Starting phenix.real_space_refine (version: dev) on Fri Feb 24 14:30:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2m_11988/02_2023/7b2m_11988_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2m_11988/02_2023/7b2m_11988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2m_11988/02_2023/7b2m_11988.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2m_11988/02_2023/7b2m_11988.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2m_11988/02_2023/7b2m_11988_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2m_11988/02_2023/7b2m_11988_trim.pdb" } resolution = 3.39 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 138": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 159": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 168": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A ARG 269": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "A ARG 484": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B ARG 791": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 830": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 847": "OE1" <-> "OE2" Residue "B GLU 850": "OE1" <-> "OE2" Residue "B ASP 925": "OD1" <-> "OD2" Residue "B GLU 942": "OE1" <-> "OE2" Residue "B GLU 959": "OE1" <-> "OE2" Residue "B ARG 1055": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 1091": "OE1" <-> "OE2" Residue "B GLU 1098": "OE1" <-> "OE2" Residue "B GLU 1137": "OE1" <-> "OE2" Residue "B GLU 1223": "OE1" <-> "OE2" Residue "B ARG 1291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 1324": "OE1" <-> "OE2" Residue "B GLU 1408": "OE1" <-> "OE2" Residue "C ARG 1465": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 1474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 1498": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 1516": "OE1" <-> "OE2" Residue "C ASP 1527": "OD1" <-> "OD2" Residue "C ARG 1533": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 1543": "OE1" <-> "OE2" Residue "C ARG 1577": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 1592": "OE1" <-> "OE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 99": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 23198 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 10023 Classifications: {'peptide': 650} Link IDs: {'PCIS': 3, 'PTRANS': 41, 'TRANS': 605} Chain: "B" Number of atoms: 9444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 9444 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 27, 'TRANS': 586} Chain breaks: 4 Chain: "C" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1984 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "D" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1691 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 11.12, per 1000 atoms: 0.48 Number of scatterers: 23198 At special positions: 0 Unit cell: (167.645, 120.334, 109.021, 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 41 16.00 O 2217 8.00 N 2016 7.00 C 7390 6.00 H 11534 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS B 820 " distance=2.03 Simple disulfide: pdb=" SG CYS A 635 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 876 " - pdb=" SG CYS C1590 " distance=2.03 Simple disulfide: pdb=" SG CYS B1394 " - pdb=" SG CYS C1566 " distance=2.03 Simple disulfide: pdb=" SG CYS C1471 " - pdb=" SG CYS C1535 " distance=2.04 Simple disulfide: pdb=" SG CYS C1583 " - pdb=" SG CYS C1588 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 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 Links applied NAG-ASN " NAG A1801 " - " ASN A 226 " " NAG B1801 " - " ASN B 862 " " NAG B1802 " - " ASN B1328 " " NAG B1803 " - " ASN B1391 " Time building additional restraints: 17.45 Conformation dependent library (CDL) restraints added in 1.7 seconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2774 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 30 sheets defined 19.3% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 114 through 120 removed outlier: 4.346A pdb=" N LYS A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 327 Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 642 through 651 Processing helix chain 'B' and resid 996 through 1003 removed outlier: 3.576A pdb=" N VAL B1000 " --> pdb=" O SER B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1032 Proline residue: B1020 - end of helix Processing helix chain 'B' and resid 1038 through 1058 removed outlier: 3.980A pdb=" N LYS B1042 " --> pdb=" O PRO B1038 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP B1043 " --> pdb=" O PRO B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1090 Processing helix chain 'B' and resid 1096 through 1111 removed outlier: 3.938A pdb=" N LEU B1100 " --> pdb=" O SER B1096 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B1110 " --> pdb=" O TRP B1106 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN B1111 " --> pdb=" O LEU B1107 " (cutoff:3.500A) Processing helix chain 'B' and resid 1126 through 1130 removed outlier: 3.819A pdb=" N GLY B1130 " --> pdb=" O SER B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1152 Processing helix chain 'B' and resid 1161 through 1185 removed outlier: 3.702A pdb=" N LYS B1165 " --> pdb=" O ALA B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1203 Processing helix chain 'B' and resid 1206 through 