Starting phenix.real_space_refine on Tue Mar 19 01:59:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dt8_27692/03_2024/8dt8_27692.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dt8_27692/03_2024/8dt8_27692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dt8_27692/03_2024/8dt8_27692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dt8_27692/03_2024/8dt8_27692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dt8_27692/03_2024/8dt8_27692.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dt8_27692/03_2024/8dt8_27692.pdb" } resolution = 3.34 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= -0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 14506 2.51 5 N 3775 2.21 5 O 4407 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22796 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7939 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 54, 'TRANS': 960} Chain breaks: 7 Chain: "H" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 982 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "D" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "C" Number of atoms: 6377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6377 Classifications: {'peptide': 818} Link IDs: {'PTRANS': 43, 'TRANS': 774} Chain breaks: 8 Chain: "B" Number of atoms: 6375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6375 Classifications: {'peptide': 818} Link IDs: {'PTRANS': 45, 'TRANS': 772} Chain breaks: 8 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 11.45, per 1000 atoms: 0.50 Number of scatterers: 22796 At special positions: 0 Unit cell: (140.03, 136.895, 204.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4407 8.00 N 3775 7.00 C 14506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=1.90 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS B 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS H 49 " - pdb=" SG CYS H 69 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 69 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 883 " - pdb=" SG CYS B 705 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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 A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 801 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A1098 " " NAG B1301 " - " ASN B 717 " " NAG B1302 " - " ASN B 801 " " NAG B1303 " - " ASN B1098 " " NAG C1301 " - " ASN C 717 " " NAG C1302 " - " ASN C 801 " " NAG C1303 " - " ASN C1134 " " NAG C1304 " - " ASN C1098 " Time building additional restraints: 8.16 Conformation dependent library (CDL) restraints added in 4.1 seconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5418 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 43 sheets defined 24.0% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.373A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.081A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.573A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.745A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.018A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.691A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.016A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.720A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.886A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.064A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.440A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.194A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.784A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.508A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 7.050A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.719A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.495A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.394A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.241A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.241A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.538A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.806A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 7 through 8 removed outlier: 3.553A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.313A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.313A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASP H 100I" --> pdb=" O TYR H 96 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.373A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ALA D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 29 through 