Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 07:54:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ut4_26754/05_2023/7ut4_26754.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ut4_26754/05_2023/7ut4_26754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ut4_26754/05_2023/7ut4_26754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ut4_26754/05_2023/7ut4_26754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ut4_26754/05_2023/7ut4_26754.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ut4_26754/05_2023/7ut4_26754.pdb" } resolution = 3.9 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= 0.002 sd= 1.500 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 74 5.16 5 C 12612 2.51 5 N 3206 2.21 5 O 3756 1.98 5 H 20092 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 324": "OD1" <-> "OD2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A ASP 538": "OD1" <-> "OD2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 755": "OE1" <-> "OE2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "A PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 908": "OD1" <-> "OD2" Residue "A PHE 912": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1167": "OE1" <-> "OE2" Residue "A PHE 1170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 162": "OD1" <-> "OD2" Residue "B TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "B PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 542": "OE1" <-> "OE2" Residue "B GLU 552": "OE1" <-> "OE2" Residue "B ASP 558": "OD1" <-> "OD2" Residue "B GLU 562": "OE1" <-> "OE2" Residue "B PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 694": "OD1" <-> "OD2" Residue "B PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B GLU 761": "OE1" <-> "OE2" Residue "B GLU 770": "OE1" <-> "OE2" Residue "B GLU 801": "OE1" <-> "OE2" Residue "B ASP 842": "OD1" <-> "OD2" Residue "B ASP 855": "OD1" <-> "OD2" Residue "B ASP 859": "OD1" <-> "OD2" Residue "B PHE 916": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 941": "OE1" <-> "OE2" Residue "B ASP 956": "OD1" <-> "OD2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B PHE 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1193": "OE1" <-> "OE2" Residue "B GLU 1204": "OE1" <-> "OE2" Residue "B GLU 1277": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 39740 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 19870 Classifications: {'peptide': 1224} Link IDs: {'PTRANS': 36, 'TRANS': 1187} Chain breaks: 7 Chain: "B" Number of atoms: 19870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 19870 Classifications: {'peptide': 1224} Link IDs: {'PTRANS': 36, 'TRANS': 1187} Chain breaks: 7 Time building chain proxies: 16.91, per 1000 atoms: 0.43 Number of scatterers: 39740 At special positions: 0 Unit cell: (311.168, 153.088, 123.136, 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 74 16.00 O 3756 8.00 N 3206 7.00 C 12612 6.00 H 20092 1.00 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: 31.86 Conformation dependent library (CDL) restraints added in 3.4 seconds 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4740 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 1 sheets defined 75.2% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 11 through 26 removed outlier: 3.953A pdb=" N ILE A 15 " --> pdb=" O PRO A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 83 removed outlier: 3.573A pdb=" N PHE A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 107 removed outlier: 3.625A pdb=" N ILE A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) Proline residue: A 100 - end of helix removed outlier: 3.558A pdb=" N LEU A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 129 Processing helix chain 'A' and resid 137 through 151 removed outlier: 3.878A pdb=" N HIS A 151 " --> pdb=" O ASN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 179 removed outlier: 3.822A pdb=" N VAL A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.639A pdb=" N LEU A 185 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 203 Processing helix chain 'A' and resid 207 through 227 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 329 through 344 removed outlier: 4.318A pdb=" N ARG A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 removed outlier: 4.536A pdb=" N LEU A 349 " --> pdb=" O GLU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 371 removed outlier: 3.685A pdb=" N PHE A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 377 through 386 removed outlier: 3.519A pdb=" N THR A 382 " --> pdb=" O PRO A 378 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 401 through 419 Processing helix chain 'A' and resid 423 through 440 removed outlier: 3.509A pdb=" N ASP A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 467 Processing helix chain 'A' and resid 467 through 472 removed outlier: 3.818A pdb=" N THR A 471 " --> pdb=" O SER A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 493 through 505 Processing helix