1221 Processing helix chain 'B' and resid 1258 through 1275 Processing helix chain 'B' and resid 1281 through 1294 removed outlier: 3.667A pdb=" N TRP B1288 " --> pdb=" O GLN B1284 " (cutoff:3.500A) Processing helix chain 'B' and resid 1302 through 1320 Processing helix chain 'C' and resid 1497 through 1507 removed outlier: 4.006A pdb=" N LEU C1504 " --> pdb=" O ASP C1500 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR C1505 " --> pdb=" O LEU C1501 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C1506 " --> pdb=" O GLU C1502 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C1507 " --> pdb=" O LYS C1503 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.581A pdb=" N LYS D 64 " --> pdb=" O ASN D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.935A pdb=" N THR D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 87 removed outlier: 7.455A pdb=" N SER A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 3.689A pdb=" N ASN A 60 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 66 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 32 Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 145 Processing sheet with id=AA5, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA6, first strand: chain 'A' and resid 185 through 192 removed outlier: 6.060A pdb=" N VAL A 178 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS A 188 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 176 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU A 190 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 174 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 241 through 247 removed outlier: 4.054A pdb=" N MET A 262 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 251 through 253 removed outlier: 5.374A pdb=" N ILE A 252 " --> pdb=" O VAL A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 293 through 295 Processing sheet with id=AB1, first strand: chain 'A' and resid 293 through 295 removed outlier: 4.495A pdb=" N TYR A 281 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 355 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.562A pdb=" N ARG A 391 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 419 through 423 removed outlier: 3.892A pdb=" N GLU A 443 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 450 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 472 through 476 removed outlier: 4.156A pdb=" N THR A 527 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 515 through 522 removed outlier: 3.605A pdb=" N PHE A 517 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 510 " --> pdb=" O TYR A 542 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 545 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS A 552 " --> pdb=" O HIS A 549 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 515 through 522 removed outlier: 3.605A pdb=" N PHE A 517 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 510 " --> pdb=" O TYR A 542 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 572 through 574 removed outlier: 3.539A pdb=" N GLU A 592 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 814 " --> pdb=" O GLY B 818 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 785 through 798 removed outlier: 3.951A pdb=" N ARG B 791 " --> pdb=" O SER A 595 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N SER A 595 " --> pdb=" O ARG B 791 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLN B 793 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N THR A 593 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU B 795 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU A 591 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU B 797 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU A 589 " --> pdb=" O LEU B 797 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 774 through 775 removed outlier: 6.996A pdb=" N VAL B 843 " --> pdb=" O GLU B 934 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 774 through 775 removed outlier: 3.546A pdb=" N VAL B 909 " --> pdb=" O LEU B 931 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 867 " --> pdb=" O GLN B 885 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 833 through 836 Processing sheet with id=AC3, first strand: chain 'B' and resid 849 through 851 removed outlier: 3.712A pdb=" N VAL B 902 " --> pdb=" O CYS B 876 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS B 876 " --> pdb=" O VAL B 902 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 938 through 945 Processing sheet with id=AC5, first strand: chain 'B' and resid 959 through 960 Processing sheet with id=AC6, first strand: chain 'B' and resid 1397 through 1405 Processing sheet with id=AC7, first strand: chain 'B' and resid 1397 through 1405 removed outlier: 3.574A pdb=" N VAL C1536 " --> pdb=" O VAL C1470 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1512 through 1518 removed outlier: 3.744A pdb=" N HIS C1514 " --> pdb=" O TYR C1525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1581 through 1583 Processing sheet with id=AD1, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.561A pdb=" N THR D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 57 through 59 removed outlier: 3.528A pdb=" N VAL D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N SER D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 57 through 59 removed outlier: 3.528A pdb=" N VAL D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N SER D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 91 " --> pdb=" O VAL D 112 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1416 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: 9.80 Time building geometry restraints manager: 18.