30 removed outlier: 7.763A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 42 through 44 removed outlier: 3.588A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.770A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.539A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.265A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.576A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.531A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.531A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.458A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 787 through 789 Processing sheet with id=AD4, first strand: chain 'C' and resid 796 through 797 Processing sheet with id=AD5, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.642A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.176A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.765A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 83 through 85 removed outlier: 7.009A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.312A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.691A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.337A pdb=" N TYR B 660 " --> pdb=" O SER B 698 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.553A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.277A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.277A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.344A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.669A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) 1031 hydrogen bonds defined for protein. 2841 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: 10.25 Time building geometry restraints manager: 8.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7330 1.35 - 1.47: 5860 1.47 - 1.59: 9978 1.59 - 1.72: 0 1.72 - 1.84: 137 Bond restraints: 23305 Sorted by residual: bond pdb=" N PRO B 986 " pdb=" CA PRO B 986 " ideal model delta sigma weight residual 1.465 1.506 -0.041 2.03e-02 2.43e+03 4.10e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.89e+00 bond pdb=" CG LEU C 916 " pdb=" CD2 LEU C 916 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.85e+00 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" CG LEU A 916 " pdb=" CD2 LEU A 916 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.70e+00 ... (remaining 23300 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.27: 725 106.27 - 113.28: 12245 113.28 - 120.28: 8994 120.28 - 127.29: 9504 127.29 - 134.30: 232 Bond angle restraints: 31700 Sorted by residual: angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.13 -5.43 1.22e+00 6.72e-01 1.98e+01 angle pdb=" N GLN C 613 " pdb=" CA GLN C 613 " pdb=" C GLN C 613 " ideal model delta sigma weight residual 111.28 116.13 -4.85 1.09e+00 8.42e-01 1.98e+01 angle pdb=" N ARG C 214 " pdb=" CA ARG C 214 " pdb=" C ARG C 214 " ideal model delta sigma weight residual 110.80 120.24 -9.44 2.13e+00 2.20e-01 1.96e+01 angle pdb=" N LEU A 117 " pdb=" CA LEU A 117 " pdb=" C LEU A 117 " ideal model delta sigma weight residual 109.46 116.16 -6.70 1.66e+00 3.63e-01 1.63e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 115.50 -4.80 1.22e+00 6.72e-01 1.55e+01 ... (remaining 31695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 13496 17.43 - 34.86: 413 34.86 - 52.28: 94 52.28 - 69.71: 60 69.71 - 87.14: 20 Dihedral angle restraints: 14083 sinusoidal: 5667 harmonic: 8416 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -160.01 74.01 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 37.28 55.72 1 1.00e+01 1.00e-02 4.19e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 136.09 -43.09 1 1.00e+01 1.00e-02 2.59e+01 ... (remaining 14080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2266 0.045 - 0.089: 948 0.089 - 0.134: 320 0.134 - 0.178: 83 0.178 - 0.223: 14 Chirality restraints: 3631 Sorted by residual: chirality pdb=" CA PHE D 67 " pdb=" N PHE D 67 " pdb=" C PHE D 67 " pdb=" CB PHE D 67 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CG LEU B 945 " pdb=" CB LEU B 945 " pdb=" CD1 LEU B 945 " pdb=" CD2 LEU B 945 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE C 203 " pdb=" N ILE C 203 " pdb=" C ILE C 203 " pdb=" CB ILE C 203 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3628 not shown) Planarity restraints: 4115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 954 " 0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C GLN B 954 " -0.066 2.00e-02 2.50e+03 pdb=" O GLN B 954 " 0.025 2.00e-02 