chain 'A' and resid 506 through 511 removed outlier: 3.590A pdb=" N LEU A 511 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 536 removed outlier: 4.077A pdb=" N ILE A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 525 " --> pdb=" O CYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 removed outlier: 3.815A pdb=" N PHE A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 540 through 546' Processing helix chain 'A' and resid 551 through 559 removed outlier: 3.568A pdb=" N ASP A 558 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 567 Processing helix chain 'A' and resid 577 through 585 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 607 through 617 removed outlier: 3.629A pdb=" N ILE A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 628 Processing helix chain 'A' and resid 629 through 631 No H-bonds generated for 'chain 'A' and resid 629 through 631' Processing helix chain 'A' and resid 637 through 647 Processing helix chain 'A' and resid 654 through 657 Processing helix chain 'A' and resid 658 through 673 Processing helix chain 'A' and resid 687 through 691 removed outlier: 3.570A pdb=" N THR A 690 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 713 removed outlier: 3.685A pdb=" N THR A 710 " --> pdb=" O ILE A 706 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 727 removed outlier: 3.730A pdb=" N SER A 727 " --> pdb=" O PHE A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 754 removed outlier: 3.723A pdb=" N TYR A 748 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A 751 " --> pdb=" O ILE A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 782 removed outlier: 4.207A pdb=" N SER A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N THR A 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 796 removed outlier: 3.674A pdb=" N ASP A 795 " --> pdb=" O SER A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 828 removed outlier: 3.718A pdb=" N ARG A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA A 808 " --> pdb=" O ASN A 804 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE A 809 " --> pdb=" O PHE A 805 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 812 " --> pdb=" O ALA A 808 " (cutoff:3.500A) Proline residue: A 815 - end of helix Processing helix chain 'A' and resid 830 through 852 Processing helix chain 'A' and resid 853 through 868 Processing helix chain 'A' and resid 906 through 915 Processing helix chain 'A' and resid 915 through 932 removed outlier: 3.840A pdb=" N GLN A 919 " --> pdb=" O SER A 915 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 956 removed outlier: 3.573A pdb=" N ASP A 956 " --> pdb=" O THR A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 972 removed outlier: 3.611A pdb=" N GLN A 968 " --> pdb=" O PHE A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1027 removed outlier: 3.584A pdb=" N ASN A1027 " --> pdb=" O ILE A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1033 removed outlier: 3.537A pdb=" N VAL A1032 " --> pdb=" O ILE A1028 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A1033 " --> pdb=" O ALA A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1050 Processing helix chain 'A' and resid 1062 through 1081 removed outlier: 3.590A pdb=" N LEU A1067 " --> pdb=" O PHE A1063 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A1068 " --> pdb=" O GLU A1064 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A1080 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1100 removed outlier: 3.546A pdb=" N HIS A1100 " --> pdb=" O PHE A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1123 removed outlier: 3.501A pdb=" N VAL A1109 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A1113 " --> pdb=" O VAL A1109 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A1114 " --> pdb=" O ARG A1110 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A1115 " --> pdb=" O ARG A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1136 Processing helix chain 'A' and resid 1146 through 1152 Processing helix chain 'A' and resid 1152 through 1165 Processing helix chain 'A' and resid 1171 through 1176 removed outlier: 3.521A pdb=" N LEU A1175 " --> pdb=" O TYR A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1191 removed outlier: 3.553A pdb=" N TRP A1182 " --> pdb=" O ASN A1178 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A1191 " --> pdb=" O LYS A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1209 removed outlier: 3.738A pdb=" N ASP A1209 " --> pdb=" O SER A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1230 removed outlier: 3.634A pdb=" N VAL A1221 " --> pdb=" O ASN A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1275 removed outlier: 4.138A pdb=" N LEU A1264 " --> pdb=" O LYS A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1279 removed outlier: 3.841A pdb=" N ASN A1279 " --> pdb=" O LEU A1276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1276 through 1279' Processing helix chain 'A' and resid 