Starting phenix.real_space_refine on Tue Mar 19 02:49:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2q_11990/03_2024/7b2q_11990_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2q_11990/03_2024/7b2q_11990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2q_11990/03_2024/7b2q_11990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2q_11990/03_2024/7b2q_11990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2q_11990/03_2024/7b2q_11990_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2q_11990/03_2024/7b2q_11990_trim.pdb" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 44 5.16 5 C 7355 2.51 5 N 2007 2.21 5 O 2205 1.98 5 H 11430 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 873": "OE1" <-> "OE2" Residue "B PHE 921": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 946": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1012": "OE1" <-> "OE2" Residue "B TYR 1027": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1263": "OE1" <-> "OE2" Residue "B GLU 1280": "OE1" <-> "OE2" Residue "B GLU 1323": "OE1" <-> "OE2" Residue "B GLU 1400": "OE1" <-> "OE2" Residue "C PHE 1526": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1559": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1560": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 106": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23041 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 10007 Classifications: {'peptide': 650} Link IDs: {'PCIS': 3, 'PTRANS': 41, 'TRANS': 605} Chain: "B" Number of atoms: 9222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 9222 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 27, 'TRANS': 572} Chain breaks: 6 Chain: "C" Number of atoms: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1958 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "D" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1784 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.14, per 1000 atoms: 0.44 Number of scatterers: 23041 At special positions: 0 Unit cell: (135.762, 122.391, 131.648, 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 44 16.00 O 2205 8.00 N 2007 7.00 C 7355 6.00 H 11430 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=2.04 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 92 " 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 BETA1-4 " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B1801 " - " ASN B 862 " " NAG B1802 " - " ASN B1328 " " NAG B1803 " - " ASN B1391 " " NAG E 1 " - " ASN A 226 " Time building additional restraints: 18.38 Conformation dependent library (CDL) restraints added in 2.3 seconds 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2762 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 28 sheets defined 19.5% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.762A pdb=" N ARG A 63 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 97 removed outlier: 3.706A pdb=" N ALA A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 315 through 327 Processing helix chain 'A' and resid 606 through 611 removed outlier: 3.771A pdb=" N ALA A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 642 through 650 Processing helix chain 'B' and resid 999 through 1004 Processing helix chain 'B' and resid 1012 through 1017 removed outlier: 3.807A pdb=" N ILE B1016 " --> pdb=" O GLU B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1032 Processing helix chain 'B' and resid 1038 through 1058 removed outlier: 3.855A pdb=" N LYS B1042 " --> pdb=" O PRO B1038 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP B1043 " --> pdb=" O PRO B1039 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP B1047 " --> pdb=" O ASP B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1090 Processing helix chain 'B' and resid 1096 through 1110 removed outlier: 3.568A pdb=" N LEU B1100 " --> pdb=" O SER B1096 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR B1103 " --> pdb=" O LYS B1099 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B1107 " --> pdb=" O THR B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1130 removed outlier: 4.012A pdb=" N MET B1128 " --> pdb=" O ASP B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1156 removed outlier: 3.701A pdb=" N LEU B1153 " --> pdb=" O LEU B1149 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B1154 " --> pdb=" O HIS B1150 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL B1155 " --> pdb=" O HIS B1151 " (cutoff:3.500A) Processing helix chain 'B' and resid 1161 through 1186 removed outlier: 3.563A pdb=" N ARG B1167 " --> pdb=" O PRO B1163 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1203 Processing helix chain 'B' and resid 1206 through 1221 removed outlier: 3.561A pdb=" N ALA B1219 " --> pdb=" O ASN B1215 " (cutoff:3.500A) Processing helix chain 'B' and resid 1258 through 1275 Processing helix chain 'B' and resid 1281 through 1294 removed outlier: 3.726A pdb=" N ALA B1287 " --> pdb=" O ASP B1283 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TRP B1288 " --> pdb=" O GLN B1284 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B1291 " --> pdb=" O ALA B1287 " (cutoff:3.500A) Processing helix chain 'B' and resid 1302 through 1320 Processing helix chain 'C' and resid 1497 through 1507 removed outlier: 3.641A pdb=" N LEU C1507 " --> pdb=" O LYS C1503 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 61 removed outlier: 3.669A pdb=" N LYS D 61 " --> pdb=" O PRO D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 58 through 61' Processing helix chain 'D' and resid 83 through 87 removed outlier: 4.253A pdb=" N