Starting phenix.real_space_refine on Thu Jul 25 00:47:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yz5_39685/07_2024/8yz5_39685.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yz5_39685/07_2024/8yz5_39685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yz5_39685/07_2024/8yz5_39685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yz5_39685/07_2024/8yz5_39685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yz5_39685/07_2024/8yz5_39685.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yz5_39685/07_2024/8yz5_39685.cif" } resolution = 3.93 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= 0.001 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 122 5.16 5 C 17620 2.51 5 N 4635 2.21 5 O 5300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 725": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 780": "OE1" <-> "OE2" Residue "D GLU 819": "OE1" <-> "OE2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "K TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 27677 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 8023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8023 Classifications: {'peptide': 1027} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 49, 'TRANS': 977} Chain breaks: 8 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 8138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8138 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 52, 'TRANS': 989} Chain breaks: 6 Chain: "D" Number of atoms: 8102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8102 Classifications: {'peptide': 1037} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 51, 'TRANS': 985} Chain breaks: 8 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 889 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 884 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 15.14, per 1000 atoms: 0.55 Number of scatterers: 27677 At special positions: 0 Unit cell: (162.68, 181.77, 150.23, 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 122 16.00 O 5300 8.00 N 4635 7.00 C 17620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 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 A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 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 D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.02 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.04 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.02 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 86 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 86 " 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 Time building additional restraints: 10.05 Conformation dependent library (CDL) restraints added in 4.9 seconds 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6616 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 47 sheets defined 20.3% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.719A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.659A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.072A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.593A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.576A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.594A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.796A pdb=" N ASP C 820 " --> pdb=" O SER C 816 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 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 968 removed outlier: 3.618A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 removed outlier: 3.981A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1031 removed outlier: 4.355A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1120 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 4.239A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.100A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 438 through 443 removed outlier: 4.070A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.765A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.564A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.802A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.173A pdb=" N ILE A 923 " --> pdb=" O ASN A 919 " (cutoff:3.500A) 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 968 removed outlier: 3.780A pdb=" N ASN A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.157A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1031 removed outlier: 4.122A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'D' and resid 294 through 304 removed outlier: 3.547A pdb=" N GLU D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 364 through 371 Processing helix chain 