1283 through 1297 removed outlier: 3.731A pdb=" N ILE A1287 " --> pdb=" O ARG A1283 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE A1288 " --> pdb=" O LYS A1284 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A1289 " --> pdb=" O ASN A1285 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN A1297 " --> pdb=" O ALA A1293 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1300 No H-bonds generated for 'chain 'A' and resid 1298 through 1300' Processing helix chain 'A' and resid 1302 through 1320 removed outlier: 3.575A pdb=" N SER A1306 " --> pdb=" O CYS A1302 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A1314 " --> pdb=" O VAL A1310 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1338 removed outlier: 4.122A pdb=" N ILE A1335 " --> pdb=" O VAL A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1344 removed outlier: 4.177A pdb=" N LEU A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A1344 " --> pdb=" O LEU A1340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1339 through 1344' Processing helix chain 'A' and resid 1349 through 1354 removed outlier: 4.138A pdb=" N GLN A1352 " --> pdb=" O GLN A1349 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A1353 " --> pdb=" O GLU A1350 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE A1354 " --> pdb=" O ASP A1351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1349 through 1354' Processing helix chain 'A' and resid 1355 through 1374 removed outlier: 3.661A pdb=" N ILE A1359 " --> pdb=" O LEU A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1391 removed outlier: 4.413A pdb=" N PHE A1381 " --> pdb=" O SER A1377 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU A1382 " --> pdb=" O ASN A1378 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A1391 " --> pdb=" O ILE A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1402 Processing helix chain 'A' and resid 1403 through 1417 removed outlier: 3.945A pdb=" N ASP A1407 " --> pdb=" O GLN A1403 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY A1416 " --> pdb=" O GLU A1412 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 25 Processing helix chain 'B' and resid 72 through 84 removed outlier: 4.101A pdb=" N PHE B 76 " --> pdb=" O PHE B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.846A pdb=" N ILE B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 93 through 98' Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 111 through 129 Processing helix chain 'B' and resid 137 through 151 removed outlier: 3.590A pdb=" N HIS B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 179 removed outlier: 3.719A pdb=" N VAL B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.579A pdb=" N LEU B 185 " --> pdb=" O GLY B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 203 Processing helix chain 'B' and resid 207 through 228 removed outlier: 3.674A pdb=" N ILE B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 344 removed outlier: 3.904A pdb=" N GLN B 334 " --> pdb=" O PRO B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 349 removed outlier: 4.506A pdb=" N LEU B 349 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 370 removed outlier: 3.810A pdb=" N SER B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.831A pdb=" N GLN B 375 " --> pdb=" O ASP B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 399 removed outlier: 3.865A pdb=" N LEU B 383 " --> pdb=" O ARG B 379 " (cutoff:3.500A) Proline residue: B 387 - end of helix Processing helix chain 'B' and resid 401 through 419 Processing helix chain 'B' and resid 425 through 440 removed outlier: 3.728A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP B 440 " --> pdb=" O SER B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 467 removed outlier: 3.842A pdb=" N GLU B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 461 " --> pdb=" O ILE B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 472 removed outlier: 3.779A pdb=" N THR B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.668A pdb=" N PHE B 484 " --> pdb=" O THR B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 506 removed outlier: 3.946A pdb=" N LEU B 506 " --> pdb=" O THR B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 513 removed outlier: 4.461A pdb=" N THR B 512 " --> pdb=" O GLU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 536 removed outlier: 4.182A pdb=" N ILE B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 529 " --> pdb=" O LEU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 545 removed outlier: 3.955A pdb=" N PHE B 544 " --> pdb=" O ASP B 540 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY B 545 " --> pdb=" O ARG B 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 540 through 545' Processing helix chain 'B' and resid 551 through 567 removed outlier: 4.203A pdb=" N THR B 561 " --> pdb=" O ARG B 557 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU B 562 " --> pdb=" O ASP B 558 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU B 565 " --> pdb=" O THR B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 585 Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 607 through 616 removed outlier: 3.735A pdb=" N ILE B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 631 removed outlier: 3.964A pdb=" N PHE B 631 " --> pdb=" O TYR B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 647 Processing helix chain 'B' and resid 654 through 672 removed outlier: 3.618A pdb=" N GLU B 659 " --> pdb=" O SER B 655 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG B 660 " --> pdb=" O GLN B 656 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE B 661 " --> pdb=" O GLN B 657 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE B 662 " --> pdb=" O ILE B 658 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA B 664 " --> pdb=" O ARG B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 713 Processing helix chain 'B' and resid 722 through 730 removed outlier: 3.899A pdb=" N GLY B 728 " --> pdb=" O GLU B 724 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN B 729 " --> pdb=" O ASP B 725 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU B 730 " --> pdb=" O TYR B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 754 removed outlier: 3.684A pdb=" N LEU B 744 " --> pdb=" O PRO B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 779 removed outlier: 4.278A pdb=" N SER B 779 " --> pdb=" O ASN B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 796 removed outlier: 3.669A pdb=" N ASP B 795 " --> pdb=" O SER B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 806 Processing helix chain 'B' and resid 806 through 828 removed outlier: 3.619A pdb=" N GLN B 812 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Proline residue: B 815 - end of helix Processing helix chain 'B' and resid 830 through 852 removed outlier: 3.596A pdb=" N SER B 834 " --> pdb=" O ASP B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 868 removed outlier: 3.649A pdb=" N LEU B 861 " --> pdb=" O PHE B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 915 removed outlier: 3.749A pdb=" N SER B 915 " --> pdb=" O ARG B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 931 removed outlier: 3.682A pdb=" N ASN B 921 " --> pdb=" O LYS B 917 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR B 922 " --> pdb=" O GLY B 918 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 923 " --> pdb=" O GLN B 919 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 956 removed outlier: 3.547A pdb=" N ASP B 956 " --> pdb=" O THR B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 972 removed outlier: 3.598A pdb=" N GLN B 968 " --> pdb=" O PHE B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1027 Processing helix chain 'B' and resid 1028 through 1033 removed outlier: 3.860A pdb=" N PHE B1033 " --> pdb=" O ALA B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1039 removed outlier: 3.605A pdb=" N ILE B1039 " --> pdb=" O GLU B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1050 Processing helix chain 'B' and resid 1056 through 1060 removed outlier: 3.864A pdb=" N SER B1060 " --> pdb=" O ALA B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1062 through 1081 removed outlier: 3.852A pdb=" N LEU B1067 " --> pdb=" O PHE B1063 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU B1068 " --> pdb=" O GLU B1064 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE B1080 " --> pdb=" O ALA B1076 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N CYS B1081 " --> pdb=" O LEU B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1086 through 1100 Processing helix chain 'B' and resid 1105 through 1123 removed outlier: 3.632A pdb=" N VAL B1109 " --> pdb=" O THR B1105 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B1113 " --> pdb=" O VAL B1109 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR B1114 " --> pdb=" O ARG B1110 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR B1115 " --> pdb=" O ARG B1111 " (cutoff:3.500A) Processing helix chain 'B' and resid 1126 through 1137 Processing helix chain 'B' and resid 1146 through 1151 Processing helix chain 'B' and resid 1152 through 1168 removed outlier: 3.574A pdb=" N LYS B1156 " --> pdb=" O THR B1152 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU B1157 " --> pdb=" O ASN B1153 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR B1166 " --> pdb=" O LEU B1162 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU B1167 " --> pdb=" O PHE B1163 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B1168 " --> pdb=" O SER B1164 " (cutoff:3.500A) Processing helix chain 'B' and resid 1171 through 1178 removed outlier: 3.666A pdb=" N GLY B1177 " --> pdb=" O GLY B1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1190 removed outlier: 3.801A pdb=" N TRP B1182 " --> pdb=" O ASN B1178 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B1190 " --> pdb=" O ARG B1186 " (cutoff:3.500A) Processing helix chain 