1.337 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C1 H1H A1701 " pdb=" O7 H1H A1701 " ideal model delta sigma weight residual 1.345 1.395 -0.050 2.00e-02 2.50e+03 6.36e+00 bond pdb=" C23 H1H A1701 " pdb=" O28 H1H A1701 " ideal model delta sigma weight residual 1.350 1.398 -0.048 2.00e-02 2.50e+03 5.88e+00 bond pdb=" C ASN C 423 " pdb=" N LEU C 424 " ideal model delta sigma weight residual 1.331 1.266 0.065 2.83e-02 1.25e+03 5.20e+00 bond pdb=" C LEU B 221 " pdb=" N PRO B 222 " ideal model delta sigma weight residual 1.335 1.314 0.021 9.40e-03 1.13e+04 5.00e+00 ... (remaining 19522 not shown) Histogram of bond angle deviations from ideal: 97.76 - 105.04: 357 105.04 - 112.33: 9883 112.33 - 119.62: 6514 119.62 - 126.91: 9523 126.91 - 134.19: 229 Bond angle restraints: 26506 Sorted by residual: angle pdb=" N SER C 311 " pdb=" CA SER C 311 " pdb=" C SER C 311 " ideal model delta sigma weight residual 111.37 119.11 -7.74 1.64e+00 3.72e-01 2.23e+01 angle pdb=" C PHE C 518 " pdb=" N SER C 519 " pdb=" CA SER C 519 " ideal model delta sigma weight residual 120.38 126.06 -5.68 1.37e+00 5.33e-01 1.72e+01 angle pdb=" C ARG A 766 " pdb=" N SER A 767 " pdb=" CA SER A 767 " ideal model delta sigma weight residual 122.19 131.42 -9.23 2.30e+00 1.89e-01 1.61e+01 angle pdb=" C THR A1132 " pdb=" N LEU A1133 " pdb=" CA LEU A1133 " ideal model delta sigma weight residual 120.09 125.09 -5.00 1.25e+00 6.40e-01 1.60e+01 angle pdb=" CA THR A1242 " pdb=" CB THR A1242 " pdb=" CG2 THR A1242 " ideal model delta sigma weight residual 110.50 117.30 -6.80 1.70e+00 3.46e-01 1.60e+01 ... (remaining 26501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 10494 17.71 - 35.41: 1059 35.41 - 53.12: 182 53.12 - 70.82: 26 70.82 - 88.53: 13 Dihedral angle restraints: 11774 sinusoidal: 4706 harmonic: 7068 Sorted by residual: dihedral pdb=" CB CYS A 711 " pdb=" SG CYS A 711 " pdb=" SG CYS A 732 " pdb=" CB CYS A 732 " ideal model delta sinusoidal sigma weight residual 93.00 177.85 -84.85 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CA LEU C 310 " pdb=" C LEU C 310 " pdb=" N SER C 311 " pdb=" CA SER C 311 " ideal model delta harmonic sigma weight residual -180.00 -142.55 -37.45 0 5.00e+00 4.00e-02 5.61e+01 dihedral pdb=" CB CYS C 634 " pdb=" SG CYS C 634 " pdb=" SG CYS C 669 " pdb=" CB CYS C 669 " ideal model delta sinusoidal sigma weight residual -86.00 -141.06 55.06 1 1.00e+01 1.00e-02 4.10e+01 ... (remaining 11771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2117 0.051 - 0.103: 672 0.103 - 0.154: 206 0.154 - 0.206: 20 0.206 - 0.257: 9 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CG LEU B 400 " pdb=" CB LEU B 400 " pdb=" CD1 LEU B 400 " pdb=" CD2 LEU B 400 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL B 192 " pdb=" CA VAL B 192 " pdb=" CG1 VAL B 192 " pdb=" CG2 VAL B 192 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL B 584 " pdb=" CA VAL B 584 " pdb=" CG1 VAL B 584 " pdb=" CG2 VAL B 584 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 3021 not shown) Planarity restraints: 3374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 165 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO C 166 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 166 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 166 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 511 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO B 512 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 512 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 512 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 358 " 0.040 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO B 359 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 359 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 359 " 0.033 5.00e-02 4.00e+02 ... (remaining 3371 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 437 2.67 - 3.23: 16247 3.23 - 3.79: 28852 3.79 - 4.34: 38815 4.34 - 4.90: 65810 Nonbonded interactions: 150161 Sorted by model distance: nonbonded pdb=" OD1 ASP B 542 " pdb="MG MG B2000 " model vdw 2.114 2.170 nonbonded pdb=" OD1 ASP B 539 " pdb="MG MG B2000 " model vdw 2.143 2.170 nonbonded pdb=" OD1 ASN A1268 " pdb=" OH TYR A1300 " model vdw 2.269 2.440 nonbonded pdb=" O PRO B 351 " pdb=" OH TYR B 360 " model vdw 2.274 2.440 nonbonded pdb=" OG1 THR C 655 " pdb=" O ASN C 658 " model vdw 2.283 2.440 ... (remaining 150156 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 75 5.16 5 C 12241 2.51 5 N 3167 2.21 5 O 3625 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 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.550 Check model and map are aligned: 0.300 Process input model: 51.960 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.160 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 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 : 0.007 0.119 19527 Z= 0.488 Angle : 0.912 12.373 26506 Z= 0.499 Chirality : 0.056 0.257 3024 Planarity : 0.007 0.072 3374 Dihedral : 14.436 88.529 7182 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.47 % Favored : 93.45 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.12 (0.14), residues: 2396 helix: -4.60 (0.11), residues: 316 sheet: -2.07 (0.15), residues: 925 loop : -2.68 (0.15), residues: 1155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 