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 11532 1.04 - 1.23: 771 1.23 - 1.43: 4229 1.43 - 1.63: 6851 1.63 - 1.83: 64 Bond restraints: 23447 Sorted by residual: bond pdb=" CG LEU A 24 " pdb=" CD2 LEU A 24 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.04e+00 bond pdb=" CB PRO A 348 " pdb=" CG PRO A 348 " ideal model delta sigma weight residual 1.506 1.474 0.032 3.90e-02 6.57e+02 6.77e-01 bond pdb=" C ALA A 450 " pdb=" N GLY A 451 " ideal model delta sigma weight residual 1.319 1.330 -0.011 1.34e-02 5.57e+03 6.73e-01 bond pdb=" C VAL C1529 " pdb=" N PRO C1530 " ideal model delta sigma weight residual 1.328 1.338 -0.010 1.25e-02 6.40e+03 6.64e-01 bond pdb=" CA PRO C1530 " pdb=" C PRO C1530 " ideal model delta sigma weight residual 1.525 1.518 0.008 9.70e-03 1.06e+04 6.50e-01 ... (remaining 23442 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.15: 322 106.15 - 113.12: 27640 113.12 - 120.10: 6906 120.10 - 127.07: 7357 127.07 - 134.05: 156 Bond angle restraints: 42381 Sorted by residual: angle pdb=" N CYS C1535 " pdb=" CA CYS C1535 " pdb=" C CYS C1535 " ideal model delta sigma weight residual 108.14 111.38 -3.24 1.52e+00 4.33e-01 4.56e+00 angle pdb=" C GLU C1534 " pdb=" N CYS C1535 " pdb=" CA CYS C1535 " ideal model delta sigma weight residual 122.09 118.48 3.61 1.86e+00 2.89e-01 3.77e+00 angle pdb=" CA PRO C1530 " pdb=" C PRO C1530 " pdb=" N THR C1531 " ideal model delta sigma weight residual 114.74 116.71 -1.97 1.03e+00 9.43e-01 3.65e+00 angle pdb=" N SER A 613 " pdb=" CA SER A 613 " pdb=" C SER A 613 " ideal model delta sigma weight residual 108.14 111.01 -2.87 1.52e+00 4.33e-01 3.57e+00 angle pdb=" N ARG A 494 " pdb=" CA ARG A 494 " pdb=" C ARG A 494 " ideal model delta sigma weight residual 108.13 111.29 -3.16 1.72e+00 3.38e-01 3.37e+00 ... (remaining 42376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.56: 8762 19.56 - 39.13: 530 39.13 - 58.69: 66 58.69 - 78.25: 17 78.25 - 97.81: 11 Dihedral angle restraints: 9386 sinusoidal: 4370 harmonic: 5016 Sorted by residual: dihedral pdb=" CB CYS A 635 " pdb=" SG CYS A 635 " pdb=" SG CYS A 669 " pdb=" CB CYS A 669 " ideal model delta sinusoidal sigma weight residual 93.00 35.32 57.68 1 1.00e+01 1.00e-02 4.47e+01 dihedral pdb=" CB CYS A 567 " pdb=" SG CYS A 567 " pdb=" SG CYS B 820 " pdb=" CB CYS B 820 " ideal model delta sinusoidal sigma weight residual 93.00 37.73 55.27 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS C1471 " pdb=" SG CYS C1471 " pdb=" SG CYS C1535 " pdb=" CB CYS C1535 " ideal model delta sinusoidal sigma weight residual 93.00 39.27 53.73 1 1.00e+01 1.00e-02 3.92e+01 ... (remaining 9383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1649 0.069 - 0.138: 188 0.138 - 0.207: 3 0.207 - 0.276: 1 0.276 - 0.344: 1 Chirality restraints: 1842 Sorted by residual: chirality pdb=" C1 NAG B1803 " pdb=" ND2 ASN B1391 " pdb=" C2 NAG B1803 " pdb=" O5 NAG B1803 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C1 NAG B1802 " pdb=" ND2 ASN B1328 " pdb=" C2 NAG B1802 " pdb=" O5 NAG B1802 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE C1485 " pdb=" N ILE C1485 " pdb=" C ILE C1485 " pdb=" CB ILE C1485 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 ... (remaining 1839 not shown) Planarity restraints: 3512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1391 " -0.015 2.00e-02 2.50e+03 1.44e-02 2.57e+00 pdb=" CG ASN B1391 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN B1391 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B1391 " 0.017 2.00e-02 2.50e+03 pdb=" C1 NAG B1803 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 452 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO A 453 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 453 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 453 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 548 " 0.015 2.00e-02 2.50e+03 8.55e-03 2.19e+00 pdb=" CG TYR A 548 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 548 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 548 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 548 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 548 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 548 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 548 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TYR A 548 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR A 548 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TYR A 548 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR A 548 " 0.001 2.00e-02 2.50e+03 ... (remaining 3509 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1124 2.18 - 2.78: 46684 2.78 - 3.39: 62522 3.39 - 3.99: 83065 3.99 - 4.60: 127593 Nonbonded interactions: 320988 Sorted by model distance: nonbonded pdb=" O LEU A 23 " pdb="HE22 GLN A 128 " model vdw 1.574 1.850 nonbonded pdb=" O LYS A 53 " pdb=" HG