THR D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 87 removed outlier: 7.823A 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: 6.097A pdb=" N VAL A 31 " --> pdb=" O SER A 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 52 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: 3.584A pdb=" N ARG A 187 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 218 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 214 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 241 through 247 removed outlier: 3.514A pdb=" N ARG A 269 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET A 262 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 252 through 253 removed outlier: 5.154A 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 279 through 280 Processing sheet with id=AB1, first strand: chain 'A' and resid 293 through 295 Processing sheet with id=AB2, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.715A pdb=" N LEU A 386 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 433 " --> pdb=" O LEU A 386 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 417 through 423 removed outlier: 3.521A pdb=" N GLU A 443 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 448 " --> pdb=" O ALA A 458 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 450 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 488 through 493 removed outlier: 4.294A 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: 3.595A pdb=" N PHE A 517 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 510 " --> pdb=" O TYR A 542 " (cutoff:3.500A) removed outlier: 4.224A 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: 3.595A pdb=" N PHE A 517 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 3.516A 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: 3.922A pdb=" N LEU B 795 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 787 through 788 removed outlier: 3.840A pdb=" N SER B 812 " --> pdb=" O CYS B 820 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS B 820 " --> pdb=" O SER B 812 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 804 through 808 Processing sheet with id=AC1, first strand: chain 'B' and resid 833 through 836 removed outlier: 3.515A pdb=" N HIS B 836 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN B 857 " --> pdb=" O SER B 893 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 885 through 889 removed outlier: 3.771A pdb=" N VAL B 867 " --> pdb=" O GLN B 885 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS B 868 " --> pdb=" O VAL B 914 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 914 " --> pdb=" O HIS B 868 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 911 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 929 " --> pdb=" O LEU B 911 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 875 through 876 removed outlier: 3.572A pdb=" N CYS B 876 " --> pdb=" O VAL B 902 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 902 " --> pdb=" O CYS B 876 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 939 through 945 removed outlier: 3.554A pdb=" N LEU B 944 " --> pdb=" O VAL B1380 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B1380 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 959 through 960 removed outlier: 3.776A pdb=" N ILE B 960 " --> pdb=" O ILE B1366 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B1366 " --> pdb=" O ILE B 960 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B1329 " --> pdb=" O LEU B1344 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1397 through 1401 removed outlier: 3.572A pdb=" N TRP C1473 " --> pdb=" O GLN B1398 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1404 through 1405 removed outlier: 3.504A pdb=" N LYS B1404 " --> pdb=" O HIS C1467 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C1541 " --> pdb=" O HIS C1495 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1512 through 1518 removed outlier: 3.752A pdb=" N HIS C1514 " --> pdb=" O TYR C1525 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C1524 " --> pdb=" O ALA C1486 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.515A pdb=" N SER D 7 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR D 74 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP D 69 " --> pdb=" O THR D 74 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR D 65 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 54 through 56 removed outlier: 7.117A pdb=" N TRP D 32 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA D 88 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL D 116 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR D 90 " --> pdb=" O THR D 114 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1122 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: 10.24 Time building geometry restraints manager: 18.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11428 1.03 - 1.23: 263 1.23 - 1.43: 4686 1.43 - 1.63: 6841 1.63 - 1.82: 70 Bond restraints: 23288 Sorted by residual: bond pdb=" C1 NAG B1801 " pdb=" O5 NAG B1801 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C1 NAG B1803 " pdb=" O5 NAG B1803 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.59e+00 bond pdb=" N THR C1469 " pdb=" CA THR C1469 " ideal model delta sigma weight residual 1.465 1.449 0.016 1.31e-02 5.83e+03 1.58e+00 bond pdb=" C GLU A 346 " pdb=" N SER A 347 " ideal model delta sigma weight residual 1.329 1.309 0.019 1.60e-02 3.91e+03 1.47e+00 ... (remaining 23283 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.62: 391 106.62 - 113.47: 27763 113.47 - 120.32: 7126 120.32 - 127.17: 6644 127.17 - 134.01: 149 Bond angle restraints: 42073 Sorted by residual: angle pdb=" N VAL A 186 " pdb=" CA VAL A 186 " pdb=" C VAL A 186 " ideal model delta sigma weight residual 113.71 111.02 2.69 9.50e-01 1.11e+00 8.01e+00 angle pdb=" CA CYS A 567 " pdb=" CB CYS A 567 " pdb=" SG CYS A 567 " ideal model delta sigma weight residual 114.40 120.07 -5.67 2.30e+00 1.89e-01 6.07e+00 angle pdb=" N PHE B 846 " pdb=" CA PHE B 846 " pdb=" C PHE B 846 " ideal model delta sigma weight residual 113.56 110.47 3.09 1.39e+00 5.18e-01 4.93e+00 angle pdb=" CA LYS D 83 " pdb=" CB LYS D 83 " pdb=" CG LYS D 83 " ideal model delta sigma weight residual 114.10 118.41 -4.31 2.00e+00 2.50e-01 4.64e+00 angle pdb=" N GLU A 568 " pdb=" CA GLU A 568 " pdb=" C GLU A 568 " ideal model delta sigma weight residual 113.97 111.24 2.73 1.28e+00 6.10e-01 4.54e+00 ... (remaining 42068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 9941 17.22 - 34.43: 821 34.43 - 51.65: 235 51.65 - 68.87: 61 68.87 - 86.09: 13 Dihedral angle restraints: 11071 sinusoidal: 6116 harmonic: 4955 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 93.00 167.55 -74.55 1 1.00e+01 1.00e-02 7.04e+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 48.23 44.77 1 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" CA LYS D 83 " pdb=" C LYS D 83 " pdb=" N PRO D 84 " pdb=" CA PRO D 84 " ideal model delta harmonic sigma weight residual 180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 11068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1518 0.049 - 0.098: 220 0.098 - 0.147: 94 0.147 - 0.196: 2 0.196 - 0.245: 1 Chirality restraints: 1835 Sorted by residual: 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 -2.16 -0.24 2.00e-01 2.50e+01 1.50e+00 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 -2.21 -0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA PRO D 84 " pdb=" N PRO D 84 " pdb=" C PRO D 84 " pdb=" CB PRO D 84 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 1832 not shown) Planarity restraints: 3485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 636 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO A 637 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 637 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 637 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B1121 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO B1122 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B1122 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B1122 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 46 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO A 47 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 47 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 47 " -0.019 5.00e-02 4.00e+02 ... (remaining 3482 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 627 2.11 - 2.74: 41664 2.74 - 3.36: 63556 3.36 - 3.98: 81668 3.98 - 4.60: 127477 Nonbonded interactions: 314992 Sorted by model distance: nonbonded pdb=" O GLN B1395 " pdb="HD21 ASN C1475 " model vdw 1.493 1.850 nonbonded pdb=" O MET B 841 " pdb="HE22 GLN B 932 " model vdw 1.497 1.850 nonbonded pdb="HH21 ARG A 22 " pdb=" OD2 ASP A 658 " model vdw 1.517 1.850 nonbonded pdb=" HG1 THR A 606 " pdb=" O THR B 805 " model vdw 1.555 1.850 nonbonded pdb="HH22 ARG A 138 " pdb=" OD2 ASP A 172 " model vdw 1.560 1.850 ... (remaining 314987 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 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: 1.660 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: 0.390 Extract box with map and model: 6.700 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 73.150 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 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 : 0.004 0.036 11858 Z= 0.239 Angle : 0.547 5.665 16097 Z= 0.295 Chirality : 0.042 0.245 1835 Planarity : 0.003 0.057 2077 Dihedral : 13.626 86.086 4413 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.23 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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 (0.22), residues: 1473 helix: 0.39 (0.34), residues: 262 sheet: -0.76 (0.24), residues: 485 loop : -0.86 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 360 HIS 0.004 0.001 HIS B1150 PHE 0.008 0.001 PHE A 82 TYR 0.015 0.001 TYR D 29 ARG 0.008 0.001 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 1.824 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 revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7117 (pp30) cc_final: 0.6797 (pp30) REVERT: A 53 LYS cc_start: 0.7713 (ptpp) cc_final: 0.7479 (ptpt) REVERT: A 57 PHE cc_start: 0.5973 (p90) cc_final: 0.5737 (p90) REVERT: A 124 THR cc_start: 0.7998 (p) cc_final: 0.7773 (t) REVERT: A 166 LYS cc_start: 0.8042 (mtmm) cc_final: 0.7819 (mtmm) REVERT: A 179 GLU cc_start: 0.7175 (tt0) cc_final: 0.6960 (tt0) REVERT: A 209 GLU cc_start: 0.7285 (mm-30) cc_final: 0.7062 (mm-30) REVERT: A 328 MET cc_start: 0.6674 (tpp) cc_final: 0.5354 (tpp) REVERT: A 378 LEU cc_start: 0.7920 (pt) cc_final: 0.7688 (pp) REVERT: A 404 LYS cc_start: 0.7143 (mttp) cc_final: 0.6845 (mtmt) REVERT: A 419 GLN cc_start: 0.7231 (tt0) cc_final: 0.6946 (tm-30) REVERT: A 523 LYS cc_start: 0.7499 (ttpt) cc_final: 0.7145 (ttpp) REVERT: A 558 LEU cc_start: 0.8586 (tp) cc_final: 0.8319 (tp) REVERT: A 632 ASP cc_start: 0.7808 (t0) cc_final: 0.7569 (t0) REVERT: A 658 ASP cc_start: 0.7207 (m-30) cc_final: 0.6970 (m-30) REVERT: B 817 LYS cc_start: 0.7618 (mmtt) cc_final: 0.7240 (mmmm) REVERT: B 833 PHE cc_start: 0.7406 (t80) cc_final: 0.7133 (t80) REVERT: B 857 ASN cc_start: 0.7403 (t0) cc_final: 0.7199 (t0) REVERT: B 866 SER cc_start: 0.8534 (t) cc_final: 0.8279 (p) REVERT: B 942 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6689 (mt-10) REVERT: B 1029 ASP cc_start: 0.7461 (t0) cc_final: 0.7171 (m-30) REVERT: B 1084 LYS cc_start: 0.8339 (ttmt) cc_final: 0.7977 (ttmm) REVERT: B 1288 TRP cc_start: 0.7739 (t60) cc_final: 0.7469 (t-100) REVERT: B 1317 ILE cc_start: 0.8283 (pt) cc_final: 0.7311 (mt) REVERT: B 1388 ASP cc_start: 0.6950 (p0) cc_final: 0.6719 (p0) REVERT: B 1389 MET cc_start: 0.5743 (pmm) cc_final: 0.5216 (pmm) REVERT: B 1411 MET cc_start: 0.6819 (ppp) cc_final: 0.6005 (ppp) REVERT: D 27 ARG cc_start: 0.6611 (ttt90) cc_final: 0.6277 (ttt-90) REVERT: D 28 THR cc_start: 0.5700 (t) cc_final: 0.5473 (t) REVERT: D 63 ARG cc_start: 0.8273 (ttp80) cc_final: 0.7878 (ttp80) REVERT: D 104 VAL cc_start: 0.7049 (m) cc_final: 0.6845 (m) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.5978 time to fit residues: 286.4373 Evaluate side-chains 321 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 0.3980 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN B 848 GLN B1129 GLN ** B1216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11858 Z= 0.272 Angle : 0.594 5.318 16097 Z= 0.316 Chirality : 0.044 0.287 1835 Planarity : 0.005 0.041 2077 Dihedral : 5.615 59.193 1715 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.11 % Allowed : 9.53 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -1.11 (0.22), residues: 1473 helix: 0.24 (0.31), residues: 264 sheet: -0.78 (0.23), residues: 508 loop : -0.96 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 32 HIS 0.006 0.001 HIS B1150 PHE 0.021 0.002 PHE A 319 TYR 0.015 0.001 TYR A 507 ARG 0.004 0.000 ARG B 791 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 332 time to evaluate : 1.542 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: A 22 ARG cc_start: 0.7352 (mtt90) cc_final: 0.7053 (mtt180) REVERT: A 44 GLN cc_start: 0.7450 (pp30) cc_final: 0.7020 (pp30) REVERT: A 53 LYS cc_start: 0.7845 (ptpp) cc_final: 0.7575 (ptpt) REVERT: A 57 PHE cc_start: 0.5928 (p90) cc_final: 0.5725 (p90) REVERT: A 60 ASN cc_start: 0.7469 (p0) cc_final: 0.6851 (p0) REVERT: A 97 CYS cc_start: 0.4570 (p) cc_final: 0.4131 (p) REVERT: A 231 PHE cc_start: 0.8545 (p90) cc_final: 0.8301 (p90) REVERT: A 269 ARG cc_start: 0.6876 (mmm160) cc_final: 0.6520 (mtm180) REVERT: A 328 MET cc_start: 0.6131 (tpp) cc_final: 0.5618 (tpp) REVERT: A 346 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6363 (tm-30) REVERT: A 363 VAL cc_start: 0.7309 (m) cc_final: 0.7102 (p) REVERT: A 378 LEU cc_start: 0.7966 (pt) cc_final: 0.7702 (pp) REVERT: A 404 LYS cc_start: 0.7623 (mttp) cc_final: 0.7314 (mtmt) REVERT: A 523 LYS cc_start: 0.7531 (ttpt) cc_final: 0.7180 (ttpp) REVERT: A 558 LEU cc_start: 0.8675 (tp) cc_final: 0.8414 (tp) REVERT: A 632 ASP cc_start: 0.7773 (t0) cc_final: 0.7558 (t0) REVERT: B 808 ILE cc_start: 0.6921 (mt) cc_final: 0.6503 (tt) REVERT: B 857 ASN cc_start: 0.7498 (t0) cc_final: 0.7223 (t0) REVERT: B 942 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6484 (mt-10) REVERT: B 1013 GLN cc_start: 0.7441 (mm110) cc_final: 0.7134 (mm110) REVERT: B 1015 MET cc_start: 0.7537 (mmm) cc_final: 0.7302 (mmm) REVERT: B 1084 LYS cc_start: 0.8434 (ttmt) cc_final: 0.7956 (ttmm) REVERT: B 1288 TRP cc_start: 0.7733 (t60) cc_final: 0.7486 (t-100) REVERT: B 1317 ILE cc_start: 0.8432 (pt) cc_final: 0.7674 (mt) REVERT: B 1388 ASP cc_start: 0.6913 (p0) cc_final: 0.6660 (p0) REVERT: B 1389 MET cc_start: 0.5851 (pmm) cc_final: 0.5300 (pmm) REVERT: C 1510 ARG cc_start: 0.6874 (ptm-80) cc_final: 0.6612 (ptm-80) REVERT: D 27 ARG cc_start: 0.6605 (ttt90) cc_final: 0.6383 (ttt-90) outliers start: 14 outliers final: 7 residues processed: 336 average time/residue: 0.6069 time to fit residues: 278.7803 Evaluate side-chains 326 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 319 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 1203 THR Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1301 SER Chi-restraints excluded: chain B residue 1367 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1129 GLN ** B1216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 11858 Z= 0.385 Angle : 0.631 5.921 16097 Z= 0.335 Chirality : 0.045 0.292 1835 Planarity : 0.005 0.054 2077 Dihedral : 5.454 56.369 1715 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.65 % Favored : 93.28 % Rotamer: Outliers : 2.14 % Allowed : 11.60 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -1.46 (0.21), residues: 1473 helix: -0.12 (0.31), residues: 264 sheet: -0.98 (0.23), residues: 504 loop : -1.19 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 116 HIS 0.006 0.001 HIS B1214 PHE 0.024 0.002 PHE A 74 TYR 0.018 0.002 TYR A 507 ARG 0.004 0.001 ARG B 791 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 337 time to evaluate : 1.723 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 revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7434 (pp30) cc_final: 0.6886 (pp30) REVERT: A 53 LYS cc_start: 0.7916 (ptpp) cc_final: 0.7643 (ptpt) REVERT: A 57 PHE cc_start: 0.5968 (p90) cc_final: 0.5752 (p90) REVERT: A 121 LEU cc_start: 0.6988 (mp) cc_final: 0.6742 (mp) REVERT: A 171 THR cc_start: 0.7532 (p) cc_final: 0.7280 (m) REVERT: A 188 LYS cc_start: 0.8047 (ttmt) cc_final: 0.7655 (ttmm) REVERT: A 231 PHE cc_start: 0.8646 (p90) cc_final: 0.8413 (p90) REVERT: A 234 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7499 (ptmt) REVERT: A 269 ARG cc_start: 0.7003 (mtm180) cc_final: 0.6682 (mtm180) REVERT: A 318 GLU cc_start: 0.6708 (tm-30) cc_final: 0.6264 (tp30) REVERT: A 328 MET cc_start: 0.6136 (tpp) cc_final: 0.5699 (tpp) REVERT: A 346 GLU cc_start: 0.6914 (tm-30) cc_final: 0.6654 (tm-30) REVERT: A 404 LYS cc_start: 0.7781 (mttp) cc_final: 0.7456 (mtmt) REVERT: A 523 LYS cc_start: 0.7655 (ttpt) cc_final: 0.7253 (ttpp) REVERT: A 583 ASN cc_start: 0.7665 (p0) cc_final: 0.7461 (p0) REVERT: A 659 GLN cc_start: 0.7817 (mt0) cc_final: 0.7561 (mt0) REVERT: A 660 TRP cc_start: 0.7763 (p-90) cc_final: 0.6445 (p90) REVERT: B 857 ASN cc_start: 0.7738 (t0) cc_final: 0.7426 (t0) REVERT: B 1084 LYS cc_start: 0.8477 (ttmt) cc_final: 0.8183 (ttpp) REVERT: B 1288 TRP cc_start: 0.7851 (t60) cc_final: 0.7592 (t-100) REVERT: B 1317 ILE cc_start: 0.8315 (pt) cc_final: 0.7821 (mt) REVERT: B 1388 ASP cc_start: 0.6989 (p0) cc_final: 0.6746 (p0) REVERT: B 1389 MET cc_start: 0.5814 (pmm) cc_final: 0.5378 (pmm) REVERT: D 33 PHE cc_start: 0.5985 (m-80) cc_final: 0.5777 (m-80) REVERT: D 53 MET cc_start: 0.4562 (mtm) cc_final: 0.4313 (mtm) REVERT: D 55 GLU cc_start: 0.4856 (pp20) cc_final: 0.4070 (pp20) outliers start: 27 outliers final: 22 residues processed: 347 average time/residue: 0.6050 time to fit residues: 290.7709 Evaluate side-chains 356 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 333 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain B residue 1203 THR Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1301 SER Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1406 HIS Chi-restraints excluded: chain C residue 1466 VAL Chi-restraints excluded: chain C residue 1536 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN B1129 GLN ** B1216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11858 Z= 0.262 Angle : 0.568 6.658 16097 Z= 0.298 Chirality : 0.043 0.266 1835 Planarity : 0.005 0.104 2077 Dihedral : 5.183 57.507 1715 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.30 % Allowed : 13.66 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -1.40 (0.22), residues: 1473 helix: 0.03 (0.31), residues: 265 sheet: -0.99 (0.23), residues: 511 loop : -1.15 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 32 HIS 0.009 0.001 HIS B1342 PHE 0.018 0.002 PHE A 74 TYR 0.014 0.001 TYR A 507 ARG 0.007 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 340 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7419 (pp30) cc_final: 0.6870 (pp30) REVERT: A 53 LYS cc_start: 0.7941 (ptpp) cc_final: 0.7677 (ptpt) REVERT: A 121 LEU cc_start: 0.7331 (mp) cc_final: 0.6960 (mp) REVERT: A 166 LYS cc_start: 0.7958 (mtmm) cc_final: 0.7601 (mtmm) REVERT: A 171 THR cc_start: 0.7463 (p) cc_final: 0.7253 (m) REVERT: A 188 LYS cc_start: 0.8037 (ttmt) cc_final: 0.7637 (ttmm) REVERT: A 234 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7469 (ptmt) REVERT: A 328 MET cc_start: 0.6113 (tpp) cc_final: 0.5732 (tpp) REVERT: A 346 GLU cc_start: 0.6943 (tm-30) cc_final: 0.6582 (tm-30) REVERT: A 404 LYS cc_start: 0.7831 (mttp) cc_final: 0.7508 (mtmt) REVERT: A 523 LYS cc_start: 0.7678 (ttpt) cc_final: 0.7279 (ttpp) REVERT: A 558 LEU cc_start: 0.8754 (tp) cc_final: 0.8480 (tp) REVERT: A 660 TRP cc_start: 0.7770 (p-90) cc_final: 0.6358 (p90) REVERT: B 857 ASN cc_start: 0.7693 (t0) cc_final: 0.7393 (t0) REVERT: B 1015 MET cc_start: 0.7512 (mmm) cc_final: 0.7102 (mmm) REVERT: B 1084 LYS cc_start: 0.8494 (ttmt) cc_final: 0.8181 (ttpp) REVERT: B 1169 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8057 (mm-30) REVERT: B 1222 GLN cc_start: 0.6722 (tm-30) cc_final: 0.6094 (tm-30) REVERT: B 1288 TRP cc_start: 0.7652 (t60) cc_final: 0.7433 (t-100) REVERT: B 1310 ASP cc_start: 0.7536 (t0) cc_final: 0.7287 (t70) REVERT: B 1389 MET cc_start: 0.5789 (pmm) cc_final: 0.5354 (pmm) REVERT: D 6 GLU cc_start: 0.6826 (tp30) cc_final: 0.6475 (tp30) outliers start: 29 outliers final: 21 residues processed: 354 average time/residue: 0.5819 time to fit residues: 283.2238 Evaluate side-chains 359 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 336 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1301 SER Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain C residue 1466 VAL Chi-restraints excluded: chain C residue 1536 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN ** B1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11858 Z= 0.274 Angle : 0.567 5.383 16097 Z= 0.298 Chirality : 0.043 0.265 1835 Planarity : 0.005 0.056 2077 Dihedral : 5.112 58.102 1715 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.38 % Allowed : 15.49 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -1.38 (0.22), residues: 1473 helix: 0.10 (0.31), residues: 265 sheet: -0.98 (0.23), residues: 515 loop : -1.15 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 782 HIS 0.006 0.001 HIS B1214 PHE 0.025 0.002 PHE D 33 TYR 0.014 0.002 TYR A 507 ARG 0.005 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 331 time to evaluate : 1.512 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: A 44 GLN cc_start: 0.7385 (pp30) cc_final: 0.6868 (pp30) REVERT: A 53 LYS cc_start: 0.7979 (ptpp) cc_final: 0.7708 (ptpt) REVERT: A 188 LYS cc_start: 0.8023 (ttmt) cc_final: 0.7615 (ttmm) REVERT: A 234 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7520 (ptmt) REVERT: A 328 MET cc_start: 0.6183 (tpp) cc_final: 0.5886 (tpp) REVERT: A 404 LYS cc_start: 0.7858 (mttp) cc_final: 0.7557 (mtmt) REVERT: A 523 LYS cc_start: 0.7706 (ttpt) cc_final: 0.7298 (ttpp) REVERT: A 558 LEU cc_start: 0.8722 (tp) cc_final: 0.8417 (tp) REVERT: A 660 TRP cc_start: 0.7831 (p-90) cc_final: 0.6350 (p90) REVERT: B 1084 LYS cc_start: 0.8487 (ttmt) cc_final: 0.7981 (ttmm) REVERT: B 1169 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7984 (mm-30) REVERT: B 1222 GLN cc_start: 0.6905 (tm-30) cc_final: 0.6220 (tm-30) REVERT: B 1288 TRP cc_start: 0.7642 (t60) cc_final: 0.7393 (t-100) REVERT: B 1310 ASP cc_start: 0.7553 (t0) cc_final: 0.7350 (t0) REVERT: B 1389 MET cc_start: 0.5841 (pmm) cc_final: 0.5468 (pmm) REVERT: D 6 GLU cc_start: 0.6811 (tp30) cc_final: 0.6499 (tp30) outliers start: 30 outliers final: 24 residues processed: 347 average time/residue: 0.6215 time to fit residues: 296.9009 Evaluate side-chains 352 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 326 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 1065 SER Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1301 SER Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1406 HIS Chi-restraints excluded: chain C residue 1466 VAL Chi-restraints excluded: chain C residue 1536 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN B1057 GLN B1129 GLN ** B1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 11858 Z= 0.392 Angle : 0.624 7.290 16097 Z= 0.332 Chirality : 0.045 0.269 1835 Planarity : 0.006 0.073 2077 Dihedral : 5.356 56.461 1715 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 2.78 % Allowed : 15.97 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -1.62 (0.21), residues: 1473 helix: -0.10 (0.31), residues: 264 sheet: -1.13 (0.23), residues: 519 loop : -1.32 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 782 HIS 0.009 0.002 HIS C1495 PHE 0.023 0.002 PHE A 74 TYR 0.018 0.002 TYR A 507 ARG 0.008 0.001 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 340 time to evaluate : 1.924 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7317 (pp30) cc_final: 0.6846 (pp30) REVERT: A 53 LYS cc_start: 0.8048 (ptpp) cc_final: 0.7769 (ptpt) REVERT: A 188 LYS cc_start: 0.8052 (ttmt) cc_final: 0.7653 (ttmm) REVERT: A 234 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7588 (ptmt) REVERT: A 318 GLU cc_start: 0.6628 (tm-30) cc_final: 0.6315 (tp30) REVERT: A 328 MET cc_start: 0.6252 (tpp) cc_final: 0.5981 (tpp) REVERT: A 352 MET cc_start: 0.6663 (ptp) cc_final: 0.6073 (ptp) REVERT: A 404 LYS cc_start: 0.7911 (mttp) cc_final: 0.7626 (mtmt) REVERT: A 417 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6505 (tm-30) REVERT: A 523 LYS cc_start: 0.7808 (ttpt) cc_final: 0.7388 (ttpp) REVERT: A 558 LEU cc_start: 0.8682 (tp) cc_final: 0.8409 (tp) REVERT: A 568 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: A 660 TRP cc_start: 0.7839 (p-90) cc_final: 0.6330 (p90) REVERT: B 1084 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8057 (ttmm) REVERT: B 1166 GLN cc_start: 0.7825 (tp40) cc_final: 0.7118 (tp40) REVERT: B 1169 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7934 (mm-30) REVERT: B 1263 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.5910 (tt0) REVERT: B 1288 TRP cc_start: 0.7792 (t60) cc_final: 0.7521 (t-100) REVERT: B 1310 ASP cc_start: 0.7584 (t0) cc_final: 0.7318 (t0) REVERT: B 1389 MET cc_start: 0.5836 (pmm) cc_final: 0.5517 (pmm) REVERT: D 6 GLU cc_start: 0.6774 (tp30) cc_final: 0.6466 (tp30) outliers start: 35 outliers final: 29 residues processed: 355 average time/residue: 0.6101 time to fit residues: 296.0446 Evaluate side-chains 366 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 333 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 1065 SER Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1147 ILE Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1263 GLU Chi-restraints excluded: chain B residue 1301 SER Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1406 HIS Chi-restraints excluded: chain C residue 1465 ARG Chi-restraints excluded: chain C residue 1466 VAL Chi-restraints excluded: chain C residue 1536 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN B1092 GLN B1129 GLN ** B1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11858 Z= 0.274 Angle : 0.580 6.015 16097 Z= 0.304 Chirality : 0.043 0.252 1835 Planarity : 0.005 0.058 2077 Dihedral : 5.230 57.469 1715 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.10 % Allowed : 16.76 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -1.51 (0.21), residues: 1473 helix: 0.12 (0.32), residues: 264 sheet: -1.11 (0.22), residues: 516 loop : -1.26 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 32 HIS 0.009 0.001 HIS C1495 PHE 0.019 0.002 PHE A 74 TYR 0.015 0.002 TYR A 548 ARG 0.007 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 330 time to evaluate : 1.861 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: A 44 GLN cc_start: 0.7267 (pp30) cc_final: 0.6803 (pp30) REVERT: A 53 LYS cc_start: 0.8040 (ptpp) cc_final: 0.7758 (ptpt) REVERT: A 188 LYS cc_start: 0.8031 (ttmt) cc_final: 0.7635 (ttmm) REVERT: A 234 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7582 (ptmt) REVERT: A 404 LYS cc_start: 0.7901 (mttp) cc_final: 0.7589 (mtmt) REVERT: A 523 LYS cc_start: 0.7797 (ttpt) cc_final: 0.7357 (ttpp) REVERT: A 558 LEU cc_start: 0.8676 (tp) cc_final: 0.8388 (tp) REVERT: A 660 TRP cc_start: 0.7849 (p-90) cc_final: 0.6300 (p90) REVERT: B 1015 MET cc_start: 0.7458 (mmm) cc_final: 0.6889 (mmm) REVERT: B 1016 ILE cc_start: 0.7729 (mm) cc_final: 0.7246 (tp) REVERT: B 1084 LYS cc_start: 0.8576 (ttmt) cc_final: 0.8249 (ttpp) REVERT: B 1169 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7956 (mm-30) REVERT: B 1263 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.5834 (tt0) REVERT: B 1288 TRP cc_start: 0.7648 (t60) cc_final: 0.7374 (t-100) REVERT: B 1310 ASP cc_start: 0.7534 (t0) cc_final: 0.7281 (t0) REVERT: B 1389 MET cc_start: 0.5828 (pmm) cc_final: 0.5502 (pmm) REVERT: D 6 GLU cc_start: 0.6769 (tp30) cc_final: 0.6479 (tp30) REVERT: D 41 ARG cc_start: 0.6759 (ptp-170) cc_final: 0.6525 (ptp-170) outliers start: 39 outliers final: 30 residues processed: 347 average time/residue: 0.6300 time to fit residues: 296.7305 Evaluate side-chains 368 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 335 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 1065 SER Chi-restraints excluded: chain B residue 1147 ILE Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1263 GLU Chi-restraints excluded: chain B residue 1301 SER Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1406 HIS Chi-restraints excluded: chain C residue 1465 ARG Chi-restraints excluded: chain C residue 1466 VAL Chi-restraints excluded: chain C residue 1536 VAL Chi-restraints excluded: chain C residue 1566 CYS Chi-restraints excluded: chain D residue 53 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN B1129 GLN ** B1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 11858 Z= 0.551 Angle : 0.720 8.262 16097 Z= 0.387 Chirality : 0.048 0.265 1835 Planarity : 0.006 0.063 2077 Dihedral : 5.763 54.178 1715 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 3.73 % Allowed : 16.68 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.21), residues: 1473 helix: -0.55 (0.31), residues: 264 sheet: -1.22 (0.23), residues: 507 loop : -1.69 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 782 HIS 0.010 0.002 HIS C1495 PHE 0.048 0.003 PHE D 33 TYR 0.023 0.003 TYR D 29 ARG 0.007 0.001 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 345 time to evaluate : 1.747 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: A 44 GLN cc_start: 0.7256 (pp30) cc_final: 0.6802 (pp30) REVERT: A 53 LYS cc_start: 0.8112 (ptpp) cc_final: 0.7844 (ptpt) REVERT: A 166 LYS cc_start: 0.7937 (mtmm) cc_final: 0.7616 (mtmm) REVERT: A 234 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7501 (ptmt) REVERT: A 318 GLU cc_start: 0.6830 (tm-30) cc_final: 0.6581 (tp30) REVERT: A 346 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6689 (tm-30) REVERT: A 378 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7882 (pt) REVERT: A 404 LYS cc_start: 0.7947 (mttp) cc_final: 0.7676 (mtmt) REVERT: A 489 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8009 (pp) REVERT: A 523 LYS cc_start: 0.7871 (ttpt) cc_final: 0.7428 (ttpp) REVERT: A 558 LEU cc_start: 0.8668 (tp) cc_final: 0.8383 (tp) REVERT: A 568 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: A 660 TRP cc_start: 0.7905 (p-90) cc_final: 0.6307 (p90) REVERT: B 793 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6619 (pm20) REVERT: B 1015 MET cc_start: 0.7542 (mmm) cc_final: 0.6951 (mmm) REVERT: B 1166 GLN cc_start: 0.7883 (tp40) cc_final: 0.7185 (tp40) REVERT: B 1169 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7921 (mm-30) REVERT: B 1263 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6100 (tt0) REVERT: B 1288 TRP cc_start: 0.7965 (t60) cc_final: 0.7671 (t-100) REVERT: B 1389 MET cc_start: 0.6006 (pmm) cc_final: 0.5699 (pmm) REVERT: D 6 GLU cc_start: 0.6836 (tp30) cc_final: 0.6533 (tp30) outliers start: 47 outliers final: 37 residues processed: 365 average time/residue: 0.6157 time to fit residues: 305.9904 Evaluate side-chains 384 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 340 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 793 GLN Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 860 ASP Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 967 ASN Chi-restraints excluded: chain B residue 1065 SER Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1147 ILE Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1263 GLU Chi-restraints excluded: chain B residue 1273 LEU Chi-restraints excluded: chain B residue 1301 SER Chi-restraints excluded: chain B residue 1329 VAL Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1406 HIS Chi-restraints excluded: chain C residue 1466 VAL Chi-restraints excluded: chain C residue 1490 LEU Chi-restraints excluded: chain C residue 1536 VAL Chi-restraints excluded: chain C residue 1566 CYS Chi-restraints excluded: chain D residue 53 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 80 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 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 659 GLN B1129 GLN ** B1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11858 Z= 0.258 Angle : 0.611 6.878 16097 Z= 0.319 Chirality : 0.044 0.240 1835 Planarity : 0.005 0.059 2077 Dihedral : 5.418 56.063 1715 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.18 % Allowed : 18.35 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -1.73 (0.21), residues: 1473 helix: -0.11 (0.31), residues: 264 sheet: -1.17 (0.22), residues: 523 loop : -1.43 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 110 HIS 0.008 0.001 HIS C1495 PHE 0.028 0.002 PHE D 33 TYR 0.013 0.002 TYR D 29 ARG 0.013 0.001 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 337 time to evaluate : 1.745 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 REVERT: A 44 GLN cc_start: 0.7203 (pp30) cc_final: 0.6761 (pp30) REVERT: A 53 LYS cc_start: 0.8036 (ptpp) cc_final: 0.7762 (ptpt) REVERT: A 234 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7442 (ptmt) REVERT: A 262 MET cc_start: 0.6077 (mtm) cc_final: 0.5850 (mtm) REVERT: A 378 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7668 (pt) REVERT: A 404 LYS cc_start: 0.7901 (mttp) cc_final: 0.7624 (mtmt) REVERT: A 489 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7962 (pp) REVERT: A 523 LYS cc_start: 0.7841 (ttpt) cc_final: 0.7390 (ttpp) REVERT: A 660 TRP cc_start: 0.7880 (p-90) cc_final: 0.6331 (p90) REVERT: B 865 VAL cc_start: 0.7555 (t) cc_final: 0.7187 (m) REVERT: B 1015 MET cc_start: 0.7446 (mmm) cc_final: 0.7047 (mmm) REVERT: B 1166 GLN cc_start: 0.7841 (tp40) cc_final: 0.7132 (tp40) REVERT: B 1169 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8020 (mm-30) REVERT: B 1263 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.5723 (tt0) REVERT: B 1288 TRP cc_start: 0.7769 (t60) cc_final: 0.7468 (t-100) REVERT: B 1389 MET cc_start: 0.5941 (pmm) cc_final: 0.5581 (pmm) REVERT: D 6 GLU cc_start: 0.6778 (tp30) cc_final: 0.6544 (tp30) outliers start: 40 outliers final: 32 residues processed: 354 average time/residue: 0.6028 time to fit residues: 291.8723 Evaluate side-chains 371 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 334 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 860 ASP Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 1065 SER Chi-restraints excluded: chain B residue 1147 ILE Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1263 GLU Chi-restraints excluded: chain B residue 1301 SER Chi-restraints excluded: chain B residue 1329 VAL Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1406 HIS Chi-restraints excluded: chain C residue 1466 VAL Chi-restraints excluded: chain C residue 1536 VAL Chi-restraints excluded: chain C residue 1566 CYS Chi-restraints excluded: chain D residue 53 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN ** B1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11858 Z= 0.283 Angle : 0.608 7.459 16097 Z= 0.317 Chirality : 0.044 0.238 1835 Planarity : 0.005 0.053 2077 Dihedral : 5.331 57.370 1715 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.18 % Allowed : 18.67 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -1.63 (0.21), residues: 1473 helix: -0.02 (0.31), residues: 265 sheet: -1.12 (0.23), residues: 510 loop : -1.38 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 110 HIS 0.008 0.001 HIS C1495 PHE 0.023 0.002 PHE D 33 TYR 0.014 0.002 TYR A 507 ARG 0.008 0.001 ARG A 582 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 340 time to evaluate : 1.746 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 REVERT: A 44 GLN cc_start: 0.7197 (pp30) cc_final: 0.6717 (pp30) REVERT: A 53 LYS cc_start: 0.8043 (ptpp) cc_final: 0.7765 (ptpt) REVERT: A 234 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7432 (ptmt) REVERT: A 314 LEU cc_start: 0.7827 (mp) cc_final: 0.7624 (mm) REVERT: A 378 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7762 (pt) REVERT: A 404 LYS cc_start: 0.7915 (mttp) cc_final: 0.7609 (mtmt) REVERT: A 489 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7987 (pp) REVERT: A 523 LYS cc_start: 0.7799 (ttpt) cc_final: 0.7430 (ttpp) REVERT: A 660 TRP cc_start: 0.7881 (p-90) cc_final: 0.6319 (p90) REVERT: B 865 VAL cc_start: 0.7527 (t) cc_final: 0.7171 (m) REVERT: B 1015 MET cc_start: 0.7462 (mmm) cc_final: 0.7065 (mmm) REVERT: B 1088 LEU cc_start: 0.7897 (tp) cc_final: 0.7597 (tt) REVERT: B 1169 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8033 (mm-30) REVERT: B 1263 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5741 (tt0) REVERT: B 1288 TRP cc_start: 0.7692 (t60) cc_final: 0.7425 (t-100) REVERT: B 1389 MET cc_start: 0.5952 (pmm) cc_final: 0.5607 (pmm) REVERT: D 6 GLU cc_start: 0.6775 (tp30) cc_final: 0.6558 (tp30) REVERT: D 97 ARG cc_start: 0.7857 (ptp-110) cc_final: 0.7131 (ttm-80) outliers start: 40 outliers final: 33 residues processed: 360 average time/residue: 0.6071 time to fit residues: 299.0681 Evaluate side-chains 378 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 340 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 860 ASP Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 1065 SER Chi-restraints excluded: chain B residue 1147 ILE Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1263 GLU Chi-restraints excluded: chain B residue 1301 SER Chi-restraints excluded: chain B residue 1329 VAL Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1406 HIS Chi-restraints excluded: chain C residue 1466 VAL Chi-restraints excluded: chain C residue 1536 VAL Chi-restraints excluded: chain C residue 1566 CYS Chi-restraints excluded: chain C residue 1588 CYS Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 80 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN ** B1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.109336 restraints weight = 54749.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.114588 restraints weight = 21182.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.117815 restraints weight = 10804.376| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.336 11858 Z= 0.366 Angle : 0.853 59.190 16097 Z= 0.512 Chirality : 0.045 0.354 1835 Planarity : 0.005 0.070 2077 Dihedral : 5.351 57.367 1715 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.26 % Allowed : 19.06 % Favored : 77.68 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.75 % 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: -1.63 (0.21), residues: 1473 helix: -0.01 (0.31), residues: 265 sheet: -1.12 (0.23), residues: 510 loop : -1.38 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 110 HIS 0.007 0.001 HIS C1495 PHE 0.020 0.002 PHE D 33 TYR 0.014 0.001 TYR A 507 ARG 0.005 0.000 ARG A 582 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6335.21 seconds wall clock time: 111 minutes 48.77 seconds (6708.77 seconds total)