'B' and resid 1191 through 1193 No H-bonds generated for 'chain 'B' and resid 1191 through 1193' Processing helix chain 'B' and resid 1194 through 1208 removed outlier: 4.126A pdb=" N THR B1208 " --> pdb=" O GLU B1204 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1230 Processing helix chain 'B' and resid 1261 through 1275 removed outlier: 3.737A pdb=" N SER B1265 " --> pdb=" O SER B1261 " (cutoff:3.500A) Processing helix chain 'B' and resid 1276 through 1278 No H-bonds generated for 'chain 'B' and resid 1276 through 1278' Processing helix chain 'B' and resid 1283 through 1297 removed outlier: 3.583A pdb=" N ILE B1287 " --> pdb=" O ARG B1283 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE B1288 " --> pdb=" O LYS B1284 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN B1297 " --> pdb=" O ALA B1293 " (cutoff:3.500A) Processing helix chain 'B' and resid 1298 through 1300 No H-bonds generated for 'chain 'B' and resid 1298 through 1300' Processing helix chain 'B' and resid 1302 through 1320 removed outlier: 3.863A pdb=" N SER B1306 " --> pdb=" O CYS B1302 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B1311 " --> pdb=" O GLU B1307 " (cutoff:3.500A) Processing helix chain 'B' and resid 1330 through 1339 removed outlier: 3.859A pdb=" N LEU B1339 " --> pdb=" O ILE B1335 " (cutoff:3.500A) Processing helix chain 'B' and resid 1339 through 1344 Processing helix chain 'B' and resid 1349 through 1352 removed outlier: 3.918A pdb=" N GLN B1352 " --> pdb=" O GLN B1349 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1349 through 1352' Processing helix chain 'B' and resid 1353 through 1374 removed outlier: 4.032A pdb=" N SER B1358 " --> pdb=" O ILE B1354 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE B1359 " --> pdb=" O LEU B1355 " (cutoff:3.500A) Processing helix chain 'B' and resid 1377 through 1392 removed outlier: 3.692A pdb=" N PHE B1381 " --> pdb=" O SER B1377 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B1391 " --> pdb=" O ILE B1387 " (cutoff:3.500A) Processing helix chain 'B' and resid 1394 through 1417 removed outlier: 5.694A pdb=" N LEU B1406 " --> pdb=" O GLN B1402 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP B1407 " --> pdb=" O GLN B1403 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE B1411 " --> pdb=" O ASP B1407 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLU B1412 " --> pdb=" O LYS B1408 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS B1413 " --> pdb=" O LYS B1409 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 154 removed outlier: 4.050A pdb=" N PHE A 154 " --> pdb=" O GLY A 258 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 1101 hydrogen bonds defined for protein. 3249 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: 15.23 Time building geometry restraints manager: 32.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 20058 1.03 - 1.23: 47 1.23 - 1.42: 7991 1.42 - 1.62: 11844 1.62 - 1.82: 114 Bond restraints: 40054 Sorted by residual: bond pdb=" CB ILE A 15 " pdb=" CG2 ILE A 15 " ideal model delta sigma weight residual 1.521 1.601 -0.080 3.30e-02 9.18e+02 5.87e+00 bond pdb=" CB ILE B 357 " pdb=" CG2 ILE B 357 " ideal model delta sigma weight residual 1.521 1.598 -0.077 3.30e-02 9.18e+02 5.51e+00 bond pdb=" CB ASP A 842 " pdb=" CG ASP A 842 " ideal model delta sigma weight residual 1.516 1.572 -0.056 2.50e-02 1.60e+03 5.07e+00 bond pdb=" CB ILE A 946 " pdb=" CG2 ILE A 946 " ideal model delta sigma weight residual 1.521 1.592 -0.071 3.30e-02 9.18e+02 4.63e+00 bond pdb=" CB ILE B 864 " pdb=" CG2 ILE B 864 " ideal model delta sigma weight residual 1.521 1.589 -0.068 3.30e-02 9.18e+02 4.29e+00 ... (remaining 40049 not shown) Histogram of bond angle deviations from ideal: 97.05 - 104.45: 257 104.45 - 111.85: 46348 111.85 - 119.24: 10687 119.24 - 126.64: 15285 126.64 - 134.04: 159 Bond angle restraints: 72736 Sorted by residual: angle pdb=" CA GLN B1194 " pdb=" CB GLN B1194 " pdb=" CG GLN B1194 " ideal model delta sigma weight residual 114.10 122.85 -8.75 2.00e+00 2.50e-01 1.92e+01 angle pdb=" CA GLU B 766 " pdb=" CB GLU B 766 " pdb=" CG GLU B 766 " ideal model delta sigma weight residual 114.10 122.67 -8.57 2.00e+00 2.50e-01 1.84e+01 angle pdb=" CA ARG B1283 " pdb=" CB ARG B1283 " pdb=" CG ARG B1283 " ideal model delta sigma weight residual 114.10 121.64 -7.54 2.00e+00 2.50e-01 1.42e+01 angle pdb=" CB ASP A 842 " pdb=" CG ASP A 842 " pdb=" OD1 ASP A 842 " ideal model delta sigma weight residual 118.40 126.94 -8.54 2.30e+00 1.89e-01 1.38e+01 angle pdb=" CA ASP A 842 " pdb=" CB ASP A 842 " pdb=" CG ASP A 842 " ideal model delta sigma weight residual 112.60 116.31 -3.71 1.00e+00 1.00e+00 1.38e+01 ... (remaining 72731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 13401 17.88 - 35.76: 2029 35.76 - 53.64: 520 53.64 - 71.52: 99 71.52 - 89.39: 37 Dihedral angle restraints: 16086 sinusoidal: 7750 harmonic: 8336 Sorted by residual: dihedral pdb=" CA ASN A 607 " pdb=" C