SER A 114 " model vdw 1.599 1.850 nonbonded pdb=" OE1 GLU A 209 " pdb=" H GLU A 209 " model vdw 1.601 1.850 nonbonded pdb=" O SER B1065 " pdb=" HG1 THR B1079 " model vdw 1.613 1.850 nonbonded pdb="HE22 GLN B 848 " pdb=" HG SER B 900 " model vdw 1.613 2.100 ... (remaining 320983 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 S 41 5.16 5 C 7390 2.51 5 N 2016 2.21 5 O 2217 1.98 5 H 11534 0.53 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: 1.390 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: 0.380 Extract box with map and model: 7.670 Check model and map are aligned: 0.390 Process input model: 72.370 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.190 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 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 : 0.003 0.034 11913 Z= 0.201 Angle : 0.485 4.918 16176 Z= 0.264 Chirality : 0.042 0.344 1842 Planarity : 0.003 0.038 2090 Dihedral : 13.786 97.813 4350 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.15 (0.22), residues: 1488 helix: 1.65 (0.34), residues: 243 sheet: -0.15 (0.24), residues: 508 loop : -0.59 (0.23), residues: 737 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 1.825 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: 0 outliers final: 0 residues processed: 380 average time/residue: 0.6330 time to fit residues: 329.8671 Evaluate side-chains 332 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.739 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 0.0270 chunk 60 optimal weight: 1.9990 chunk 117 optimal weight: 0.0980 chunk 45 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 GLN D 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 11913 Z= 0.201 Angle : 0.547 5.463 16176 Z= 0.286 Chirality : 0.043 0.163 1842 Planarity : 0.004 0.043 2090 Dihedral : 5.263 97.843 1643 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.09 (0.22), residues: 1488 helix: 1.57 (0.32), residues: 264 sheet: -0.03 (0.23), residues: 510 loop : -0.63 (0.23), residues: 714 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 345 time to evaluate : 1.760 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: 10 outliers final: 7 residues processed: 348 average time/residue: 0.6446 time to fit residues: 303.8789 Evaluate side-chains 332 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 325 time to evaluate : 1.958 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2840 time to fit residues: 6.2419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 309 GLN ** B 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 11913 Z= 0.408 Angle : 0.617 5.898 16176 Z= 0.325 Chirality : 0.044 0.192 1842 Planarity : 0.005 0.044 2090 Dihedral : 5.845 97.847 1643 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.52 (0.22), residues: 1488 helix: 1.20 (0.32), residues: 264 sheet: -0.27 (0.23), residues: 516 loop : -0.93 (0.23), residues: 708 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 345 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 353 average time/residue: 0.6464 time to fit residues: 308.9146 Evaluate side-chains 353 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 338 time to evaluate : 1.941 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2769 time to fit residues: 9.9167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 65 optimal weight: 0.3980 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1050 GLN B1292 GLN D 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 11913 Z= 0.256 Angle : 0.554 6.470 16176 Z= 0.287 Chirality : 0.043 0.165 1842 Planarity : 0.004 0.043 2090 Dihedral : 5.651 96.679 1643 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.36 (0.22), residues: 1488 helix: 1.49 (0.32), residues: 264 sheet: -0.21 (0.23), residues: 506 loop : -0.88 (0.23), residues: 718 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 345 time to evaluate : 2.014 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 outliers start: 13 outliers final: 6 residues processed: 347 average time/residue: 0.6528 time to fit residues: 307.1393 Evaluate side-chains 340 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 334 time to evaluate : 1.799 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2749 time to fit residues: 5.3046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B1129 GLN B1292 GLN B1359 GLN D 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.079 11913 Z= 0.460 Angle : 0.629 6.624 16176 Z= 0.331 Chirality : 0.045 0.233 1842 Planarity : 0.005 0.050 2090 Dihedral : 6.060 96.319 1643 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.85 (0.21), residues: 1488 helix: 1.06 (0.31), residues: 264 sheet: -0.59 (0.23), residues: 525 loop : -1.11 (0.23), residues: 699 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 350 time to evaluate : 1.895 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 outliers start: 28 outliers final: 19 residues processed: 356 average time/residue: 0.6456 time to fit residues: 310.9198 Evaluate side-chains 359 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 340 time to evaluate : 2.012 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3359 time to fit residues: 13.1533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN D 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 