2.50e+03 pdb=" N ASN B 955 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C1098 " -0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C ASN C1098 " 0.066 2.00e-02 2.50e+03 pdb=" O ASN C1098 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY C1099 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 948 " 0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C LEU A 948 " -0.064 2.00e-02 2.50e+03 pdb=" O LEU A 948 " 0.024 2.00e-02 2.50e+03 pdb=" N GLN A 949 " 0.022 2.00e-02 2.50e+03 ... (remaining 4112 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 275 2.65 - 3.21: 20001 3.21 - 3.77: 34691 3.77 - 4.34: 49382 4.34 - 4.90: 81618 Nonbonded interactions: 185967 Sorted by model distance: nonbonded pdb=" O THR C 108 " pdb=" OG1 THR C 236 " model vdw 2.083 2.440 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 158 " model vdw 2.161 2.520 nonbonded pdb=" NZ LYS B1028 " pdb=" O PHE B1042 " model vdw 2.252 2.520 nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 219 " model vdw 2.274 2.440 nonbonded pdb=" OG1 THR C1077 " pdb=" O PHE C1095 " model vdw 2.293 2.440 ... (remaining 185962 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 28 through 1144 or resid 1301 through 1303)) selection = (chain 'C' and (resid 28 through 143 or resid 154 through 331 or resid 531 throu \ gh 1144 or resid 1302 through 1304)) } ncs_group { reference = (chain 'D' and (resid 2 through 33 or resid 35 through 94 or resid 99 or resid 1 \ 00C or resid 100F or resid 100H through 112)) selection = (chain 'H' and (resid 2 through 33 or resid 35 through 94 or resid 99 or resid 1 \ 00C or resid 100F or resid 100J through 112)) } 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.080 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 60.790 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 : 0.005 0.065 23305 Z= 0.361 Angle : 0.974 9.435 31700 Z= 0.572 Chirality : 0.056 0.223 3631 Planarity : 0.006 0.039 4102 Dihedral : 10.603 87.138 8554 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.20 % Allowed : 1.06 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.14), residues: 2844 helix: 1.11 (0.19), residues: 603 sheet: 1.06 (0.20), residues: 628 loop : -0.00 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP H 47 HIS 0.009 0.002 HIS B 655 PHE 0.031 0.002 PHE B 133 TYR 0.047 0.003 TYR H 100D ARG 0.009 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 464 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.5993 (mt) cc_final: 0.5172 (tp) REVERT: A 153 MET cc_start: 0.2745 (tpt) cc_final: 0.2174 (ptp) REVERT: A 558 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7596 (ptpt) REVERT: A 581 THR cc_start: 0.8104 (m) cc_final: 0.7878 (p) REVERT: H 32 TYR cc_start: 0.4590 (m-80) cc_final: 0.4105 (m-10) REVERT: H 37 TYR cc_start: 0.5515 (t80) cc_final: 0.4945 (t80) REVERT: H 58 TYR cc_start: 0.7677 (t80) cc_final: 0.7438 (t80) REVERT: H 89 VAL cc_start: 0.7162 (t) cc_final: 0.6709 (p) REVERT: D 36 TRP cc_start: 0.7023 (m100) cc_final: 0.5629 (m100) REVERT: D 37 TYR cc_start: 0.7727 (m-80) cc_final: 0.7489 (m-80) REVERT: D 71 ARG cc_start: 0.6846 (ppt90) cc_final: 0.6416 (ptt90) REVERT: D 78 LEU cc_start: 0.7706 (tp) cc_final: 0.5926 (tp) REVERT: D 80 LEU cc_start: 0.7754 (tt) cc_final: 0.7029 (tt) REVERT: C 153 MET cc_start: 0.5757 (mmm) cc_final: 0.4588 (ttt) REVERT: C 190 ARG cc_start: 0.5692 (mtm-85) cc_final: 0.5489 (tpp80) REVERT: C 539 VAL cc_start: 0.8190 (t) cc_final: 0.7894 (p) REVERT: C 646 ARG cc_start: 0.7243 (tpt90) cc_final: 0.6659 (tpt90) REVERT: C 856 ASN cc_start: 0.7230 (m-40) cc_final: 0.6921 (p0) REVERT: B 761 THR cc_start: 0.8528 (m) cc_final: 0.8303 (p) REVERT: B 1029 MET cc_start: 0.8891 (tpp) cc_final: 0.8595 (tpp) outliers start: 5 outliers final: 3 residues processed: 467 average time/residue: 0.3875 time to fit residues: 267.9061 Evaluate side-chains 212 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 209 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 5.9990 chunk 217 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 224 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 chunk 260 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 607 GLN A 613 GLN A 710 ASN A 955 ASN H 39 GLN H 82AASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 532 ASN C 655 HIS C 926 GLN C 935 GLN C 955 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1101 HIS B 165 ASN B 188 ASN B 655 HIS ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 