ASN A 607 " pdb=" N LYS A 608 " pdb=" CA LYS A 608 " ideal model delta harmonic sigma weight residual -180.00 -152.14 -27.86 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA LEU B 329 " pdb=" C LEU B 329 " pdb=" N PRO B 330 " pdb=" CA PRO B 330 " ideal model delta harmonic sigma weight residual -180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA LEU A 329 " pdb=" C LEU A 329 " pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta harmonic sigma weight residual -180.00 -157.09 -22.91 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 16083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2458 0.046 - 0.092: 580 0.092 - 0.139: 145 0.139 - 0.185: 17 0.185 - 0.231: 4 Chirality restraints: 3204 Sorted by residual: chirality pdb=" CB THR A 820 " pdb=" CA THR A 820 " pdb=" OG1 THR A 820 " pdb=" CG2 THR A 820 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE B1091 " pdb=" CA ILE B1091 " pdb=" CG1 ILE B1091 " pdb=" CG2 ILE B1091 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CG LEU A1225 " pdb=" CB LEU A1225 " pdb=" CD1 LEU A1225 " pdb=" CD2 LEU A1225 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3201 not shown) Planarity restraints: 5756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 333 " 0.267 9.50e-02 1.11e+02 8.95e-02 9.53e+00 pdb=" NE ARG B 333 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 333 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 333 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 333 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 333 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG B 333 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG B 333 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG B 333 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 617 " 0.048 5.00e-02 4.00e+02 7.33e-02 8.61e+00 pdb=" N PRO B 618 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 618 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 618 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 665 " 0.014 2.00e-02 2.50e+03 1.48e-02 6.61e+00 pdb=" CG PHE A 665 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 665 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 665 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A 665 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 665 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 665 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 665 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE A 665 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE A 665 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 665 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 665 " -0.001 2.00e-02 2.50e+03 ... (remaining 5753 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.29: 7798 2.29 - 2.87: 89589 2.87 - 3.45: 102130 3.45 - 4.02: 128247 4.02 - 4.60: 196950 Nonbonded interactions: 524714 Sorted by model distance: nonbonded pdb=" OE1 GLU A 562 " pdb=" H GLU A 562 " model vdw 1.719 1.850 nonbonded pdb=" OE1 GLU A 941 " pdb=" H GLU A 941 " model vdw 1.722 1.850 nonbonded pdb=" OE1 GLU B1286 " pdb=" H GLU B1286 " model vdw 1.731 1.850 nonbonded pdb=" OD1 ASN A1178 " pdb=" H PHE A1181 " model vdw 1.732 1.850 nonbonded pdb=" OD1 ASN B1178 " pdb=" H PHE B1181 " model vdw 1.746 1.850 ... (remaining 524709 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.560 Extract box with map and model: 9.110 Check model and map are aligned: 0.560 Set scattering table: 0.360 Process input model: 116.700 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 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 : 0.006 0.080 19962 Z= 0.377 Angle : 0.933 8.867 26956 Z= 0.474 Chirality : 0.044 0.231 3204 Planarity : 0.006 0.118 3392 Dihedral : 18.883 89.394 7528 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.05 % Favored : 94.91 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.16), residues: 2416 helix: 0.33 (0.12), residues: 1538 sheet: None (None), residues: 0 loop : -1.24 (0.21), residues: 878 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 669 time to evaluate : 3.298 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 672 average time/residue: 0.6040 time to fit residues: 651.7099 Evaluate side-chains 656 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 647 time to evaluate : 3.164 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.4890 time to fit residues: 12.0845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.1980 chunk 184 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 63 optimal weight: 0.1980 chunk 124 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 191 optimal weight: 0.6980 chunk 74 optimal weight: 0.0870 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 221 optimal weight: 0.9980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 919 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 19962 Z= 0.160 Angle : 0.519 6.333 26956 Z= 0.276 Chirality : 0.034 0.130 3204 Planarity : 0.004 0.059 3392 Dihedral : 4.759 23.011 2574 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer Outliers : 2.