11913 Z= 0.265 Angle : 0.558 7.763 16176 Z= 0.289 Chirality : 0.043 0.174 1842 Planarity : 0.004 0.044 2090 Dihedral : 5.816 95.633 1643 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.65 (0.22), residues: 1488 helix: 1.40 (0.32), residues: 265 sheet: -0.52 (0.23), residues: 535 loop : -1.02 (0.23), residues: 688 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 341 time to evaluate : 1.866 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 outliers start: 12 outliers final: 7 residues processed: 346 average time/residue: 0.6480 time to fit residues: 302.9523 Evaluate side-chains 333 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 326 time to evaluate : 1.884 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.2815 time to fit residues: 5.8667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 0.0870 chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 chunk 89 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11913 Z= 0.214 Angle : 0.539 5.621 16176 Z= 0.277 Chirality : 0.043 0.160 1842 Planarity : 0.004 0.046 2090 Dihedral : 5.662 95.485 1643 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.47 (0.22), residues: 1488 helix: 1.64 (0.32), residues: 265 sheet: -0.40 (0.23), residues: 533 loop : -0.95 (0.23), residues: 690 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 342 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 345 average time/residue: 0.6711 time to fit residues: 312.6215 Evaluate side-chains 339 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 330 time to evaluate : 1.704 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.2845 time to fit residues: 6.9813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 11913 Z= 0.389 Angle : 0.599 7.950 16176 Z= 0.311 Chirality : 0.044 0.213 1842 Planarity : 0.004 0.045 2090 Dihedral : 5.915 95.275 1643 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.85 (0.22), residues: 1488 helix: 1.32 (0.31), residues: 264 sheet: -0.67 (0.22), residues: 548 loop : -1.16 (0.23), residues: 676 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 336 time to evaluate : 2.111 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 outliers start: 17 outliers final: 11 residues processed: 340 average time/residue: 0.6805 time to fit residues: 311.3912 Evaluate side-chains 340 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 329 time to evaluate : 1.775 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.3313 time to fit residues: 8.4599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.2980 chunk 138 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 11913 Z= 0.236 Angle : 0.560 8.537 16176 Z= 0.286 Chirality : 0.043 0.162 1842 Planarity : 0.004 0.048 2090 Dihedral : 5.732 95.143 1643 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.67 (0.22), residues: 1488 helix: 1.56 (0.31), residues: 263 sheet: -0.63 (0.22), residues: 548 loop : -1.00 (0.24), residues: 677 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 344 time to evaluate : 1.718 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 outliers start: 6 outliers final: 4 residues processed: 345 average time/residue: 0.6692 time to fit residues: 312.2953 Evaluate side-chains 343 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 339 time to evaluate : 1.855 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2662 time to fit residues: 4.3719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 137 optimal weight: 0.1980 chunk 118 optimal weight: 2.9990 chunk 12 optimal weight: 0.0770 chunk 91 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 126 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS D 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11913 Z= 0.209 Angle : 0.552 7.229 16176 Z= 0.281 Chirality : 0.043 0.154 1842 Planarity : 0.004 0.050 2090 Dihedral : 5.650 95.074 1643 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.59 (0.22), residues: 1488 helix: 1.61 (0.32), residues: 263 sheet: -0.54 (0.22), residues: 542 loop : -0.99 (0.24), residues: 683 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 334 time to evaluate : 1.849 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 outliers start: 4 outliers final: 2 residues processed: 336 average time/residue: 0.6646 time to fit residues: 301.6015 Evaluate side-chains 333 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 331 time to evaluate : 1.923 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.2796 time to fit residues: 3.4525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 119 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.103385 restraints weight = 54969.562| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.43 r_work: 0.3181 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 11913 Z= 0.253 Angle : 0.569 9.029 16176 Z= 0.290 Chirality : 0.043 0.170 1842 Planarity : 0.004 0.040 2090 Dihedral : 5.698 94.973 1643 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.69 (0.22), residues: 1488 helix: 1.48 (0.31), residues: 264 sheet: -0.59 (0.22), residues: 545 loop : -1.05 (0.24), residues: 679 =============================================================================== Job complete usr+sys time: 7038.44 seconds wall clock time: 123 minutes 58.70 seconds (7438.70 seconds total)