'D' and resid 385 through 390 removed outlier: 4.025A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 390 " --> pdb=" O LEU D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 408 removed outlier: 3.599A pdb=" N VAL D 407 " --> pdb=" O ARG D 403 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG D 408 " --> pdb=" O GLY D 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 403 through 408' Processing helix chain 'D' and resid 417 through 422 removed outlier: 4.284A pdb=" N TYR D 421 " --> pdb=" O LYS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 506 Processing helix chain 'D' and resid 746 through 755 Processing helix chain 'D' and resid 758 through 781 Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 866 through 883 Processing helix chain 'D' and resid 897 through 908 removed outlier: 3.816A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 941 removed outlier: 4.309A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 968 removed outlier: 3.657A pdb=" N ALA D 958 " --> pdb=" O GLN D 954 " (cutoff:3.500A) Processing helix chain 'D' and resid 977 through 982 removed outlier: 4.388A pdb=" N LEU D 981 " --> pdb=" O LEU D 977 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER D 982 " --> pdb=" O ASN D 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 977 through 982' Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.714A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1120 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.609A pdb=" N THR G 87 " --> pdb=" O ALA G 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 81 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.503A pdb=" N ILE J 81 " --> pdb=" O PRO J 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 5.830A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.508A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.869A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.664A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 141 through 142 removed outlier: 6.427A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 312 through 319 removed outlier: 5.443A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 325 through 327 Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.058A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.663A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 712 through 727 removed outlier: 6.679A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 3.822A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AB6, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.085A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.111A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 141 through 143 removed outlier: 3.973A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.527A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.411A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'A' and resid 664 through 667 removed outlier: 5.883A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 712 through 727 removed outlier: 6.794A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1120 through 1123 Processing sheet with id=AC7, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AC8, first strand: chain 'D' and resid 29 through 31 removed outlier: 8.891A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA D 93 " --> pdb=" O TYR D 266 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY D 268 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 190 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU D 224 " --> pdb=" O SER D 205 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 47 through 55 removed outlier: 4.111A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 83 through 84 removed outlier: 4.080A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 311 through 318 removed outlier: 3.592A pdb=" N GLY D 311 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR D 599 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS D 649 " --> pdb=" O TYR D 612 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 324 through 326 removed outlier: 6.872A pdb=" N GLU D 324 " --> pdb=" O ASN D 540 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASN D 542 " --> pdb=" O GLU D 324 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE D 326 " --> pdb=" O ASN D 542 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 587 " --> pdb=" O ASP D 574 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AD5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'D' and resid 664 through 667 removed outlier: 5.831A pdb=" N ALA D 672 " --> pdb=" O PRO D 665 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 711 through 727 removed outlier: 6.516A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASN D 717 " --> pdb=" O ALA D1070 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA D1070 " --> pdb=" O ASN D 717 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS D1064 " --> pdb=" O THR D 723 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'D' and resid 1081 through 1082 removed outlier: 4.263A pdb=" N ILE D1081 " --> pdb=" O HIS D1088 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'G' and resid 57 through 59 removed outlier: 3.590A pdb=" N TYR G 58 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AE5, first strand: chain 'K' and resid 19 through 22 Processing sheet with id=AE6, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.738A pdb=" N ASN K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR K 49 " --> pdb=" O ASN K 53 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN K 87 " --> pdb=" O ASN K 34 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'I' and resid 57 through 59 removed outlier: 4.841A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.806A pdb=" N LEU J 11 " --> pdb=" O LYS J 101 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU J 103 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 19 through 23 Processing sheet with id=AF2, first strand: chain 'J' and resid 34 through 37 removed outlier: 5.969A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) 993 hydrogen bonds defined for protein. 2697 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: 13.21 Time building geometry restraints manager: 11.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8938 1.34 - 1.46: 6592 1.46 - 1.58: 12610 1.58 - 1.70: 1 1.70 - 1.83: 158 Bond restraints: 28299 Sorted by residual: bond pdb=" N ASN D 331 " pdb=" CA ASN D 331 " ideal model delta sigma weight residual 1.458 1.488 -0.029 1.14e-02 7.69e+03 6.56e+00 bond pdb=" N LEU D 335 " pdb=" CA LEU D 335 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.35e+00 bond pdb=" N ASN D 334 " pdb=" CA ASN D 334 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.30e-02 5.92e+03 5.26e+00 bond pdb=" N THR D 333 " pdb=" CA THR D 333 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.30e-02 5.92e+03 4.76e+00 bond pdb=" N ILE D 332 " pdb=" CA ILE D 332 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.25e-02 6.40e+03 4.40e+00 ... (remaining 28294 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.42: 758 106.42 - 113.31: 15106 113.31 - 120.21: 9740 120.21 - 127.11: 12646 127.11 - 134.01: 239 Bond angle restraints: 38489 Sorted by residual: angle pdb=" N GLN A 954 " pdb=" CA GLN A 954 " pdb=" CB GLN A 954 " ideal model delta sigma weight residual 110.12 116.65 -6.53 1.47e+00 4.63e-01 1.98e+01 angle pdb=" C ASN C 953 " pdb=" N GLN C 954 " pdb=" CA GLN C 954 " ideal model delta sigma weight residual 121.18 113.02 8.16 1.98e+00 2.55e-01 1.70e+01 angle pdb=" C TYR K 49 " pdb=" N ASP K 50 " pdb=" CA ASP K 50 " ideal model delta sigma weight residual 121.54 129.13 -7.59 1.91e+00 2.74e-01 1.58e+01 angle pdb=" CA ARG C 765 " pdb=" CB ARG C 765 " pdb=" CG ARG C 765 " ideal model delta sigma weight residual 114.10 121.91 -7.81 2.00e+00 2.50e-01 1.53e+01 angle pdb=" CA PRO D1057 " pdb=" N PRO D1057 " pdb=" CD PRO D1057 " ideal model delta sigma weight residual 112.00 106.90 5.10 1.40e+00 5.10e-01 1.32e+01 ... (remaining 38484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 15486 17.86 - 35.71: 1092 35.71 - 53.57: 178 53.57 - 71.42: 46 71.42 - 89.28: 26 Dihedral angle restraints: 16828 sinusoidal: 6526 harmonic: 10302 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -161.26 75.26 1 1.00e+01 1.00e-02 7.16e+01 dihedral pdb=" CB CYS D 662 " pdb=" SG CYS D 662 " pdb=" SG CYS D 671 " pdb=" CB CYS D 671 " ideal model delta sinusoidal sigma weight residual 93.00 162.68 -69.68 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -19.72 -66.28 1 1.00e+01 1.00e-02 5.74e+01 ... (remaining 16825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3090 0.044 - 0.088: 889 0.088 - 0.132: 325 0.132 - 0.177: 42 0.177 - 0.221: 7 Chirality restraints: 4353 Sorted by residual: chirality pdb=" CG LEU D 948 " pdb=" CB LEU D 948 " pdb=" CD1 LEU D 948 " pdb=" CD2 LEU D 948 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CG LEU I 78 " pdb=" CB LEU I 78 " pdb=" CD1 LEU I 78 " pdb=" CD2 LEU I 78 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLN D 957 " pdb=" N GLN D 957 " pdb=" C GLN D 957 " pdb=" CB GLN D 957 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 4350 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D1056 " -0.074 