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.60 (0.17), residues: 2416 helix: 1.13 (0.13), residues: 1576 sheet: None (None), residues: 0 loop : -0.96 (0.22), residues: 840 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 668 time to evaluate : 3.408 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 54 residues processed: 688 average time/residue: 0.6221 time to fit residues: 691.5877 Evaluate side-chains 712 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 658 time to evaluate : 3.325 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 54 outliers final: 1 residues processed: 54 average time/residue: 0.4312 time to fit residues: 48.1388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 239 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 220 optimal weight: 0.5980 chunk 75 optimal weight: 0.0270 chunk 178 optimal weight: 0.0570 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 HIS A 736 HIS ** A 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 ASN B 142 HIS ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 19962 Z= 0.170 Angle : 0.509 5.453 26956 Z= 0.272 Chirality : 0.034 0.134 3204 Planarity : 0.003 0.059 3392 Dihedral : 4.493 20.985 2574 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.42 % Favored : 94.54 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.97 (0.18), residues: 2416 helix: 1.43 (0.13), residues: 1576 sheet: None (None), residues: 0 loop : -0.86 (0.22), residues: 840 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 671 time to evaluate : 3.099 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 32 residues processed: 695 average time/residue: 0.6128 time to fit residues: 683.9072 Evaluate side-chains 683 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 651 time to evaluate : 3.247 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 32 outliers final: 1 residues processed: 32 average time/residue: 0.4515 time to fit residues: 30.8800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.7980 chunk 166 optimal weight: 0.5980 chunk 115 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 105 optimal weight: 0.0670 chunk 149 optimal weight: 0.9990 chunk 222 optimal weight: 1.9990 chunk 235 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 211 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 GLN ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 19962 Z= 0.160 Angle : 0.497 6.477 26956 Z= 0.264 Chirality : 0.034 0.209 3204 Planarity : 0.003 0.053 3392 Dihedral : 4.356 21.085 2574 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.42 % Favored : 94.54 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.05 (0.18), residues: 2416 helix: 1.51 (0.13), residues: 1586 sheet: None (None), residues: 0 loop : -0.88 (0.22), residues: 830 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 673 time to evaluate : 3.360 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 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: 50 outliers final: 33 residues processed: 692 average time/residue: 0.6185 time to fit residues: 690.7625 Evaluate side-chains 690 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 657 time to evaluate : 3.440 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 33 outliers final: 1 residues processed: 33 average time/residue: 0.4515 time to fit residues: 31.5879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 175 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 201 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 120 optimal weight: 0.0980 chunk 211 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN ** A 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 19962 Z= 0.196 Angle : 0.511 6.344 26956 Z= 0.273 Chirality : 0.034 0.149 3204 Planarity : 0.003 0.052 3392 Dihedral : 4.334 20.387 2574 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.67 % Favored : 94.29 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.17), residues: 2416 helix: 1.51 (0.13), residues: 1586 sheet: None (None), residues: 0 loop : -0.98 (0.22), residues: 830 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 663 time to evaluate : 3.101 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 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: 41 outliers final: 33 residues processed: 682 average time/residue: 0.6266 time to fit residues: 689.7630 Evaluate side-chains 685 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 652 time to evaluate : 3.132 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 33 outliers final: 1 residues processed: 33 average time/residue: 0.4323 time to fit residues: 30.5730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 0.9980 chunk 212 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 0.0980 chunk 123 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 HIS A 571 ASN ** A 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 ASN B1154 GLN ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 19962 Z= 0.226 Angle : 0.528 6.274 26956 Z= 0.284 Chirality : 0.034 0.145 3204 Planarity : 0.003 0.050 3392 Dihedral : 4.366 20.901 2574 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.00 % Favored : 93.96 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.17), residues: 2416 helix: 1.42 (0.13), residues: 1600 sheet: None (None), residues: 0 loop : -1.09 (0.22), residues: 816 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 664 time to evaluate : 3.231 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 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: 56 outliers final: 40 residues processed: 678 average time/residue: 0.6129 time to fit residues: 664.4090 Evaluate side-chains 684 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 644 time to evaluate : 3.184 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 40 outliers final: 1 residues processed: 40 average time/residue: 0.4771 time to fit residues: 38.4012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 235 optimal weight: 0.0870 chunk 147 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 19962 Z= 0.221 Angle : 0.531 6.092 26956 Z= 0.284 Chirality : 0.035 0.153 3204 Planarity : 0.003 0.055 3392 Dihedral : 4.364 19.719 2574 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.21 % Favored : 93.75 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.83 (0.17), residues: 2416 helix: 1.39 (0.13), residues: 1598 sheet: None (None), residues: 0 loop : -1.12 (0.22), residues: 818 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 653 time to evaluate : 3.226 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 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: 38 outliers final: 30 residues processed: 667 average time/residue: 0.6167 time to fit residues: 664.7164 Evaluate side-chains 667 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 637 time to evaluate : 3.271 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 30 outliers final: 1 residues processed: 30 average time/residue: 0.4334 time to fit residues: 28.1006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 chunk 70 optimal weight: 0.0870 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 149 optimal weight: 0.5980 chunk 160 optimal weight: 0.1980 chunk 116 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19962 Z= 0.170 Angle : 0.514 6.749 26956 Z= 0.271 Chirality : 0.034 0.230 3204 Planarity : 0.003 0.049 3392 Dihedral : 4.268 19.802 2574 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.75 % Favored : 94.21 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.18), residues: 2416 helix: 1.47 (0.13), residues: 1610 sheet: None (None), residues: 0 loop : -1.02 (0.23), residues: 806 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 660 time to evaluate : 3.351 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 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: 21 outliers final: 14 residues processed: 666 average time/residue: 0.5183 time to fit residues: 560.9169 Evaluate side-chains 658 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 644 time to evaluate : 2.388 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3622 time to fit residues: 12.2647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.6980 chunk 225 optimal weight: 0.8980 chunk 205 optimal weight: 0.7980 chunk 219 optimal weight: 0.9990 chunk 131 optimal weight: 0.0980 chunk 95 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 218 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS ** A 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 HIS ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 19962 Z= 0.221 Angle : 0.538 8.676 26956 Z= 0.287 Chirality : 0.035 0.194 3204 Planarity : 0.003 0.049 3392 Dihedral : 4.305 19.381 2574 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.46 % Favored : 93.50 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.17), residues: 2416 helix: 1.40 (0.13), residues: 1600 sheet: None (None), residues: 0 loop : -1.09 (0.22), residues: 816 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 650 time to evaluate : 2.769 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 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: 15 outliers final: 12 residues processed: 654 average time/residue: 0.5547 time to fit residues: 588.8046 Evaluate side-chains 659 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 647 time to evaluate : 3.119 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3432 time to fit residues: 10.8593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.9980 chunk 231 optimal weight: 0.0670 chunk 141 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 161 optimal weight: 0.9980 chunk 243 optimal weight: 0.1980 chunk 223 optimal weight: 0.9990 chunk 193 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: