Starting phenix.real_space_refine on Tue Mar 19 04:09:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2m_11988/03_2024/7b2m_11988_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2m_11988/03_2024/7b2m_11988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2m_11988/03_2024/7b2m_11988.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2m_11988/03_2024/7b2m_11988.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2m_11988/03_2024/7b2m_11988_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2m_11988/03_2024/7b2m_11988_trim.pdb" } resolution = 3.39 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 41 5.16 5 C 7390 2.51 5 N 2016 2.21 5 O 2217 1.98 5 H 11534 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 138": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 159": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 168": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A ARG 269": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "A ARG 484": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B ARG 791": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 830": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 847": "OE1" <-> "OE2" Residue "B GLU 850": "OE1" <-> "OE2" Residue "B ASP 925": "OD1" <-> "OD2" Residue "B GLU 942": "OE1" <-> "OE2" Residue "B GLU 959": "OE1" <-> "OE2" Residue "B ARG 1055": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 1091": "OE1" <-> "OE2" Residue "B GLU 1098": "OE1" <-> "OE2" Residue "B GLU 1137": "OE1" <-> "OE2" Residue "B GLU 1223": "OE1" <-> "OE2" Residue "B ARG 1291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 1324": "OE1" <-> "OE2" Residue "B GLU 1408": "OE1" <-> "OE2" Residue "C ARG 1465": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 1474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 1498": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 1516": "OE1" <-> "OE2" Residue "C ASP 1527": "OD1" <-> "OD2" Residue "C ARG 1533": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 1543": "OE1" <-> "OE2" Residue "C ARG 1577": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 1592": "OE1" <-> "OE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 99": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23198 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 10023 Classifications: {'peptide': 650} Link IDs: {'PCIS': 3, 'PTRANS': 41, 'TRANS': 605} Chain: "B" Number of atoms: 9444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 9444 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 27, 'TRANS': 586} Chain breaks: 4 Chain: "C" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1984 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "D" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1691 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.46, per 1000 atoms: 0.45 Number of scatterers: 23198 At special positions: 0 Unit cell: (167.645, 120.334, 109.021, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 O 2217 8.00 N 2016 7.00 C 7390 6.00 H 11534 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS B 820 " distance=2.03 Simple disulfide: pdb=" SG CYS A 635 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 876 " - pdb=" SG CYS C1590 " distance=2.03 Simple disulfide: pdb=" SG CYS B1394 " - pdb=" SG CYS C1566 " distance=2.03 Simple disulfide: pdb=" SG CYS C1471 " - pdb=" SG CYS C1535 " distance=2.04 Simple disulfide: pdb=" SG CYS C1583 " - pdb=" SG CYS C1588 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1801 " - " ASN A 226 " " NAG B1801 " - " ASN B 862 " " NAG B1802 " - " ASN B1328 " " NAG B1803 " - " ASN B1391 " Time building additional restraints: 16.91 Conformation dependent library (CDL) restraints added in 1.9 seconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2774 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 30 sheets defined 19.3% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 114 through 120 removed outlier: 4.346A pdb=" N LYS A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 327 Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 642 through 651 Processing helix chain 'B' and resid 996 through 1003 removed outlier: 3.576A pdb=" N VAL B1000 " --> pdb=" O SER B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1032 Proline residue: B1020 - end of helix Processing helix chain 'B' and resid 1038 through 1058 removed outlier: 3.980A pdb=" N LYS B1042 " --> pdb=" O PRO B1038 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP B1043 " --> pdb=" O PRO B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1090 Processing helix chain 'B' and resid 1096 through 1111 removed outlier: 3.938A pdb=" N LEU B1100 " --> pdb=" O SER B1096 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B1110 " --> pdb=" O TRP B1106 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN B1111 " --> pdb=" O LEU B1107 " (cutoff:3.500A) Processing helix chain 'B' and resid 1126 through 1130 removed outlier: 3.819A pdb=" N GLY B1130 " --> pdb=" O SER B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1152 Processing helix chain 'B' and resid 1161 through 1185 removed outlier: 3.702A pdb=" N LYS B1165 " --> pdb=" O ALA B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1203 Processing helix chain 'B' and resid 1206 through 1221 Processing helix chain 'B' and resid 1258 through 1275 Processing helix chain 'B' and resid 1281 through 1294 removed outlier: 3.667A pdb=" N TRP B1288 " --> pdb=" O GLN B1284 " (cutoff:3.500A) Processing helix chain 'B' and resid 1302 through 1320 Processing helix chain 'C' and resid 1497 through 1507 removed outlier: 4.006A pdb=" N LEU C1504 " --> pdb=" O ASP C1500 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR C1505 " --> pdb=" O LEU C1501 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C1506 " --> pdb=" O GLU C1502 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C1507 " --> pdb=" O LYS C1503 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.581A pdb=" N LYS D 64 " --> pdb=" O ASN D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.935A pdb=" N THR D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 87 removed outlier: 7.455A pdb=" N SER A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 3.689A pdb=" N ASN A 60 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 66 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 32 Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 145 Processing sheet with id=AA5, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA6, first strand: chain 'A' and resid 185 through 192 removed outlier: 6.060A pdb=" N VAL A 178 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS A 188 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 176 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU A 190 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 174 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 241 through 247 removed outlier: 4.054A pdb=" N MET A 262 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 251 through 253 removed outlier: 5.374A pdb=" N ILE A 252 " --> pdb=" O VAL A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 293 through 295 Processing sheet with id=AB1, first strand: chain 'A' and resid 293 through 295 removed outlier: 4.495A pdb=" N TYR A 281 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 355 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.562A pdb=" N ARG A 391 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 419 through 423 removed outlier: 3.892A pdb=" N GLU A 443 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 450 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 472 through 476 removed outlier: 4.156A pdb=" N THR A 527 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 515 through 522 removed outlier: 3.605A pdb=" N PHE A 517 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 510 " --> pdb=" O TYR A 542 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 545 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS A 552 " --> pdb=" O HIS A 549 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 515 through 522 removed outlier: 3.605A pdb=" N PHE A 517 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 510 " --> pdb=" O TYR A 542 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 572 through 574 removed outlier: 3.539A pdb=" N GLU A 592 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 814 " --> pdb=" O GLY B 818 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 785 through 798 removed outlier: 3.951A pdb=" N ARG B 791 " --> pdb=" O SER A 595 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N SER A 595 " --> pdb=" O ARG B 791 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLN B 793 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N THR A 593 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU B 795 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU A 591 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU B 797 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU A 589 " --> pdb=" O LEU B 797 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 774 through 775 removed outlier: 6.996A pdb=" N VAL B 843 " --> pdb=" O GLU B 934 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 774 through 775 removed outlier: 3.546A pdb=" N VAL B 909 " --> pdb=" O LEU B 931 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 867 " --> pdb=" O GLN B 885 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 833 through 836 Processing sheet with id=AC3, first strand: chain 'B' and resid 849 through 851 removed outlier: 3.712A pdb=" N VAL B 902 " --> pdb=" O CYS B 876 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS B 876 " --> pdb=" O VAL B 902 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 938 through 945 Processing sheet with id=AC5, first strand: chain 'B' and resid 959 through 960 Processing sheet with id=AC6, first strand: chain 'B' and resid 1397 through 1405 Processing sheet with id=AC7, first strand: chain 'B' and resid 1397 through 1405 removed outlier: 3.574A pdb=" N VAL C1536 " --> pdb=" O VAL C1470 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1512 through 1518 removed outlier: 3.744A pdb=" N HIS C1514 " --> pdb=" O TYR C1525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1581 through 1583 Processing sheet with id=AD1, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.561A pdb=" N THR D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 57 through 59 removed outlier: 3.528A pdb=" N VAL D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N SER D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 57 through 59 removed outlier: 3.528A pdb=" N VAL D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N SER D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 91 " --> pdb=" O VAL D 112 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.80 Time building geometry restraints manager: 17.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 11532 1.04 - 1.23: 771 1.23 - 1.43: 4229 1.43 - 1.63: 6851 1.63 - 1.83: 64 Bond restraints: 23447 Sorted by residual: bond pdb=" C1 NAG B1801 " pdb=" O5 NAG B1801 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.40e+00 bond pdb=" C1 NAG B1803 " pdb=" O5 NAG B1803 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.31e+00 bond pdb=" C5 NAG B1801 " pdb=" O5 NAG B1801 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.25e+00 bond pdb=" C5 NAG B1803 " pdb=" O5 NAG B1803 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" C5 NAG A1801 " pdb=" O5 NAG A1801 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.10e+00 ... (remaining 23442 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.15: 322 106.15 - 113.12: 27640 113.12 - 120.10: 6906 120.10 - 127.07: 7357 127.07 - 134.05: 156 Bond angle restraints: 42381 Sorted by residual: angle pdb=" N CYS C1535 " pdb=" CA CYS C1535 " pdb=" C CYS C1535 " ideal model delta sigma weight residual 108.14 111.38 -3.24 1.52e+00 4.33e-01 4.56e+00 angle pdb=" C GLU C1534 " pdb=" N CYS C1535 " pdb=" CA CYS C1535 " ideal model delta sigma weight residual 122.09 118.48 3.61 1.86e+00 2.89e-01 3.77e+00 angle pdb=" CA PRO C1530 " pdb=" C PRO C1530 " pdb=" N THR C1531 " ideal model delta sigma weight residual 114.74 116.71 -1.97 1.03e+00 9.43e-01 3.65e+00 angle pdb=" N SER A 613 " pdb=" CA SER A 613 " pdb=" C SER A 613 " ideal model delta sigma weight residual 108.14 111.01 -2.87 1.52e+00 4.33e-01 3.57e+00 angle pdb=" N ARG A 494 " pdb=" CA ARG A 494 " pdb=" C ARG A 494 " ideal model delta sigma weight residual 108.13 111.29 -3.16 1.72e+00 3.38e-01 3.37e+00 ... (remaining 42376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.32: 10256 20.32 - 40.64: 664 40.64 - 60.96: 199 60.96 - 81.27: 14 81.27 - 101.59: 13 Dihedral angle restraints: 11146 sinusoidal: 6130 harmonic: 5016 Sorted by residual: dihedral pdb=" CB CYS A 635 " pdb=" SG CYS A 635 " pdb=" SG CYS A 669 " pdb=" CB CYS A 669 " ideal model delta sinusoidal sigma weight residual 93.00 35.32 57.68 1 1.00e+01 1.00e-02 4.47e+01 dihedral pdb=" CB CYS A 567 " pdb=" SG CYS A 567 " pdb=" SG CYS B 820 " pdb=" CB CYS B 820 " ideal model delta sinusoidal sigma weight residual 93.00 37.73 55.27 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS C1471 " pdb=" SG CYS C1471 " pdb=" SG CYS C1535 " pdb=" CB CYS C1535 " ideal model delta sinusoidal sigma weight residual 93.00 39.27 53.73 1 1.00e+01 1.00e-02 3.92e+01 ... (remaining 11143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1645 0.069 - 0.138: 192 0.138 - 0.207: 3 0.207 - 0.276: 1 0.276 - 0.344: 1 Chirality restraints: 1842 Sorted by residual: chirality pdb=" C1 NAG B1803 " pdb=" ND2 ASN B1391 " pdb=" C2 NAG B1803 " pdb=" O5 NAG B1803 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C1 NAG B1802 " pdb=" ND2 ASN B1328 " pdb=" C2 NAG B1802 " pdb=" O5 NAG B1802 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE C1485 " pdb=" N ILE C1485 " pdb=" C ILE C1485 " pdb=" CB ILE C1485 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 ... (remaining 1839 not shown) Planarity restraints: 3512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1391 " -0.015 2.00e-02 2.50e+03 1.44e-02 2.57e+00 pdb=" CG ASN B1391 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN B1391 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B1391 " 0.017 2.00e-02 2.50e+03 pdb=" C1 NAG B1803 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 452 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO A 453 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 453 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 453 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 548 " 0.015 2.00e-02 2.50e+03 8.55e-03 2.19e+00 pdb=" CG TYR A 548 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 548 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 548 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 548 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 548 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 548 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 548 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TYR A 548 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR A 548 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TYR A 548 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR A 548 " 0.001 2.00e-02 2.50e+03 ... (remaining 3509 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1124 2.18 - 2.78: 46684 2.78 - 3.39: 62522 3.39 - 3.99: 83065 3.99 - 4.60: 127593 Nonbonded interactions: 320988 Sorted by model distance: nonbonded pdb=" O LEU A 23 " pdb="HE22 GLN A 128 " model vdw 1.574 1.850 nonbonded pdb=" O LYS A 53 " pdb=" HG SER A 114 " model vdw 1.599 1.850 nonbonded pdb=" OE1 GLU A 209 " pdb=" H GLU A 209 " model vdw 1.601 1.850 nonbonded pdb=" O SER B1065 " pdb=" HG1 THR B1079 " model vdw 1.613 1.850 nonbonded pdb="HE22 GLN B 848 " pdb=" HG SER B 900 " model vdw 1.613 2.100 ... (remaining 320983 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 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: 0.370 Extract box with map and model: 6.920 Check model and map are aligned: 0.380 Set scattering table: 0.250 Process input model: 72.270 Find NCS groups from input model: 0.480 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: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11913 Z= 0.208 Angle : 0.493 4.918 16176 Z= 0.264 Chirality : 0.043 0.344 1842 Planarity : 0.003 0.038 2090 Dihedral : 14.434 101.593 4410 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.22), residues: 1488 helix: 1.65 (0.34), residues: 243 sheet: -0.15 (0.24), residues: 508 loop : -0.59 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 360 HIS 0.003 0.001 HIS B1191 PHE 0.008 0.001 PHE A 296 TYR 0.024 0.001 TYR A 548 ARG 0.015 0.000 ARG C1564 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 1.716 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: A 55 SER cc_start: 0.7642 (p) cc_final: 0.7251 (m) REVERT: A 57 PHE cc_start: 0.8079 (p90) cc_final: 0.7810 (p90) REVERT: A 63 ARG cc_start: 0.6810 (tpp80) cc_final: 0.6511 (ttm110) REVERT: A 77 SER cc_start: 0.7722 (t) cc_final: 0.7460 (p) REVERT: A 82 PHE cc_start: 0.7108 (p90) cc_final: 0.6862 (p90) REVERT: A 116 TRP cc_start: 0.7744 (t60) cc_final: 0.7520 (t60) REVERT: A 125 THR cc_start: 0.7833 (t) cc_final: 0.7627 (p) REVERT: A 126 ASN cc_start: 0.8103 (p0) cc_final: 0.7877 (p0) REVERT: A 137 ARG cc_start: 0.7685 (ttt90) cc_final: 0.7439 (ttt-90) REVERT: A 138 ARG cc_start: 0.7907 (ptt90) cc_final: 0.7689 (ttp-110) REVERT: A 188 LYS cc_start: 0.7650 (tttp) cc_final: 0.7424 (ttmm) REVERT: A 234 LYS cc_start: 0.8013 (ttpp) cc_final: 0.7720 (ttpt) REVERT: A 251 TYR cc_start: 0.7948 (p90) cc_final: 0.7607 (p90) REVERT: A 269 ARG cc_start: 0.7446 (ttm-80) cc_final: 0.7238 (ttm-80) REVERT: A 270 TYR cc_start: 0.7775 (m-80) cc_final: 0.7298 (m-10) REVERT: A 346 GLU cc_start: 0.6855 (pt0) cc_final: 0.6539 (pt0) REVERT: A 353 GLU cc_start: 0.6824 (tp30) cc_final: 0.6606 (tp30) REVERT: A 364 SER cc_start: 0.8272 (p) cc_final: 0.7689 (t) REVERT: A 378 LEU cc_start: 0.7694 (pt) cc_final: 0.7475 (pp) REVERT: A 530 SER cc_start: 0.8359 (t) cc_final: 0.8139 (p) REVERT: A 534 ASP cc_start: 0.7421 (t0) cc_final: 0.7135 (m-30) REVERT: A 547 TYR cc_start: 0.8129 (p90) cc_final: 0.7913 (p90) REVERT: A 549 HIS cc_start: 0.7619 (t70) cc_final: 0.6613 (t-170) REVERT: A 570 LYS cc_start: 0.7347 (tmtt) cc_final: 0.7073 (tmtt) REVERT: A 656 ASP cc_start: 0.6843 (p0) cc_final: 0.6609 (p0) REVERT: B 809 HIS cc_start: 0.7127 (p-80) cc_final: 0.6805 (p-80) REVERT: B 811 LEU cc_start: 0.8247 (mt) cc_final: 0.7983 (mt) REVERT: B 858 TYR cc_start: 0.8450 (m-80) cc_final: 0.8145 (m-10) REVERT: B 930 VAL cc_start: 0.7970 (m) cc_final: 0.7733 (p) REVERT: B 1050 GLN cc_start: 0.7704 (tp40) cc_final: 0.7307 (tp40) REVERT: B 1053 TYR cc_start: 0.7653 (t80) cc_final: 0.7269 (t80) REVERT: B 1057 GLN cc_start: 0.7502 (tp40) cc_final: 0.7184 (mm-40) REVERT: B 1066 TYR cc_start: 0.7840 (m-80) cc_final: 0.7239 (m-80) REVERT: B 1084 LYS cc_start: 0.7667 (ttmt) cc_final: 0.7363 (tttt) REVERT: B 1101 GLN cc_start: 0.6697 (mt0) cc_final: 0.6494 (mt0) REVERT: B 1128 MET cc_start: 0.6844 (ptm) cc_final: 0.6639 (ptm) REVERT: B 1137 GLU cc_start: 0.6471 (mp0) cc_final: 0.5952 (mp0) REVERT: B 1165 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7920 (mttt) REVERT: B 1262 ILE cc_start: 0.8611 (tp) cc_final: 0.8342 (mt) REVERT: B 1267 TYR cc_start: 0.8397 (m-80) cc_final: 0.8004 (m-80) REVERT: B 1355 GLU cc_start: 0.7073 (mp0) cc_final: 0.6550 (mp0) REVERT: B 1360 PHE cc_start: 0.6790 (p90) cc_final: 0.6348 (p90) REVERT: D 81 GLN cc_start: 0.7680 (tt0) cc_final: 0.7465 (tt0) REVERT: D 102 ILE cc_start: 0.8298 (tt) cc_final: 0.7948 (tp) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.6138 time to fit residues: 318.9608 Evaluate side-chains 344 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 2.9990 chunk 113 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 GLN D 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11913 Z= 0.331 Angle : 0.601 7.560 16176 Z= 0.311 Chirality : 0.044 0.188 1842 Planarity : 0.005 0.047 2090 Dihedral : 6.574 58.459 1703 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.42 % Allowed : 9.15 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1488 helix: 1.33 (0.32), residues: 263 sheet: -0.17 (0.23), residues: 506 loop : -0.78 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 360 HIS 0.007 0.001 HIS B 834 PHE 0.018 0.002 PHE A 74 TYR 0.026 0.002 TYR A 548 ARG 0.006 0.000 ARG B 895 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 360 time to evaluate : 1.894 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: A 55 SER cc_start: 0.7682 (p) cc_final: 0.7296 (m) REVERT: A 57 PHE cc_start: 0.8063 (p90) cc_final: 0.7818 (p90) REVERT: A 63 ARG cc_start: 0.6875 (tpp80) cc_final: 0.6636 (ttm110) REVERT: A 116 TRP cc_start: 0.7558 (t60) cc_final: 0.7251 (t60) REVERT: A 119 ASP cc_start: 0.7091 (p0) cc_final: 0.6577 (p0) REVERT: A 125 THR cc_start: 0.7941 (t) cc_final: 0.7723 (p) REVERT: A 137 ARG cc_start: 0.7702 (ttt90) cc_final: 0.7468 (ttt-90) REVERT: A 188 LYS cc_start: 0.7677 (tttp) cc_final: 0.7442 (ttmm) REVERT: A 234 LYS cc_start: 0.7890 (ttpp) cc_final: 0.7645 (ttpt) REVERT: A 270 TYR cc_start: 0.7828 (m-80) cc_final: 0.7302 (m-10) REVERT: A 346 GLU cc_start: 0.6860 (pt0) cc_final: 0.6585 (pt0) REVERT: A 353 GLU cc_start: 0.6919 (tp30) cc_final: 0.6547 (mm-30) REVERT: A 364 SER cc_start: 0.8315 (p) cc_final: 0.7739 (t) REVERT: A 404 LYS cc_start: 0.8066 (mmmt) cc_final: 0.7708 (ttmm) REVERT: A 424 ASN cc_start: 0.7487 (t0) cc_final: 0.7118 (t0) REVERT: A 534 ASP cc_start: 0.7320 (t0) cc_final: 0.7044 (m-30) REVERT: A 648 GLN cc_start: 0.7324 (mm-40) cc_final: 0.7057 (mm110) REVERT: B 811 LEU cc_start: 0.8203 (mt) cc_final: 0.7985 (mt) REVERT: B 858 TYR cc_start: 0.8314 (m-80) cc_final: 0.8000 (m-10) REVERT: B 1013 GLN cc_start: 0.6649 (tt0) cc_final: 0.6415 (tp40) REVERT: B 1016 ILE cc_start: 0.7943 (mm) cc_final: 0.7679 (mm) REVERT: B 1030 LYS cc_start: 0.7961 (mttm) cc_final: 0.7752 (mttm) REVERT: B 1050 GLN cc_start: 0.7588 (tp40) cc_final: 0.7263 (tp-100) REVERT: B 1063 ASP cc_start: 0.6734 (t0) cc_final: 0.6333 (t0) REVERT: B 1066 TYR cc_start: 0.7964 (m-80) cc_final: 0.7349 (m-80) REVERT: B 1101 GLN cc_start: 0.6629 (mt0) cc_final: 0.6422 (mt0) REVERT: B 1102 GLU cc_start: 0.7556 (tt0) cc_final: 0.7332 (mt-10) REVERT: B 1137 GLU cc_start: 0.6436 (mp0) cc_final: 0.5890 (mp0) REVERT: B 1267 TYR cc_start: 0.8372 (m-80) cc_final: 0.8143 (m-80) REVERT: B 1313 SER cc_start: 0.7366 (t) cc_final: 0.6816 (p) REVERT: B 1355 GLU cc_start: 0.7022 (mp0) cc_final: 0.6429 (mp0) REVERT: B 1357 GLU cc_start: 0.6967 (tt0) cc_final: 0.6716 (tt0) REVERT: B 1360 PHE cc_start: 0.6937 (p90) cc_final: 0.6674 (p90) REVERT: C 1483 MET cc_start: 0.6438 (ptp) cc_final: 0.5775 (ptp) REVERT: C 1505 THR cc_start: 0.7208 (p) cc_final: 0.7004 (p) REVERT: C 1575 LYS cc_start: 0.7722 (mmtm) cc_final: 0.7494 (mmtp) REVERT: D 81 GLN cc_start: 0.7813 (tt0) cc_final: 0.7517 (tt0) outliers start: 18 outliers final: 13 residues processed: 364 average time/residue: 0.6559 time to fit residues: 324.0552 Evaluate side-chains 356 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 343 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 967 ASN Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain D residue 60 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.1980 chunk 42 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 147 optimal weight: 0.3980 chunk 121 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11913 Z= 0.224 Angle : 0.541 6.243 16176 Z= 0.279 Chirality : 0.043 0.194 1842 Planarity : 0.004 0.048 2090 Dihedral : 5.438 57.210 1703 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.89 % Allowed : 12.54 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.22), residues: 1488 helix: 1.58 (0.32), residues: 264 sheet: -0.08 (0.23), residues: 512 loop : -0.78 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 360 HIS 0.024 0.001 HIS A 536 PHE 0.013 0.001 PHE D 29 TYR 0.017 0.001 TYR A 548 ARG 0.004 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 352 time to evaluate : 1.775 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: A 45 ASP cc_start: 0.6568 (t0) cc_final: 0.6336 (t70) REVERT: A 55 SER cc_start: 0.7688 (p) cc_final: 0.7291 (m) REVERT: A 57 PHE cc_start: 0.8079 (p90) cc_final: 0.7565 (p90) REVERT: A 63 ARG cc_start: 0.6868 (tpp80) cc_final: 0.6623 (ttm110) REVERT: A 116 TRP cc_start: 0.7510 (t60) cc_final: 0.7195 (t60) REVERT: A 119 ASP cc_start: 0.7137 (p0) cc_final: 0.6581 (p0) REVERT: A 125 THR cc_start: 0.7986 (t) cc_final: 0.7708 (p) REVERT: A 137 ARG cc_start: 0.7746 (ttt90) cc_final: 0.7484 (ttt-90) REVERT: A 188 LYS cc_start: 0.7715 (tttp) cc_final: 0.7501 (ttmm) REVERT: A 234 LYS cc_start: 0.7916 (ttpp) cc_final: 0.7667 (ttpt) REVERT: A 270 TYR cc_start: 0.7834 (m-80) cc_final: 0.7305 (m-10) REVERT: A 346 GLU cc_start: 0.6914 (pt0) cc_final: 0.6683 (pt0) REVERT: A 353 GLU cc_start: 0.6928 (tp30) cc_final: 0.6672 (tp30) REVERT: A 364 SER cc_start: 0.8326 (p) cc_final: 0.7770 (t) REVERT: A 404 LYS cc_start: 0.8061 (mmmt) cc_final: 0.7749 (ttpp) REVERT: A 424 ASN cc_start: 0.7501 (t0) cc_final: 0.7209 (t0) REVERT: A 648 GLN cc_start: 0.7296 (mm-40) cc_final: 0.7012 (mm110) REVERT: B 811 LEU cc_start: 0.8163 (mt) cc_final: 0.7933 (mt) REVERT: B 847 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6750 (mt-10) REVERT: B 852 ARG cc_start: 0.7687 (ttp-170) cc_final: 0.7470 (ttm110) REVERT: B 858 TYR cc_start: 0.8320 (m-80) cc_final: 0.8016 (m-10) REVERT: B 1013 GLN cc_start: 0.6617 (tt0) cc_final: 0.6370 (tp40) REVERT: B 1016 ILE cc_start: 0.7960 (mm) cc_final: 0.7748 (mm) REVERT: B 1050 GLN cc_start: 0.7582 (tp40) cc_final: 0.7253 (tp-100) REVERT: B 1063 ASP cc_start: 0.6746 (t0) cc_final: 0.6521 (t0) REVERT: B 1066 TYR cc_start: 0.7880 (m-80) cc_final: 0.7410 (m-80) REVERT: B 1102 GLU cc_start: 0.7489 (tt0) cc_final: 0.7144 (mt-10) REVERT: B 1137 GLU cc_start: 0.6438 (mp0) cc_final: 0.6194 (mp0) REVERT: B 1313 SER cc_start: 0.7344 (t) cc_final: 0.6784 (p) REVERT: B 1355 GLU cc_start: 0.6925 (mp0) cc_final: 0.6376 (mp0) REVERT: B 1357 GLU cc_start: 0.6970 (tt0) cc_final: 0.6677 (tt0) REVERT: C 1483 MET cc_start: 0.6296 (ptp) cc_final: 0.5760 (ptp) REVERT: C 1505 THR cc_start: 0.7174 (p) cc_final: 0.6945 (p) REVERT: C 1575 LYS cc_start: 0.7711 (mmtm) cc_final: 0.7442 (mmtp) REVERT: D 81 GLN cc_start: 0.7768 (tt0) cc_final: 0.7518 (tt0) REVERT: D 102 ILE cc_start: 0.8250 (tp) cc_final: 0.7852 (tp) outliers start: 24 outliers final: 19 residues processed: 357 average time/residue: 0.6302 time to fit residues: 305.5863 Evaluate side-chains 364 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 345 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 967 ASN Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain B residue 1330 THR Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain C residue 1553 SER Chi-restraints excluded: chain C residue 1578 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11913 Z= 0.281 Angle : 0.542 5.393 16176 Z= 0.280 Chirality : 0.043 0.168 1842 Planarity : 0.004 0.046 2090 Dihedral : 5.224 55.722 1703 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.37 % Allowed : 13.88 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.22), residues: 1488 helix: 1.61 (0.32), residues: 264 sheet: -0.33 (0.23), residues: 537 loop : -0.89 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 360 HIS 0.006 0.001 HIS B1150 PHE 0.016 0.002 PHE A 74 TYR 0.013 0.001 TYR A 507 ARG 0.005 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 353 time to evaluate : 1.753 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: A 45 ASP cc_start: 0.6591 (t0) cc_final: 0.6384 (t70) REVERT: A 55 SER cc_start: 0.7748 (p) cc_final: 0.7356 (m) REVERT: A 63 ARG cc_start: 0.6888 (tpp80) cc_final: 0.6680 (ttm110) REVERT: A 116 TRP cc_start: 0.7549 (t60) cc_final: 0.7206 (t60) REVERT: A 119 ASP cc_start: 0.7196 (p0) cc_final: 0.6722 (p0) REVERT: A 125 THR cc_start: 0.7948 (t) cc_final: 0.7692 (p) REVERT: A 137 ARG cc_start: 0.7745 (ttt90) cc_final: 0.7536 (ttt90) REVERT: A 188 LYS cc_start: 0.7727 (tttp) cc_final: 0.7518 (ttmm) REVERT: A 234 LYS cc_start: 0.7911 (ttpp) cc_final: 0.7702 (ttpt) REVERT: A 270 TYR cc_start: 0.7904 (m-80) cc_final: 0.7377 (m-10) REVERT: A 346 GLU cc_start: 0.6941 (pt0) cc_final: 0.6685 (pt0) REVERT: A 353 GLU cc_start: 0.6941 (tp30) cc_final: 0.6708 (tp30) REVERT: A 364 SER cc_start: 0.8319 (p) cc_final: 0.7771 (t) REVERT: A 404 LYS cc_start: 0.8050 (mmmt) cc_final: 0.7770 (ttpp) REVERT: A 424 ASN cc_start: 0.7541 (t0) cc_final: 0.7236 (t0) REVERT: B 858 TYR cc_start: 0.8317 (m-80) cc_final: 0.8005 (m-10) REVERT: B 1013 GLN cc_start: 0.6647 (tt0) cc_final: 0.6398 (tp40) REVERT: B 1050 GLN cc_start: 0.7572 (tp40) cc_final: 0.7221 (tp-100) REVERT: B 1066 TYR cc_start: 0.7954 (m-80) cc_final: 0.7516 (m-80) REVERT: B 1102 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7079 (mt-10) REVERT: B 1137 GLU cc_start: 0.6468 (mp0) cc_final: 0.6056 (mp0) REVERT: B 1313 SER cc_start: 0.7329 (t) cc_final: 0.6756 (p) REVERT: B 1355 GLU cc_start: 0.6961 (mp0) cc_final: 0.6375 (mp0) REVERT: B 1357 GLU cc_start: 0.6969 (tt0) cc_final: 0.6627 (tt0) REVERT: B 1389 MET cc_start: 0.5740 (OUTLIER) cc_final: 0.5376 (ptt) REVERT: C 1483 MET cc_start: 0.6365 (ptp) cc_final: 0.5859 (ptp) REVERT: C 1575 LYS cc_start: 0.7725 (mmtm) cc_final: 0.7453 (mmtp) REVERT: D 56 ASN cc_start: 0.7901 (m-40) cc_final: 0.7544 (m110) REVERT: D 81 GLN cc_start: 0.7745 (tt0) cc_final: 0.7490 (tt0) REVERT: D 102 ILE cc_start: 0.8264 (tp) cc_final: 0.7819 (tp) outliers start: 30 outliers final: 21 residues processed: 361 average time/residue: 0.6405 time to fit residues: 313.7106 Evaluate side-chains 367 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 344 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 967 ASN Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1330 THR Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain C residue 1553 SER Chi-restraints excluded: chain D residue 60 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 0 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1129 GLN B1359 GLN D 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 11913 Z= 0.515 Angle : 0.646 7.104 16176 Z= 0.341 Chirality : 0.046 0.212 1842 Planarity : 0.005 0.055 2090 Dihedral : 5.690 53.746 1703 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.00 % Allowed : 14.91 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.21), residues: 1488 helix: 0.93 (0.31), residues: 264 sheet: -0.67 (0.22), residues: 533 loop : -1.23 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 360 HIS 0.010 0.002 HIS B 834 PHE 0.027 0.003 PHE A 74 TYR 0.022 0.002 TYR A 158 ARG 0.006 0.001 ARG A 664 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 368 time to evaluate : 1.943 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: A 26 PHE cc_start: 0.8001 (m-80) cc_final: 0.7738 (m-80) REVERT: A 55 SER cc_start: 0.7826 (p) cc_final: 0.7343 (m) REVERT: A 77 SER cc_start: 0.7978 (t) cc_final: 0.7730 (p) REVERT: A 116 TRP cc_start: 0.7643 (t60) cc_final: 0.7294 (t60) REVERT: A 119 ASP cc_start: 0.7063 (p0) cc_final: 0.6468 (p0) REVERT: A 137 ARG cc_start: 0.7783 (ttt90) cc_final: 0.7554 (ttt90) REVERT: A 188 LYS cc_start: 0.7721 (tttp) cc_final: 0.7448 (ttmm) REVERT: A 234 LYS cc_start: 0.7887 (ttpp) cc_final: 0.7677 (ttpt) REVERT: A 252 ILE cc_start: 0.7761 (mm) cc_final: 0.7482 (mp) REVERT: A 270 TYR cc_start: 0.7928 (m-80) cc_final: 0.7663 (m-80) REVERT: A 346 GLU cc_start: 0.6994 (pt0) cc_final: 0.6776 (pt0) REVERT: A 364 SER cc_start: 0.8316 (p) cc_final: 0.7789 (t) REVERT: A 404 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7786 (ttpp) REVERT: A 424 ASN cc_start: 0.7632 (t0) cc_final: 0.7328 (t0) REVERT: A 534 ASP cc_start: 0.7346 (t0) cc_final: 0.6985 (m-30) REVERT: A 587 VAL cc_start: 0.8238 (p) cc_final: 0.7907 (m) REVERT: B 764 GLU cc_start: 0.5150 (mp0) cc_final: 0.4899 (mp0) REVERT: B 801 ASP cc_start: 0.7559 (m-30) cc_final: 0.7316 (m-30) REVERT: B 858 TYR cc_start: 0.8315 (m-80) cc_final: 0.7925 (m-10) REVERT: B 895 ARG cc_start: 0.7998 (mmt-90) cc_final: 0.7650 (mmt-90) REVERT: B 1013 GLN cc_start: 0.6714 (tt0) cc_final: 0.6475 (tp40) REVERT: B 1050 GLN cc_start: 0.7590 (tp40) cc_final: 0.7252 (tp40) REVERT: B 1102 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7139 (mt-10) REVERT: B 1275 HIS cc_start: 0.6996 (OUTLIER) cc_final: 0.6260 (t-90) REVERT: B 1291 ARG cc_start: 0.7293 (ttp80) cc_final: 0.6795 (ttp-110) REVERT: B 1313 SER cc_start: 0.7287 (t) cc_final: 0.7074 (t) REVERT: B 1355 GLU cc_start: 0.7123 (mp0) cc_final: 0.6661 (mp0) REVERT: B 1357 GLU cc_start: 0.7010 (tt0) cc_final: 0.6751 (tt0) REVERT: B 1360 PHE cc_start: 0.7072 (p90) cc_final: 0.6633 (p90) REVERT: B 1389 MET cc_start: 0.5780 (OUTLIER) cc_final: 0.5431 (ptt) REVERT: C 1483 MET cc_start: 0.6419 (ptp) cc_final: 0.6201 (ptp) REVERT: D 56 ASN cc_start: 0.7966 (m-40) cc_final: 0.7594 (m110) REVERT: D 81 GLN cc_start: 0.7758 (tt0) cc_final: 0.7456 (tt0) REVERT: D 102 ILE cc_start: 0.8287 (tp) cc_final: 0.7894 (tp) outliers start: 38 outliers final: 30 residues processed: 379 average time/residue: 0.6285 time to fit residues: 324.3228 Evaluate side-chains 397 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 364 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 967 ASN Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1275 HIS Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain B residue 1302 THR Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1330 THR Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1370 VAL Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain C residue 1497 LEU Chi-restraints excluded: chain C residue 1553 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 67 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11913 Z= 0.269 Angle : 0.558 7.731 16176 Z= 0.288 Chirality : 0.043 0.163 1842 Planarity : 0.004 0.054 2090 Dihedral : 5.333 49.806 1703 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.52 % Allowed : 16.56 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.22), residues: 1488 helix: 1.29 (0.32), residues: 265 sheet: -0.59 (0.23), residues: 523 loop : -1.07 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 360 HIS 0.005 0.001 HIS B1150 PHE 0.017 0.002 PHE A 74 TYR 0.012 0.002 TYR A 507 ARG 0.007 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 360 time to evaluate : 1.561 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: A 26 PHE cc_start: 0.8013 (m-80) cc_final: 0.7752 (m-80) REVERT: A 55 SER cc_start: 0.7824 (p) cc_final: 0.7346 (m) REVERT: A 77 SER cc_start: 0.8022 (t) cc_final: 0.7780 (p) REVERT: A 116 TRP cc_start: 0.7655 (t60) cc_final: 0.7297 (t60) REVERT: A 119 ASP cc_start: 0.7183 (p0) cc_final: 0.6707 (p0) REVERT: A 125 THR cc_start: 0.7912 (t) cc_final: 0.7669 (p) REVERT: A 137 ARG cc_start: 0.7732 (ttt90) cc_final: 0.7522 (ttt90) REVERT: A 188 LYS cc_start: 0.7715 (tttp) cc_final: 0.7471 (ttmm) REVERT: A 252 ILE cc_start: 0.7767 (mm) cc_final: 0.7506 (mp) REVERT: A 270 TYR cc_start: 0.7923 (m-80) cc_final: 0.7652 (m-80) REVERT: A 356 GLU cc_start: 0.6393 (mm-30) cc_final: 0.5943 (mm-30) REVERT: A 364 SER cc_start: 0.8293 (p) cc_final: 0.7775 (t) REVERT: A 404 LYS cc_start: 0.8087 (mmmt) cc_final: 0.7662 (ttmm) REVERT: A 424 ASN cc_start: 0.7517 (t0) cc_final: 0.7242 (t0) REVERT: A 587 VAL cc_start: 0.8243 (p) cc_final: 0.7946 (m) REVERT: B 764 GLU cc_start: 0.4981 (mp0) cc_final: 0.4663 (mp0) REVERT: B 848 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7370 (tp40) REVERT: B 858 TYR cc_start: 0.8279 (m-80) cc_final: 0.7952 (m-10) REVERT: B 895 ARG cc_start: 0.8002 (mmt-90) cc_final: 0.7565 (mmt-90) REVERT: B 944 LEU cc_start: 0.7843 (mt) cc_final: 0.7624 (mt) REVERT: B 1013 GLN cc_start: 0.6716 (tt0) cc_final: 0.6489 (tp40) REVERT: B 1050 GLN cc_start: 0.7509 (tp40) cc_final: 0.7142 (tp40) REVERT: B 1102 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7111 (mt-10) REVERT: B 1291 ARG cc_start: 0.7224 (ttp80) cc_final: 0.6810 (ttm110) REVERT: B 1313 SER cc_start: 0.7271 (t) cc_final: 0.7044 (t) REVERT: B 1355 GLU cc_start: 0.6955 (mp0) cc_final: 0.6537 (mp0) REVERT: B 1357 GLU cc_start: 0.6934 (tt0) cc_final: 0.6667 (tt0) REVERT: B 1360 PHE cc_start: 0.7001 (p90) cc_final: 0.6687 (p90) REVERT: B 1381 LEU cc_start: 0.7729 (pp) cc_final: 0.7514 (pp) REVERT: B 1389 MET cc_start: 0.5745 (OUTLIER) cc_final: 0.5413 (ptt) REVERT: B 1411 MET cc_start: 0.5101 (mmm) cc_final: 0.4893 (mmp) REVERT: D 56 ASN cc_start: 0.7948 (m-40) cc_final: 0.7557 (m110) REVERT: D 81 GLN cc_start: 0.7741 (tt0) cc_final: 0.7474 (tt0) REVERT: D 102 ILE cc_start: 0.8286 (tp) cc_final: 0.7887 (tp) outliers start: 32 outliers final: 24 residues processed: 373 average time/residue: 0.6148 time to fit residues: 311.4726 Evaluate side-chains 385 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 358 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 967 ASN Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1328 ASN Chi-restraints excluded: chain B residue 1330 THR Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain D residue 60 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11913 Z= 0.312 Angle : 0.565 6.410 16176 Z= 0.293 Chirality : 0.043 0.178 1842 Planarity : 0.005 0.046 2090 Dihedral : 5.219 49.610 1703 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.15 % Allowed : 16.48 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.22), residues: 1488 helix: 1.31 (0.32), residues: 265 sheet: -0.59 (0.23), residues: 529 loop : -1.16 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 360 HIS 0.006 0.001 HIS B 834 PHE 0.019 0.002 PHE A 74 TYR 0.021 0.002 TYR B1267 ARG 0.006 0.000 ARG B1072 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 359 time to evaluate : 1.814 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: A 26 PHE cc_start: 0.8005 (m-80) cc_final: 0.7747 (m-80) REVERT: A 55 SER cc_start: 0.7837 (p) cc_final: 0.7355 (m) REVERT: A 77 SER cc_start: 0.8038 (t) cc_final: 0.7797 (p) REVERT: A 116 TRP cc_start: 0.7665 (t60) cc_final: 0.7298 (t60) REVERT: A 119 ASP cc_start: 0.7173 (p0) cc_final: 0.6683 (p0) REVERT: A 137 ARG cc_start: 0.7738 (ttt90) cc_final: 0.7509 (ttt90) REVERT: A 188 LYS cc_start: 0.7702 (tttp) cc_final: 0.7459 (ttmm) REVERT: A 356 GLU cc_start: 0.6384 (mm-30) cc_final: 0.5897 (mm-30) REVERT: A 364 SER cc_start: 0.8285 (p) cc_final: 0.7784 (t) REVERT: A 404 LYS cc_start: 0.8085 (mmmt) cc_final: 0.7779 (ttpp) REVERT: A 424 ASN cc_start: 0.7528 (t0) cc_final: 0.7234 (t0) REVERT: A 430 GLN cc_start: 0.7044 (mt0) cc_final: 0.6758 (mt0) REVERT: A 587 VAL cc_start: 0.8273 (p) cc_final: 0.7945 (m) REVERT: B 764 GLU cc_start: 0.5070 (OUTLIER) cc_final: 0.4708 (mp0) REVERT: B 771 ASP cc_start: 0.7373 (t0) cc_final: 0.7097 (t70) REVERT: B 848 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7363 (tp40) REVERT: B 858 TYR cc_start: 0.8298 (m-80) cc_final: 0.8018 (m-10) REVERT: B 895 ARG cc_start: 0.8002 (mmt-90) cc_final: 0.7514 (mmt-90) REVERT: B 1013 GLN cc_start: 0.6734 (tt0) cc_final: 0.6509 (tp40) REVERT: B 1050 GLN cc_start: 0.7497 (tp40) cc_final: 0.7167 (tp40) REVERT: B 1102 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7127 (mt-10) REVERT: B 1181 GLU cc_start: 0.6801 (pm20) cc_final: 0.6572 (mp0) REVERT: B 1291 ARG cc_start: 0.7239 (ttp80) cc_final: 0.6723 (ttp-110) REVERT: B 1313 SER cc_start: 0.7268 (t) cc_final: 0.7054 (t) REVERT: B 1355 GLU cc_start: 0.6952 (mp0) cc_final: 0.6212 (mp0) REVERT: B 1357 GLU cc_start: 0.6957 (tt0) cc_final: 0.6672 (tt0) REVERT: B 1360 PHE cc_start: 0.6986 (p90) cc_final: 0.6708 (p90) REVERT: B 1381 LEU cc_start: 0.7737 (pp) cc_final: 0.7519 (pp) REVERT: B 1389 MET cc_start: 0.5713 (OUTLIER) cc_final: 0.5391 (ptt) REVERT: C 1483 MET cc_start: 0.6360 (ptp) cc_final: 0.5907 (ptp) REVERT: D 56 ASN cc_start: 0.7949 (m-40) cc_final: 0.7559 (m110) REVERT: D 81 GLN cc_start: 0.7737 (tt0) cc_final: 0.7467 (tt0) REVERT: D 102 ILE cc_start: 0.8293 (tp) cc_final: 0.7893 (tp) outliers start: 40 outliers final: 31 residues processed: 376 average time/residue: 0.6212 time to fit residues: 319.6398 Evaluate side-chains 394 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 359 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 967 ASN Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1128 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1328 ASN Chi-restraints excluded: chain B residue 1330 THR Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1370 VAL Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain C residue 1497 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 60 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 0.0980 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN ** B 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11913 Z= 0.263 Angle : 0.546 6.315 16176 Z= 0.281 Chirality : 0.043 0.162 1842 Planarity : 0.004 0.058 2090 Dihedral : 5.003 50.020 1703 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.08 % Allowed : 16.88 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1488 helix: 1.47 (0.32), residues: 265 sheet: -0.60 (0.22), residues: 532 loop : -1.08 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 360 HIS 0.005 0.001 HIS B 834 PHE 0.016 0.002 PHE A 74 TYR 0.012 0.001 TYR A 507 ARG 0.009 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 358 time to evaluate : 1.696 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: A 55 SER cc_start: 0.7835 (p) cc_final: 0.7344 (m) REVERT: A 63 ARG cc_start: 0.6932 (tpp80) cc_final: 0.6669 (ttm110) REVERT: A 77 SER cc_start: 0.8044 (t) cc_final: 0.7822 (p) REVERT: A 119 ASP cc_start: 0.7188 (p0) cc_final: 0.6680 (p0) REVERT: A 137 ARG cc_start: 0.7732 (ttt90) cc_final: 0.7504 (ttt90) REVERT: A 188 LYS cc_start: 0.7714 (tttp) cc_final: 0.7367 (ttmm) REVERT: A 356 GLU cc_start: 0.6410 (mm-30) cc_final: 0.5946 (mm-30) REVERT: A 364 SER cc_start: 0.8263 (p) cc_final: 0.7764 (t) REVERT: A 404 LYS cc_start: 0.8081 (mmmt) cc_final: 0.7790 (ttpp) REVERT: A 424 ASN cc_start: 0.7574 (t0) cc_final: 0.7246 (t0) REVERT: A 430 GLN cc_start: 0.6995 (mt0) cc_final: 0.6609 (mt0) REVERT: A 587 VAL cc_start: 0.8258 (p) cc_final: 0.7928 (m) REVERT: B 764 GLU cc_start: 0.4958 (OUTLIER) cc_final: 0.4618 (mp0) REVERT: B 771 ASP cc_start: 0.7383 (t0) cc_final: 0.7171 (t70) REVERT: B 848 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7367 (tp40) REVERT: B 858 TYR cc_start: 0.8261 (m-80) cc_final: 0.8030 (m-10) REVERT: B 895 ARG cc_start: 0.7993 (mmt-90) cc_final: 0.7467 (mmt-90) REVERT: B 1013 GLN cc_start: 0.6736 (tt0) cc_final: 0.6428 (tp40) REVERT: B 1050 GLN cc_start: 0.7498 (tp40) cc_final: 0.7086 (tm-30) REVERT: B 1072 ARG cc_start: 0.6451 (ttp80) cc_final: 0.5774 (ttp80) REVERT: B 1102 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7114 (mt-10) REVERT: B 1137 GLU cc_start: 0.6720 (mp0) cc_final: 0.6443 (mp0) REVERT: B 1291 ARG cc_start: 0.7216 (ttp80) cc_final: 0.6710 (ttp-110) REVERT: B 1313 SER cc_start: 0.7268 (t) cc_final: 0.7040 (t) REVERT: B 1355 GLU cc_start: 0.6909 (mp0) cc_final: 0.6084 (mp0) REVERT: B 1357 GLU cc_start: 0.6929 (tt0) cc_final: 0.6679 (tt0) REVERT: B 1360 PHE cc_start: 0.6952 (p90) cc_final: 0.6703 (p90) REVERT: B 1381 LEU cc_start: 0.7790 (pp) cc_final: 0.7512 (pp) REVERT: B 1389 MET cc_start: 0.5711 (OUTLIER) cc_final: 0.5389 (ptt) REVERT: D 56 ASN cc_start: 0.7950 (m-40) cc_final: 0.7562 (m110) REVERT: D 81 GLN cc_start: 0.7730 (tt0) cc_final: 0.7470 (tt0) REVERT: D 102 ILE cc_start: 0.8279 (tp) cc_final: 0.7890 (tp) outliers start: 39 outliers final: 31 residues processed: 373 average time/residue: 0.6513 time to fit residues: 334.6111 Evaluate side-chains 387 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 352 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 967 ASN Chi-restraints excluded: chain B residue 1030 LYS Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1173 SER Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1328 ASN Chi-restraints excluded: chain B residue 1330 THR Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1370 VAL Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain B residue 1410 THR Chi-restraints excluded: chain C residue 1466 VAL Chi-restraints excluded: chain C residue 1497 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 60 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 81 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 127 optimal weight: 0.0270 chunk 88 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11913 Z= 0.207 Angle : 0.539 7.878 16176 Z= 0.274 Chirality : 0.043 0.152 1842 Planarity : 0.004 0.050 2090 Dihedral : 4.768 50.111 1703 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.15 % Allowed : 16.72 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.22), residues: 1488 helix: 1.64 (0.32), residues: 264 sheet: -0.54 (0.23), residues: 521 loop : -0.97 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 784 HIS 0.003 0.001 HIS B 834 PHE 0.014 0.001 PHE A 74 TYR 0.010 0.001 TYR B1267 ARG 0.006 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 354 time to evaluate : 1.936 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: A 55 SER cc_start: 0.7833 (p) cc_final: 0.7359 (m) REVERT: A 77 SER cc_start: 0.8051 (t) cc_final: 0.7840 (p) REVERT: A 119 ASP cc_start: 0.7200 (p0) cc_final: 0.6682 (p0) REVERT: A 125 THR cc_start: 0.7913 (t) cc_final: 0.7657 (p) REVERT: A 137 ARG cc_start: 0.7745 (ttt90) cc_final: 0.7514 (ttt90) REVERT: A 188 LYS cc_start: 0.7705 (tttp) cc_final: 0.7478 (ttmm) REVERT: A 346 GLU cc_start: 0.6621 (pt0) cc_final: 0.6314 (pt0) REVERT: A 364 SER cc_start: 0.8242 (p) cc_final: 0.7769 (t) REVERT: A 404 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7780 (ttpp) REVERT: A 424 ASN cc_start: 0.7557 (t0) cc_final: 0.7225 (t0) REVERT: A 430 GLN cc_start: 0.6973 (mt0) cc_final: 0.6599 (mt0) REVERT: A 505 TYR cc_start: 0.7449 (m-80) cc_final: 0.6905 (m-10) REVERT: A 605 ASP cc_start: 0.6861 (t0) cc_final: 0.6554 (t70) REVERT: B 764 GLU cc_start: 0.4844 (OUTLIER) cc_final: 0.4483 (mm-30) REVERT: B 771 ASP cc_start: 0.7337 (t0) cc_final: 0.7029 (t70) REVERT: B 848 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7350 (tp40) REVERT: B 858 TYR cc_start: 0.8238 (m-80) cc_final: 0.7978 (m-10) REVERT: B 895 ARG cc_start: 0.7977 (mmt-90) cc_final: 0.7629 (mmt180) REVERT: B 943 GLU cc_start: 0.7212 (tp30) cc_final: 0.7011 (tp30) REVERT: B 1013 GLN cc_start: 0.6709 (tt0) cc_final: 0.6472 (tp40) REVERT: B 1050 GLN cc_start: 0.7503 (tp40) cc_final: 0.7062 (tm-30) REVERT: B 1072 ARG cc_start: 0.6493 (ttp80) cc_final: 0.5812 (ttp80) REVERT: B 1102 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7113 (mt-10) REVERT: B 1313 SER cc_start: 0.7268 (t) cc_final: 0.7056 (t) REVERT: B 1355 GLU cc_start: 0.6879 (mp0) cc_final: 0.6080 (mp0) REVERT: B 1357 GLU cc_start: 0.6896 (tt0) cc_final: 0.6625 (tt0) REVERT: B 1360 PHE cc_start: 0.6911 (p90) cc_final: 0.6658 (p90) REVERT: B 1381 LEU cc_start: 0.7824 (pp) cc_final: 0.7415 (pp) REVERT: B 1389 MET cc_start: 0.5692 (OUTLIER) cc_final: 0.5383 (ptt) REVERT: D 56 ASN cc_start: 0.7939 (m-40) cc_final: 0.7629 (m-40) REVERT: D 81 GLN cc_start: 0.7728 (tt0) cc_final: 0.7470 (tt0) REVERT: D 102 ILE cc_start: 0.8276 (tp) cc_final: 0.7890 (tp) outliers start: 40 outliers final: 30 residues processed: 370 average time/residue: 0.6006 time to fit residues: 305.5583 Evaluate side-chains 382 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 348 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 967 ASN Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain B residue 1328 ASN Chi-restraints excluded: chain B residue 1330 THR Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1370 VAL Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain C residue 1497 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 91 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** B 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11913 Z= 0.247 Angle : 0.546 8.390 16176 Z= 0.279 Chirality : 0.043 0.161 1842 Planarity : 0.004 0.048 2090 Dihedral : 4.780 50.109 1703 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.52 % Allowed : 17.51 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.22), residues: 1488 helix: 1.57 (0.31), residues: 265 sheet: -0.52 (0.23), residues: 520 loop : -1.00 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 782 HIS 0.005 0.001 HIS B1150 PHE 0.019 0.002 PHE A 319 TYR 0.012 0.001 TYR A 507 ARG 0.006 0.000 ARG A 269 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 342 time to evaluate : 1.612 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: A 55 SER cc_start: 0.7855 (p) cc_final: 0.7376 (m) REVERT: A 77 SER cc_start: 0.8089 (t) cc_final: 0.7867 (p) REVERT: A 119 ASP cc_start: 0.7198 (p0) cc_final: 0.6679 (p0) REVERT: A 137 ARG cc_start: 0.7747 (ttt90) cc_final: 0.7518 (ttt90) REVERT: A 188 LYS cc_start: 0.7708 (tttp) cc_final: 0.7367 (ttmm) REVERT: A 346 GLU cc_start: 0.6650 (pt0) cc_final: 0.6348 (pt0) REVERT: A 364 SER cc_start: 0.8293 (p) cc_final: 0.7798 (t) REVERT: A 404 LYS cc_start: 0.8083 (mmmt) cc_final: 0.7655 (ttmm) REVERT: A 424 ASN cc_start: 0.7571 (t0) cc_final: 0.7233 (t0) REVERT: A 430 GLN cc_start: 0.6976 (mt0) cc_final: 0.6618 (mt0) REVERT: A 505 TYR cc_start: 0.7455 (m-80) cc_final: 0.6933 (m-10) REVERT: B 764 GLU cc_start: 0.4862 (OUTLIER) cc_final: 0.4499 (mm-30) REVERT: B 771 ASP cc_start: 0.7357 (t0) cc_final: 0.7045 (t70) REVERT: B 848 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7351 (tp40) REVERT: B 858 TYR cc_start: 0.8168 (m-80) cc_final: 0.7911 (m-10) REVERT: B 895 ARG cc_start: 0.7974 (mmt-90) cc_final: 0.7628 (mmt180) REVERT: B 1050 GLN cc_start: 0.7523 (tp40) cc_final: 0.7109 (tm-30) REVERT: B 1072 ARG cc_start: 0.6485 (ttp80) cc_final: 0.5833 (ttp80) REVERT: B 1102 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7113 (mt-10) REVERT: B 1137 GLU cc_start: 0.6702 (mp0) cc_final: 0.6454 (mp0) REVERT: B 1313 SER cc_start: 0.7284 (t) cc_final: 0.7064 (t) REVERT: B 1355 GLU cc_start: 0.6895 (mp0) cc_final: 0.6104 (mp0) REVERT: B 1357 GLU cc_start: 0.6896 (tt0) cc_final: 0.6652 (tt0) REVERT: B 1381 LEU cc_start: 0.7806 (pp) cc_final: 0.7541 (pp) REVERT: B 1389 MET cc_start: 0.5691 (OUTLIER) cc_final: 0.5386 (ptt) REVERT: C 1557 TYR cc_start: 0.7566 (m-80) cc_final: 0.6509 (m-10) REVERT: D 73 ASN cc_start: 0.7113 (m-40) cc_final: 0.6891 (m110) REVERT: D 81 GLN cc_start: 0.7728 (tt0) cc_final: 0.7474 (tt0) REVERT: D 102 ILE cc_start: 0.8278 (tp) cc_final: 0.7890 (tp) outliers start: 32 outliers final: 27 residues processed: 359 average time/residue: 0.6138 time to fit residues: 302.3669 Evaluate side-chains 373 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 342 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 967 ASN Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain B residue 1328 ASN Chi-restraints excluded: chain B residue 1330 THR Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1370 VAL Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain C residue 1497 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.102055 restraints weight = 55274.931| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.44 r_work: 0.3142 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11913 Z= 0.246 Angle : 0.543 6.051 16176 Z= 0.279 Chirality : 0.043 0.157 1842 Planarity : 0.004 0.059 2090 Dihedral : 4.759 49.890 1703 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.60 % Allowed : 17.74 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.22), residues: 1488 helix: 1.49 (0.31), residues: 270 sheet: -0.55 (0.23), residues: 523 loop : -0.99 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 782 HIS 0.004 0.001 HIS B1150 PHE 0.015 0.002 PHE A 74 TYR 0.012 0.001 TYR A 507 ARG 0.008 0.000 ARG A 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7206.66 seconds wall clock time: 126 minutes 24.15 seconds (7584.15 seconds total)