23305 Z= 0.336 Angle : 0.643 13.846 31700 Z= 0.345 Chirality : 0.047 0.308 3631 Planarity : 0.005 0.052 4102 Dihedral : 5.240 58.544 3374 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.93 % Allowed : 5.04 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.15), residues: 2844 helix: 2.47 (0.20), residues: 607 sheet: 1.02 (0.19), residues: 646 loop : -0.29 (0.14), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.006 0.001 HIS B 655 PHE 0.021 0.002 PHE B 133 TYR 0.028 0.002 TYR H 37 ARG 0.017 0.001 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 221 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.5237 (t0) cc_final: 0.4996 (t0) REVERT: A 141 LEU cc_start: 0.5947 (mt) cc_final: 0.5507 (tp) REVERT: A 153 MET cc_start: 0.2903 (tpt) cc_final: 0.2337 (ptp) REVERT: A 558 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7655 (ptpt) REVERT: H 59 TYR cc_start: 0.6145 (m-80) cc_final: 0.5745 (m-80) REVERT: D 36 TRP cc_start: 0.6634 (m100) cc_final: 0.6276 (m100) REVERT: D 71 ARG cc_start: 0.7026 (ppt90) cc_final: 0.6671 (ptt90) REVERT: D 100 PHE cc_start: 0.7825 (m-10) cc_final: 0.7466 (m-10) REVERT: C 131 CYS cc_start: 0.4327 (OUTLIER) cc_final: 0.3500 (m) REVERT: C 153 MET cc_start: 0.5756 (mmm) cc_final: 0.4571 (ttt) REVERT: C 190 ARG cc_start: 0.5755 (mtm-85) cc_final: 0.5504 (tpp80) REVERT: C 646 ARG cc_start: 0.7288 (tpt90) cc_final: 0.6684 (tpt90) REVERT: B 115 GLN cc_start: 0.7254 (mt0) cc_final: 0.6976 (mm-40) outliers start: 49 outliers final: 28 residues processed: 257 average time/residue: 0.3407 time to fit residues: 137.2566 Evaluate side-chains 192 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 988 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 144 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 216 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 261 optimal weight: 0.0570 chunk 282 optimal weight: 0.4980 chunk 232 optimal weight: 5.9990 chunk 258 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 209 optimal weight: 8.9990 overall best weight: 1.4900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A1005 GLN D 76 ASN C 926 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23305 Z= 0.228 Angle : 0.548 10.156 31700 Z= 0.291 Chirality : 0.044 0.256 3631 Planarity : 0.004 0.045 4102 Dihedral : 4.755 50.184 3370 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.57 % Favored : 97.40 % Rotamer: Outliers : 1.89 % Allowed : 6.58 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.15), residues: 2844 helix: 2.90 (0.20), residues: 609 sheet: 0.95 (0.19), residues: 639 loop : -0.48 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 36 HIS 0.004 0.001 HIS B1058 PHE 0.020 0.002 PHE B 133 TYR 0.021 0.002 TYR H 100D ARG 0.004 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 191 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.5172 (t0) cc_final: 0.4939 (t0) REVERT: A 141 LEU cc_start: 0.6123 (mt) cc_final: 0.5443 (tp) REVERT: A 153 MET cc_start: 0.3162 (tpt) cc_final: 0.2414 (ptp) REVERT: A 558 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7678 (ptpt) REVERT: H 89 VAL cc_start: 0.7507 (t) cc_final: 0.7266 (p) REVERT: D 37 TYR cc_start: 0.8063 (m-80) cc_final: 0.7632 (m-80) REVERT: D 43 LYS cc_start: 0.7060 (mppt) cc_final: 0.6652 (mmmt) REVERT: D 47 TRP cc_start: 0.7741 (t60) cc_final: 0.7487 (t60) REVERT: D 100 PHE cc_start: 0.7950 (m-10) cc_final: 0.7484 (m-10) REVERT: C 81 ASN cc_start: 0.6906 (t0) cc_final: 0.6672 (t0) REVERT: C 131 CYS cc_start: 0.4427 (OUTLIER) cc_final: 0.3707 (m) REVERT: C 153 MET cc_start: 0.5735 (mmm) cc_final: 0.4595 (ttt) REVERT: C 190 ARG cc_start: 0.5876 (mtm-85) cc_final: 0.5088 (tpt-90) REVERT: C 646 ARG cc_start: 0.7302 (tpt90) cc_final: 0.6718 (tpt90) REVERT: C 1038 LYS cc_start: 0.8987 (mttm) cc_final: 0.8599 (mmtm) REVERT: B 115 GLN cc_start: 0.7313 (mt0) cc_final: 0.6970 (mm-40) outliers start: 48 outliers final: 34 residues processed: 226 average time/residue: 0.3517 time to fit residues: 124.5555 Evaluate side-chains 202 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 988 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 257 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 175 optimal weight: 0.4980 chunk 262 optimal weight: 5.9990 chunk 277 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN D 73 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN B 901 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23305 Z= 0.243 Angle : 0.542 