286 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 299 average time/residue: 0.3445 time to fit residues: 155.2522 Evaluate side-chains 183 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 174 time to evaluate : 2.395 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1845 time to fit residues: 6.3627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 188 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 217 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN C 500 ASN C 533 ASN C 644 ASN C 658 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1121 ASN B 59 HIS B 112 GLN B 181 ASN B 333 GLN B 405 ASN B 416 ASN B 465 ASN B 501 GLN B 507 ASN B 554 ASN B 557 GLN B 869 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 19527 Z= 0.185 Angle : 0.554 9.913 26506 Z= 0.288 Chirality : 0.045 0.171 3024 Planarity : 0.004 0.052 3374 Dihedral : 5.330 45.717 2608 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.05 % Favored : 94.87 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.07 (0.15), residues: 2396 helix: -3.07 (0.21), residues: 321 sheet: -1.40 (0.16), residues: 951 loop : -2.21 (0.16), residues: 1124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 218 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 26 residues processed: 247 average time/residue: 0.3020 time to fit residues: 118.0171 Evaluate side-chains 203 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 177 time to evaluate : 2.373 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 1 residues processed: 26 average time/residue: 0.1704 time to fit residues: 11.6865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.0980 chunk 67 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 chunk 235 optimal weight: 0.2980 chunk 194 optimal weight: 2.9990 chunk 216 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 GLN C 656 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 GLN A1360 HIS ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 19527 Z= 0.267 Angle : 0.565 11.257 26506 Z= 0.289 Chirality : 0.046 0.175 3024 Planarity : 0.004 0.048 3374 Dihedral : 5.089 38.663 2608 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.09 % Favored : 93.86 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.47 (0.16), residues: 2396 helix: -2.18 (0.25), residues: 320 sheet: -0.95 (0.16), residues: 943 loop : -2.02 (0.17), residues: 1133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 193 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 29 residues processed: 226 average time/residue: 0.3017 time to fit residues: 109.1863 Evaluate side-chains 205 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 176 time to evaluate : 2.402 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 29 outliers final: 1 residues processed: 29 average time/residue: 0.1872 time to fit residues: 13.7390 ------------------------------------------------------------------------------- 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: 54.3665 > 50: distance: 37 - 195: 30.137 distance: 40 - 192: 26.073 distance: 133 - 157: 17.409 distance: 138 - 167: 22.476 distance: 148 - 157: 16.051 distance: 157 - 158: 3.978 distance: 158 - 159: 12.700 distance: 158 - 161: 3.010 distance: 159 - 160: 14.403 distance: 159 - 167: 15.208 distance: 161 - 162: 9.596 distance: 162 - 163: 15.142 distance: 162 - 164: 18.450 distance: 163 - 165: 10.253 distance: 164 - 166: 3.653 distance: 165 - 166: 15.112 distance: 167 - 168: 13.916 distance: 168 - 169: 15.032 distance: 168 - 171: 10.333 distance: 169 - 170: 39.953 distance: 169 - 175: 5.673 distance: 171 - 172: 9.770 distance: 172 - 173: 7.773 distance: 172 - 174: 11.819 distance: 175 - 176: 3.510 distance: 176 - 177: 25.868 distance: 176 - 179: 26.896 distance: 177 - 178: 23.592 distance: 177 - 180: 22.057 distance: 180 - 181: 42.696 distance: 181 - 182: 26.558 distance: 182 - 183: 36.049 distance: 182 - 184: 22.245 distance: 184 - 185: 17.835 distance: 185 - 186: 11.643 distance: 185 - 188: 25.300 distance: 186 - 187: 8.731 distance: 186 - 192: 18.032 distance: 188 - 189: 18.130 distance: 189 - 190: 28.297 distance: 189 - 191: 20.155 distance: 192 - 193: 22.479 distance: 193 - 194: 26.784 distance: 193 - 196: 14.931 distance: 194 - 195: 6.545 distance: 194 - 199: 25.400 distance: 196 - 197: 6.101 distance: 196 - 198: 18.646 distance: 199 - 200: 17.459 distance: 200 - 201: 12.564 distance: 200 - 203: 17.154 distance: 201 - 202: 7.124 distance: 201 - 210: 14.910 distance: 203 - 204: 11.580 distance: 204 - 205: 18.803 distance: 204 - 206: 5.294 distance: 205 - 207: 12.131 distance: 206 - 208: 9.960 distance: 207 - 209: 8.710 distance: 208 - 209: 16.707 distance: 210 - 211: 11.987 distance: 211 - 212: 9.322 distance: 211 - 214: 11.665 distance: 212 - 213: 19.986 distance: 212 - 218: 8.808 distance: 214 - 215: 18.280 distance: 215 - 216: 5.382 distance: 215 - 217: 13.251 distance: 218 - 219: 15.704 distance: 219 - 220: 33.277 distance: 219 - 222: 27.076 distance: 220 - 221: 24.005 distance: 220 - 225: 18.332 distance: 222 - 223: 36.470 distance: 222 - 224: 18.018 distance: 225 - 226: 7.855 distance: 226 - 227: 9.030 distance: 226 - 229: 6.591 distance: 227 - 228: 9.739 distance: 227 - 233: 9.281 distance: 229 - 230: 13.986 distance: 230 - 231: 18.591 distance: 230 - 232: 4.190