12.612 31700 Z= 0.285 Chirality : 0.044 0.247 3631 Planarity : 0.004 0.044 4102 Dihedral : 4.681 42.066 3370 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 2.13 % Allowed : 7.13 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 2844 helix: 2.92 (0.20), residues: 618 sheet: 0.75 (0.19), residues: 672 loop : -0.56 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 36 HIS 0.006 0.001 HIS B1058 PHE 0.019 0.002 PHE A 140 TYR 0.022 0.002 TYR H 100D ARG 0.006 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 181 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.5330 (t0) cc_final: 0.5072 (t0) REVERT: A 141 LEU cc_start: 0.6230 (mt) cc_final: 0.5476 (tp) REVERT: A 153 MET cc_start: 0.3318 (tpt) cc_final: 0.2440 (ptp) REVERT: A 271 GLN cc_start: 0.7606 (mp10) cc_final: 0.7354 (mp10) REVERT: A 400 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.7993 (p90) REVERT: A 558 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7738 (ptpt) REVERT: H 89 VAL cc_start: 0.7515 (t) cc_final: 0.7228 (p) REVERT: D 37 TYR cc_start: 0.8116 (m-80) cc_final: 0.7564 (m-80) REVERT: D 43 LYS cc_start: 0.7185 (mppt) cc_final: 0.6821 (mmtp) REVERT: D 47 TRP cc_start: 0.7831 (t60) cc_final: 0.7529 (t60) REVERT: D 100 PHE cc_start: 0.8147 (m-10) cc_final: 0.7703 (m-10) REVERT: C 131 CYS cc_start: 0.4331 (OUTLIER) cc_final: 0.3542 (m) REVERT: C 140 PHE cc_start: 0.5097 (m-80) cc_final: 0.4834 (m-80) REVERT: C 153 MET cc_start: 0.5691 (mmm) cc_final: 0.4607 (ttt) REVERT: C 190 ARG cc_start: 0.5681 (mtm-85) cc_final: 0.5218 (mtm-85) REVERT: C 646 ARG cc_start: 0.7348 (tpt90) cc_final: 0.6769 (tpt90) REVERT: C 1038 LYS cc_start: 0.9001 (mttm) cc_final: 0.8613 (mmtm) REVERT: B 115 GLN cc_start: 0.7365 (mt0) cc_final: 0.7021 (mm-40) outliers start: 54 outliers final: 36 residues processed: 224 average time/residue: 0.3436 time to fit residues: 121.9157 Evaluate side-chains 202 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 164 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 988 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 231 optimal weight: 5.9990 chunk 157 optimal weight: 0.0270 chunk 4 optimal weight: 20.0000 chunk 206 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 236 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 chunk 70 optimal weight: 0.1980 overall best weight: 2.4444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** H 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 23305 Z= 0.320 Angle : 0.573 12.529 31700 Z= 0.300 Chirality : 0.045 0.265 3631 Planarity : 0.004 0.044 4102 Dihedral : 4.807 40.123 3370 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.34 % Favored : 96.62 % Rotamer: Outliers : 2.64 % Allowed : 7.29 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 2844 helix: 2.87 (0.20), residues: 612 sheet: 0.52 (0.19), residues: 698 loop : -0.65 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 36 HIS 0.008 0.001 HIS B1058 PHE 0.020 0.002 PHE B 898 TYR 0.021 0.002 TYR H 37 ARG 0.005 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 166 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.5287 (t0) cc_final: 0.5055 (t0) REVERT: A 400 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8523 (p90) REVERT: A 558 LYS cc_start: 0.8074 (mmtt) cc_final: 0.7793 (ptpt) REVERT: H 48 VAL cc_start: 0.7777 (t) cc_final: 0.7493 (t) REVERT: H 103 TRP cc_start: 0.6454 (OUTLIER) cc_final: 0.5791 (m-90) REVERT: D 37 TYR cc_start: 0.8020 (m-80) cc_final: 0.7496 (m-80) REVERT: D 43 LYS cc_start: 0.7107 (mppt) cc_final: 0.6797 (mmtt) REVERT: D 47 TRP cc_start: 0.7991 (t60) cc_final: 0.7684 (t60) REVERT: D 100 PHE cc_start: 0.8241 (m-10) cc_final: 0.7886 (m-10) REVERT: C 81 ASN cc_start: 0.6485 (t0) cc_final: 0.6086 (t0) REVERT: C 131 CYS cc_start: 0.4196 (OUTLIER) cc_final: 0.3305 (m) REVERT: C 140 PHE cc_start: 0.5173 (m-80) cc_final: 0.4882 (m-80) REVERT: C 153 MET cc_start: 0.5739 (mmm) cc_final: 0.4695 (ttt) REVERT: C 157 PHE cc_start: 0.5445 (OUTLIER) cc_final: 0.5190 (m-80) REVERT: C 190 ARG cc_start: 0.5677 (mtm-85) cc_final: 0.5223 (mtm-85) REVERT: C 266 TYR cc_start: 0.6762 (m-80) cc_final: 0.5937 (m-80) REVERT: C 646 ARG cc_start: 0.7353 (tpt90) cc_final: 0.6805 (tpt90) REVERT: B 115 GLN cc_start: 0.7267 (mt0) cc_final: 0.6977 (mm-40) REVERT: B 1138 TYR cc_start: 0.8423 (t80) cc_final: 0.8202 (t80) outliers start: 67 outliers final: 50 residues processed: 217 average time/residue: 0.3496 time to fit residues: 118.8657 Evaluate side-chains 209 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 155 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 93 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 162 optimal weight: 0.0570 chunk 68 optimal weight: 0.0040 chunk 277 optimal weight: 4.9990 chunk 230 optimal weight: 0.9980 chunk 128 optimal weight: 0.0670 chunk 23 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 overall best weight: 0.8250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN A1005 GLN H 82AASN D 73 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 23305 Z= 0.162 Angle : 0.499 11.799 31700 Z= 0.262 Chirality : 0.043 0.239 3631 Planarity : 0.004 0.067 4102 Dihedral : 4.453 39.347 3370 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.64 % Favored : 97.33 % Rotamer: Outliers : 1.89 % Allowed : 8.23 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.15), residues: 2844 helix: 3.12 (0.20), residues: 614 sheet: 0.69 (0.19), residues: 665 loop : -0.64 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 64 HIS 0.002 0.001 HIS B1058 PHE 0.018 0.001 PHE D 67 TYR 0.018 0.001 TYR A1067 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 180 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.5134 (t0) cc_final: 0.4833 (t0) REVERT: A 141 LEU cc_start: 0.6125 (mt) cc_final: 0.5286 (tp) REVERT: A 558 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7793 (ptpt) REVERT: A 599 THR cc_start: 0.9342 (OUTLIER) cc_final: 0.9068 (p) REVERT: H 44 GLU cc_start: 0.6716 (mp0) cc_final: 0.6507 (mp0) REVERT: H 48 VAL cc_start: 0.7631 (t) cc_final: 0.7322 (t) REVERT: H 87 THR cc_start: 0.5105 (p) cc_final: 0.4849 (p) REVERT: H 103 TRP cc_start: 0.6472 (OUTLIER) cc_final: 0.5904 (m-90) REVERT: D 5 GLN cc_start: 0.6457 (tp40) cc_final: 0.6065 (mp10) REVERT: D 37 TYR cc_start: 0.8082 (m-80) cc_final: 0.7447 (m-80) REVERT: D 43 LYS cc_start: 0.7194 (mppt) cc_final: 0.6781 (mmtp) REVERT: D 47 TRP cc_start: 0.7885 (t60) cc_final: 0.7625 (t60) REVERT: D 100 PHE cc_start: 0.8218 (m-10) cc_final: 0.7884 (m-10) REVERT: C 81 ASN cc_start: 0.6477 (t0) cc_final: 0.6113 (t0) REVERT: C 131 CYS cc_start: 0.4133 (OUTLIER) cc_final: 0.3288 (m) REVERT: C 153 MET cc_start: 0.5726 (mmm) cc_final: 0.4649 (ttt) REVERT: C 157 PHE cc_start: 0.5519 (OUTLIER) cc_final: 0.5293 (m-80) REVERT: C 266 TYR cc_start: 0.6781 (m-80) cc_final: 0.5955 (m-80) REVERT: C 646 ARG cc_start: 0.7343 (tpt90) cc_final: 0.6797 (tpt90) REVERT: C 1038 LYS cc_start: 0.8991 (mttm) cc_final: 0.8604 (mmtm) REVERT: B 115 GLN cc_start: 0.7388 (mt0) cc_final: 0.7006 (mm-40) REVERT: B 1138 TYR cc_start: 0.8439 (t80) cc_final: 0.8218 (t80) outliers start: 48 outliers final: 34 residues processed: 219 average time/residue: 0.3444 time to fit residues: 118.7236 Evaluate side-chains 198 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 160 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 988 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 267 optimal weight: 0.4980 chunk 31 optimal weight: 0.1980 chunk 158 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 233 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 276 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 23305 Z= 0.260 Angle : 0.531 11.075 31700 Z= 0.278 Chirality : 0.044 0.244 3631 Planarity : 0.004 0.060 4102 Dihedral : 4.543 38.887 3368 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.91 % Rotamer: Outliers : 2.05 % Allowed : 8.51 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.16), residues: 2844 helix: 2.96 (0.20), residues: 620 sheet: 0.55 (0.19), residues: 691 loop : -0.66 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 64 HIS 0.006 0.001 HIS B1058 PHE 0.019 0.001 PHE B 898 TYR 0.024 0.001 TYR H 100F ARG 0.004 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 160 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.5163 (t0) cc_final: 0.4946 (t0) REVERT: A 160 TYR cc_start: 0.4257 (m-80) cc_final: 0.4005 (m-80) REVERT: A 558 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7820 (ptpt) REVERT: A 599 THR cc_start: 0.9337 (OUTLIER) cc_final: 0.9033 (p) REVERT: H 44 GLU cc_start: 0.6745 (mp0) cc_final: 0.6503 (mp0) REVERT: H 48 VAL cc_start: 0.7654 (t) cc_final: 0.7370 (t) REVERT: H 87 THR cc_start: 0.4999 (p) cc_final: 0.4771 (p) REVERT: H 103 TRP cc_start: 0.6543 (OUTLIER) cc_final: 0.6026 (m-90) REVERT: D 37 TYR cc_start: 0.8099 (m-80) cc_final: 0.7405 (m-80) REVERT: D 47 TRP cc_start: 0.8049 (t60) cc_final: 0.7718 (t60) REVERT: D 100 PHE cc_start: 0.8207 (m-10) cc_final: 0.7936 (m-10) REVERT: C 81 ASN cc_start: 0.6466 (t0) cc_final: 0.6117 (t0) REVERT: C 131 CYS cc_start: 0.4146 (OUTLIER) cc_final: 0.3301 (m) REVERT: C 140 PHE cc_start: 0.5151 (m-80) cc_final: 0.4801 (m-80) REVERT: C 153 MET cc_start: 0.5747 (mmm) cc_final: 0.4664 (ttt) REVERT: C 266 TYR cc_start: 0.6654 (m-80) cc_final: 0.5827 (m-80) REVERT: C 646 ARG cc_start: 0.7382 (tpt90) cc_final: 0.6834 (tpt90) REVERT: B 115 GLN cc_start: 0.7291 (mt0) cc_final: 0.6999 (mm-40) outliers start: 52 outliers final: 41 residues processed: 199 average time/residue: 0.3802 time to fit residues: 120.2410 Evaluate side-chains 196 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 152 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 988 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 171 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 136 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 690 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 23305 Z= 0.253 Angle : 0.532 12.942 31700 Z= 0.278 Chirality : 0.044 0.254 3631 Planarity : 0.004 0.059 4102 Dihedral : 4.614 40.425 3368 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.23 % Favored : 96.73 % Rotamer: Outliers : 2.36 % Allowed : 8.35 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.16), residues: 2844 helix: 2.90 (0.20), residues: 622 sheet: 0.55 (0.19), residues: 683 loop : -0.72 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 64 HIS 0.006 0.001 HIS B1058 PHE 0.020 0.001 PHE B 898 TYR 0.024 0.001 TYR H 100F ARG 0.004 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 164 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.4347 (m-80) cc_final: 0.4061 (m-80) REVERT: A 558 LYS cc_start: 0.8019 (mmtt) cc_final: 0.7792 (ptpt) REVERT: A 599 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.9042 (p) REVERT: H 37 TYR cc_start: 0.6444 (OUTLIER) cc_final: 0.6161 (t80) REVERT: H 48 VAL cc_start: 0.7581 (t) cc_final: 0.7288 (t) REVERT: H 87 THR cc_start: 0.4855 (p) cc_final: 0.4654 (p) REVERT: H 100 ASP cc_start: 0.7225 (m-30) cc_final: 0.6936 (m-30) REVERT: H 103 TRP cc_start: 0.6632 (OUTLIER) cc_final: 0.6235 (m-90) REVERT: D 37 TYR cc_start: 0.8193 (m-80) cc_final: 0.7490 (m-80) REVERT: D 100 PHE cc_start: 0.8174 (m-10) cc_final: 0.7920 (m-10) REVERT: C 81 ASN cc_start: 0.6464 (t0) cc_final: 0.6118 (t0) REVERT: C 131 CYS cc_start: 0.4166 (OUTLIER) cc_final: 0.3313 (m) REVERT: C 153 MET cc_start: 0.5603 (mmm) cc_final: 0.4599 (ttt) REVERT: C 266 TYR cc_start: 0.6678 (m-80) cc_final: 0.5878 (m-80) REVERT: C 646 ARG cc_start: 0.7365 (tpt90) cc_final: 0.6814 (tpt90) REVERT: B 115 GLN cc_start: 0.7289 (mt0) cc_final: 0.6987 (mm-40) outliers start: 60 outliers final: 52 residues processed: 213 average time/residue: 0.3264 time to fit residues: 110.9454 Evaluate side-chains 211 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 155 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 251 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 257 optimal weight: 0.0270 chunk 264 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 202 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 243 optimal weight: 0.1980 overall best weight: 1.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN H 97 GLN D 73 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 23305 Z= 0.180 Angle : 0.502 12.731 31700 Z= 0.263 Chirality : 0.043 0.240 3631 Planarity : 0.004 0.058 4102 Dihedral : 4.419 39.348 3368 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.23 % Favored : 96.73 % Rotamer: Outliers : 2.01 % Allowed : 9.02 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.16), residues: 2844 helix: 3.04 (0.20), residues: 623 sheet: 0.57 (0.19), residues: 676 loop : -0.67 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.003 0.001 HIS B1058 PHE 0.017 0.001 PHE D 67 TYR 0.028 0.001 TYR B1138 ARG 0.006 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 168 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.4366 (m-80) cc_final: 0.4096 (m-80) REVERT: A 558 LYS cc_start: 0.8000 (mmtt) cc_final: 0.7792 (ptpt) REVERT: A 581 THR cc_start: 0.8140 (m) cc_final: 0.7808 (p) REVERT: A 599 THR cc_start: 0.9331 (OUTLIER) cc_final: 0.9055 (p) REVERT: H 37 TYR cc_start: 0.6383 (OUTLIER) cc_final: 0.6116 (t80) REVERT: H 48 VAL cc_start: 0.7542 (t) cc_final: 0.7221 (t) REVERT: H 87 THR cc_start: 0.4707 (p) cc_final: 0.4483 (p) REVERT: H 96 TYR cc_start: 0.6610 (t80) cc_final: 0.6195 (t80) REVERT: H 103 TRP cc_start: 0.6519 (OUTLIER) cc_final: 0.5960 (m-90) REVERT: D 5 GLN cc_start: 0.6456 (tp40) cc_final: 0.6027 (mp10) REVERT: D 37 TYR cc_start: 0.8182 (m-80) cc_final: 0.7398 (m-80) REVERT: D 47 TRP cc_start: 0.8066 (t60) cc_final: 0.7726 (t60) REVERT: D 100 PHE cc_start: 0.8217 (m-10) cc_final: 0.7998 (m-10) REVERT: C 81 ASN cc_start: 0.6411 (t0) cc_final: 0.6082 (t0) REVERT: C 131 CYS cc_start: 0.4179 (OUTLIER) cc_final: 0.3326 (m) REVERT: C 153 MET cc_start: 0.5606 (mmm) cc_final: 0.4671 (ttp) REVERT: C 266 TYR cc_start: 0.6686 (m-80) cc_final: 0.5892 (m-80) REVERT: C 646 ARG cc_start: 0.7240 (tpt90) cc_final: 0.6681 (tpt90) REVERT: B 115 GLN cc_start: 0.7380 (mt0) cc_final: 0.7002 (mm-40) outliers start: 51 outliers final: 40 residues processed: 208 average time/residue: 0.3371 time to fit residues: 111.2448 Evaluate side-chains 199 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 155 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 256 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 chunk 272 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 285 optimal weight: 5.9990 chunk 263 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 23 optimal weight: 0.0970 chunk 175 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 23305 Z= 0.155 Angle : 0.494 12.979 31700 Z= 0.259 Chirality : 0.042 0.232 3631 Planarity : 0.004 0.059 4102 Dihedral : 4.272 36.632 3368 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 1.77 % Allowed : 9.34 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.16), residues: 2844 helix: 3.08 (0.20), residues: 624 sheet: 0.62 (0.19), residues: 664 loop : -0.63 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 64 HIS 0.003 0.001 HIS C 207 PHE 0.018 0.001 PHE D 67 TYR 0.027 0.001 TYR H 100F ARG 0.006 0.000 ARG D 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 164 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.7514 (mp) cc_final: 0.7312 (mt) REVERT: A 160 TYR cc_start: 0.4494 (m-80) cc_final: 0.4091 (m-80) REVERT: A 599 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.9050 (p) REVERT: H 37 TYR cc_start: 0.6272 (OUTLIER) cc_final: 0.6054 (t80) REVERT: H 48 VAL cc_start: 0.7547 (t) cc_final: 0.7244 (t) REVERT: H 87 THR cc_start: 0.5031 (p) cc_final: 0.4806 (p) REVERT: H 96 TYR cc_start: 0.6624 (t80) cc_final: 0.6332 (t80) REVERT: H 103 TRP cc_start: 0.6492 (OUTLIER) cc_final: 0.5871 (m-90) REVERT: D 5 GLN cc_start: 0.6448 (tp40) cc_final: 0.6030 (mp10) REVERT: D 37 TYR cc_start: 0.8183 (m-80) cc_final: 0.7347 (m-80) REVERT: D 47 TRP cc_start: 0.8085 (t60) cc_final: 0.7766 (t60) REVERT: D 64 LYS cc_start: 0.3996 (mttm) cc_final: 0.3666 (mttm) REVERT: D 100 PHE cc_start: 0.8219 (m-10) cc_final: 0.7989 (m-10) REVERT: C 81 ASN cc_start: 0.6310 (t0) cc_final: 0.6037 (t0) REVERT: C 131 CYS cc_start: 0.4230 (OUTLIER) cc_final: 0.3484 (m) REVERT: C 153 MET cc_start: 0.5588 (mmm) cc_final: 0.4695 (ttp) REVERT: C 266 TYR cc_start: 0.6673 (m-80) cc_final: 0.5908 (m-80) REVERT: B 115 GLN cc_start: 0.7297 (mt0) cc_final: 0.6978 (mm-40) outliers start: 45 outliers final: 36 residues processed: 200 average time/residue: 0.3377 time to fit residues: 107.8671 Evaluate side-chains 194 residues out of total 2538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 154 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 139 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 234 optimal weight: 0.0070 chunk 28 optimal weight: 0.9980 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.107290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.073547 restraints weight = 52705.222| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.31 r_work: 0.2940 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23305 Z= 0.181 Angle : 0.498 12.532 31700 Z= 0.260 Chirality : 0.043 0.234 3631 Planarity : 0.004 0.058 4102 Dihedral : 4.287 35.824 3368 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.23 % Favored : 96.73 % Rotamer: Outliers : 1.85 % Allowed : 9.30 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.16), residues: 2844 helix: 3.08 (0.20), residues: 625 sheet: 0.64 (0.19), residues: 670 loop : -0.64 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 36 HIS 0.004 0.001 HIS B1058 PHE 0.018 0.001 PHE B 898 TYR 0.027 0.001 TYR H 100F ARG 0.005 0.000 ARG D 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4861.08 seconds wall clock time: 88 minutes 34.38 seconds (5314.38 seconds total)