5.00e-02 4.00e+02 1.09e-01 1.92e+01 pdb=" N PRO D1057 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO D1057 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO D1057 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 560 " 0.059 5.00e-02 4.00e+02 8.99e-02 1.29e+01 pdb=" N PRO C 561 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO C 561 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 561 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 896 " 0.050 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO D 897 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 897 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 897 " 0.042 5.00e-02 4.00e+02 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 7 2.16 - 2.85: 9516 2.85 - 3.53: 37429 3.53 - 4.22: 63012 4.22 - 4.90: 106716 Nonbonded interactions: 216680 Sorted by model distance: nonbonded pdb=" OD2 ASP D 142 " pdb=" CZ3 TRP D 258 " model vdw 1.479 3.340 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.053 2.440 nonbonded pdb=" OE2 GLU D 725 " pdb=" NZ LYS D1028 " model vdw 2.094 2.520 nonbonded pdb=" O VAL A 951 " pdb=" ND2 ASN A 955 " model vdw 2.101 2.520 nonbonded pdb=" OD2 ASP A 142 " pdb=" CZ2 TRP A 258 " model vdw 2.120 3.340 ... (remaining 216675 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 143 or resid 161 or resid 166 through 332 or re \ sid 335 through 356 or (resid 357 and (name N or name CA or name C or name O or \ name CB )) or resid 358 through 377 or (resid 378 and (name N or name CA or name \ C or name O or name CB )) or resid 379 through 390 or (resid 391 and (name N or \ name CA or name C or name O or name CB )) or resid 392 through 518 or resid 530 \ through 579 or (resid 580 and (name N or name CA or name C or name O or name CB \ )) or resid 581 through 1141)) selection = (chain 'C' and (resid 20 through 143 or resid 161 or resid 166 through 1141)) selection = (chain 'D' and (resid 20 through 143 or resid 151 or resid 166 through 332 or re \ sid 335 through 518 or resid 530 through 579 or (resid 580 and (name N or name C \ A or name C or name O or name CB )) or resid 581 through 1141)) } ncs_group { reference = (chain 'G' and resid 1 through 113) selection = chain 'I' } ncs_group { reference = (chain 'J' and resid 1 through 104) selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.100 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 75.300 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.150 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5060 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 28299 Z= 0.206 Angle : 0.661 12.182 38489 Z= 0.355 Chirality : 0.047 0.221 4353 Planarity : 0.005 0.109 4992 Dihedral : 12.984 89.276 10089 Min Nonbonded Distance : 1.479 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.95 % Favored : 93.97 % Rotamer: Outliers : 0.07 % Allowed : 0.29 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.14), residues: 3498 helix: -0.58 (0.21), residues: 592 sheet: -0.45 (0.19), residues: 750 loop : -1.66 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 64 HIS 0.011 0.001 HIS D1101 PHE 0.032 0.002 PHE C 275 TYR 0.029 0.002 TYR A 873 ARG 0.016 0.001 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 374 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 658 ASN cc_start: 0.5996 (p0) cc_final: 0.5754 (p0) REVERT: A 43 PHE cc_start: 0.7469 (m-10) cc_final: 0.7150 (m-80) REVERT: A 815 ARG cc_start: 0.5600 (ptt-90) cc_final: 0.4166 (mtm110) REVERT: D 237 ARG cc_start: 0.4408 (ppt170) cc_final: 0.4110 (tmm160) REVERT: D 754 LEU cc_start: 0.6408 (mm) cc_final: 0.6096 (mt) REVERT: D 1107 ARG cc_start: 0.4523 (mtm180) cc_final: 0.3888 (tpt90) outliers start: 2 outliers final: 0 residues processed: 376 average time/residue: 0.3901 time to fit residues: 235.0720 Evaluate side-chains 294 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 2.9990 chunk 266 optimal weight: 0.8980 chunk 147 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 275 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 167 optimal weight: 0.5980 chunk 204 optimal weight: 20.0000 chunk 318 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 GLN ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN C 926 GLN A 66 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5167 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28299 Z= 0.205 Angle : 0.610 13.032 38489 Z= 0.321 Chirality : 0.046 0.281 4353 Planarity : 0.005 0.069 4992 Dihedral : 5.071 23.316 3812 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.97 % Favored : 94.00 % Rotamer: Outliers : 1.24 % Allowed : 6.41 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 3498 helix: -0.45 (0.20), residues: 616 sheet: -0.40 (0.19), residues: 759 loop : -1.68 (0.13), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 64 HIS 0.007 0.001 HIS D1101 PHE 0.018 0.002 PHE D 906 TYR 0.034 0.002 TYR A 873 ARG 0.007 0.000 ARG D 905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 318 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 658 ASN cc_start: 0.6140 (p0) cc_final: 0.5894 (p0) REVERT: C 720 ILE cc_start: 0.8002 (mm) cc_final: 0.7762 (mt) REVERT: A 815 ARG cc_start: 0.5685 (ptt-90) cc_final: 0.5091 (ptt90) REVERT: A 869 MET cc_start: 0.5977 (OUTLIER) cc_final: 0.5671 (ttp) REVERT: D 775 ASP cc_start: 0.6940 (m-30) cc_final: 0.6671 (m-30) REVERT: D 1089 PHE cc_start: -0.0324 (m-10) cc_final: -0.0961 (m-10) outliers start: 38 outliers final: 28 residues processed: 337 average time/residue: 0.3843 time to fit residues: 208.7193 Evaluate side-chains 320 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 291 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 991 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 177 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 265 optimal weight: 0.9990 chunk 217 optimal weight: 0.1980 chunk 87 optimal weight: 3.9990 chunk 319 optimal weight: 20.0000 chunk 344 optimal weight: 20.0000 chunk 284 optimal weight: 7.9990 chunk 316 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN C 953 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 GLN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 ASN ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 GLN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5240 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28299 Z= 0.217 Angle : 0.587 11.393 38489 Z= 0.311 Chirality : 0.045 0.316 4353 Planarity : 0.004 0.066 4992 Dihedral : 5.010 22.350 3812 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.92 % Allowed : 9.72 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.14), residues: 3498 helix: -0.40 (0.21), residues: 613 sheet: -0.35 (0.19), residues: 751 loop : -1.70 (0.13), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 64 HIS 0.005 0.001 HIS D1101 PHE 0.024 0.002 PHE C 888 TYR 0.028 0.002 TYR A 873 ARG 0.008 0.000 ARG D 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 315 time to evaluate : 2.707 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: C 314 GLN cc_start: 0.6324 (OUTLIER) cc_final: 0.6059 (tt0) REVERT: C 658 ASN cc_start: 0.6265 (p0) cc_final: 0.6058 (p0) REVERT: C 720 ILE cc_start: 0.8294 (mm) cc_final: 0.8091 (mt) REVERT: A 772 VAL cc_start: 0.7948 (m) cc_final: 0.7733 (m) REVERT: A 815 ARG cc_start: 0.5726 (ptt-90) cc_final: 0.3978 (mtm180) REVERT: D 740 MET cc_start: 0.5197 (tpp) cc_final: 0.4621 (tpp) REVERT: D 774 GLN cc_start: 0.7522 (mt0) cc_final: 0.7281 (mp10) REVERT: D 775 ASP cc_start: 0.6832 (m-30) cc_final: 0.6604 (m-30) REVERT: D 1089 PHE cc_start: -0.0081 (m-10) cc_final: -0.0735 (m-10) outliers start: 59 outliers final: 40 residues processed: 344 average time/residue: 0.3994 time to fit residues: 220.4622 Evaluate side-chains 334 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 293 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 902 MET Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 975 SER Chi-restraints excluded: chain D residue 1116 THR Chi-restraints excluded: chain G residue 111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 315 optimal weight: 9.9990 chunk 240 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 152 optimal weight: 20.0000 chunk 214 optimal weight: 10.0000 chunk 320 optimal weight: 30.0000 chunk 339 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 chunk 303 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 ASN ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5440 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 28299 Z= 0.341 Angle : 0.674 12.151 38489 Z= 0.361 Chirality : 0.047 0.244 4353 Planarity : 0.005 0.072 4992 Dihedral : 5.393 27.318 3812 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 2.83 % Allowed : 11.32 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.13), residues: 3498 helix: -0.61 (0.20), residues: 606 sheet: -0.38 (0.19), residues: 738 loop : -1.84 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 64 HIS 0.005 0.001 HIS A1048 PHE 0.031 0.002 PHE A 898 TYR 0.046 0.002 TYR D1047 ARG 0.008 0.001 ARG D 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 315 time to evaluate : 2.855 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: C 353 TRP cc_start: 0.5971 (p-90) cc_final: 0.5509 (p-90) REVERT: C 658 ASN cc_start: 0.6691 (p0) cc_final: 0.6421 (p0) REVERT: C 720 ILE cc_start: 0.8436 (mm) cc_final: 0.8203 (mt) REVERT: A 43 PHE cc_start: 0.7911 (m-80) cc_final: 0.7527 (m-80) REVERT: A 815 ARG cc_start: 0.5868 (ptt-90) cc_final: 0.3998 (mtm180) REVERT: D 740 MET cc_start: 0.5433 (tpp) cc_final: 0.4811 (tpp) REVERT: D 774 GLN cc_start: 0.7720 (mt0) cc_final: 0.7485 (mp10) REVERT: D 1089 PHE cc_start: 0.0012 (m-10) cc_final: -0.0641 (m-10) outliers start: 87 outliers final: 64 residues processed: 364 average time/residue: 0.3956 time to fit residues: 232.6531 Evaluate side-chains 353 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 289 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 777 ASN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 902 MET Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 975 SER Chi-restraints excluded: chain D residue 1116 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 4 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 282 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 252 optimal weight: 40.0000 chunk 139 optimal weight: 20.0000 chunk 289 optimal weight: 0.1980 chunk 234 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 173 optimal weight: 7.9990 chunk 304 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN C1011 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5432 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28299 Z= 0.272 Angle : 0.638 12.557 38489 Z= 0.339 Chirality : 0.046 0.272 4353 Planarity : 0.005 0.075 4992 Dihedral : 5.349 25.104 3812 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 2.96 % Allowed : 13.01 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.13), residues: 3498 helix: -0.55 (0.21), residues: 594 sheet: -0.43 (0.19), residues: 756 loop : -1.87 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1102 HIS 0.005 0.001 HIS A1064 PHE 0.024 0.002 PHE C 888 TYR 0.032 0.002 TYR D1047 ARG 0.007 0.001 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 315 time to evaluate : 2.904 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: C 353 TRP cc_start: 0.5997 (p-90) cc_final: 0.5761 (p-90) REVERT: C 658 ASN cc_start: 0.6690 (p0) cc_final: 0.6471 (p0) REVERT: C 720 ILE cc_start: 0.8516 (mm) cc_final: 0.8273 (mt) REVERT: C 902 MET cc_start: 0.5534 (mmp) cc_final: 0.3685 (ttp) REVERT: C 1045 LYS cc_start: 0.7659 (mmmt) cc_final: 0.7347 (mmmt) REVERT: A 43 PHE cc_start: 0.7793 (m-80) cc_final: 0.7394 (m-80) REVERT: A 789 TYR cc_start: 0.5967 (OUTLIER) cc_final: 0.5421 (m-80) REVERT: A 815 ARG cc_start: 0.5498 (ptt-90) cc_final: 0.4095 (mtm180) REVERT: A 909 ILE cc_start: 0.1396 (OUTLIER) cc_final: 0.0860 (mp) REVERT: D 740 MET cc_start: 0.5430 (tpp) cc_final: 0.4810 (tpp) REVERT: D 902 MET cc_start: 0.1926 (OUTLIER) cc_final: 0.1717 (ttm) REVERT: D 904 TYR cc_start: 0.4742 (OUTLIER) cc_final: 0.2775 (t80) REVERT: D 977 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5967 (pt) REVERT: D 1089 PHE cc_start: 0.0256 (m-10) cc_final: -0.0379 (m-10) REVERT: I 98 GLU cc_start: 0.1431 (OUTLIER) cc_final: 0.0241 (tm-30) outliers start: 91 outliers final: 70 residues processed: 370 average time/residue: 0.3779 time to fit residues: 226.8987 Evaluate side-chains 371 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 295 time to evaluate : 2.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 655 HIS Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 733 LYS Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 902 MET Chi-restraints excluded: chain D residue 904 TYR Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 975 SER Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1032 CYS Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1116 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 98 GLU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 4 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 114 optimal weight: 0.8980 chunk 305 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 339 optimal weight: 8.9990 chunk 281 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 784 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5375 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28299 Z= 0.218 Angle : 0.603 12.477 38489 Z= 0.319 Chirality : 0.045 0.241 4353 Planarity : 0.004 0.072 4992 Dihedral : 5.181 27.242 3812 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.38 % Favored : 92.60 % Rotamer: Outliers : 2.99 % Allowed : 13.98 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.14), residues: 3498 helix: -0.52 (0.21), residues: 598 sheet: -0.45 (0.19), residues: 771 loop : -1.78 (0.13), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 104 HIS 0.007 0.001 HIS A1048 PHE 0.025 0.001 PHE C 888 TYR 0.023 0.002 TYR D1047 ARG 0.005 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 316 time to evaluate : 3.424 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: C 214 ARG cc_start: 0.2331 (OUTLIER) cc_final: 0.2102 (ptp90) REVERT: C 658 ASN cc_start: 0.6677 (p0) cc_final: 0.6466 (p0) REVERT: C 720 ILE cc_start: 0.8459 (mm) cc_final: 0.8202 (mt) REVERT: C 901 GLN cc_start: 0.5071 (OUTLIER) cc_final: 0.3509 (tt0) REVERT: C 902 MET cc_start: 0.5744 (mmp) cc_final: 0.2738 (ttt) REVERT: C 1045 LYS cc_start: 0.7629 (mmmt) cc_final: 0.7324 (mmmt) REVERT: C 1050 MET cc_start: 0.6304 (ptp) cc_final: 0.5998 (ptp) REVERT: A 802 PHE cc_start: 0.6789 (m-10) cc_final: 0.6482 (m-80) REVERT: A 815 ARG cc_start: 0.5616 (ptt-90) cc_final: 0.3930 (mtm180) REVERT: A 909 ILE cc_start: 0.1167 (OUTLIER) cc_final: 0.0583 (mp) REVERT: A 948 LEU cc_start: 0.7478 (mt) cc_final: 0.7253 (mp) REVERT: D 740 MET cc_start: 0.5415 (tpp) cc_final: 0.4842 (tpp) REVERT: D 765 ARG cc_start: 0.6145 (ptm160) cc_final: 0.5535 (ptm160) REVERT: D 948 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8102 (mp) REVERT: D 1089 PHE cc_start: 0.0228 (m-10) cc_final: -0.0342 (m-10) REVERT: J 86 CYS cc_start: 0.1023 (OUTLIER) cc_final: 0.0669 (m) outliers start: 92 outliers final: 71 residues processed: 376 average time/residue: 0.3795 time to fit residues: 231.6265 Evaluate side-chains 373 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 297 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 655 HIS Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 733 LYS Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 975 SER Chi-restraints excluded: chain D residue 1032 CYS Chi-restraints excluded: chain D residue 1116 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 86 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 327 optimal weight: 50.0000 chunk 38 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 chunk 285 optimal weight: 1.9990 chunk 189 optimal weight: 0.2980 chunk 338 optimal weight: 20.0000 chunk 211 optimal weight: 8.9990 chunk 206 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN C 978 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5498 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 28299 Z= 0.312 Angle : 0.668 12.100 38489 Z= 0.356 Chirality : 0.047 0.285 4353 Planarity : 0.005 0.074 4992 Dihedral : 5.401 26.566 3812 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 3.54 % Allowed : 14.41 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.14), residues: 3498 helix: -0.77 (0.20), residues: 612 sheet: -0.55 (0.19), residues: 772 loop : -1.85 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 353 HIS 0.006 0.001 HIS C1048 PHE 0.022 0.002 PHE A 898 TYR 0.037 0.002 TYR D1047 ARG 0.007 0.001 ARG D 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 303 time to evaluate : 2.784 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: C 214 ARG cc_start: 0.2302 (OUTLIER) cc_final: 0.2071 (ptp90) REVERT: C 658 ASN cc_start: 0.6860 (p0) cc_final: 0.6620 (p0) REVERT: C 720 ILE cc_start: 0.8427 (mm) cc_final: 0.8195 (mt) REVERT: C 901 GLN cc_start: 0.5231 (OUTLIER) cc_final: 0.2983 (mt0) REVERT: C 902 MET cc_start: 0.6176 (mmp) cc_final: 0.5778 (mmp) REVERT: C 1045 LYS cc_start: 0.7540 (mmmt) cc_final: 0.7195 (mmmt) REVERT: A 43 PHE cc_start: 0.7712 (m-80) cc_final: 0.7464 (m-80) REVERT: A 297 SER cc_start: 0.8514 (OUTLIER) cc_final: 0.8059 (t) REVERT: A 725 GLU cc_start: 0.7986 (tt0) cc_final: 0.7727 (tt0) REVERT: A 789 TYR cc_start: 0.6119 (OUTLIER) cc_final: 0.5445 (m-80) REVERT: A 802 PHE cc_start: 0.7104 (m-10) cc_final: 0.6746 (m-80) REVERT: A 815 ARG cc_start: 0.5761 (ptt-90) cc_final: 0.4037 (mtm180) REVERT: A 909 ILE cc_start: 0.1768 (OUTLIER) cc_final: 0.1144 (mp) REVERT: D 740 MET cc_start: 0.5506 (tpp) cc_final: 0.4879 (tpp) REVERT: D 765 ARG cc_start: 0.6056 (ptm160) cc_final: 0.5847 (ptm160) REVERT: D 904 TYR cc_start: 0.4667 (OUTLIER) cc_final: 0.2609 (t80) REVERT: D 1089 PHE cc_start: 0.0256 (m-10) cc_final: -0.0326 (m-10) outliers start: 109 outliers final: 79 residues processed: 377 average time/residue: 0.3772 time to fit residues: 230.1569 Evaluate side-chains 382 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 297 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 733 LYS Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 904 TYR Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 975 SER Chi-restraints excluded: chain D residue 1032 CYS Chi-restraints excluded: chain D residue 1116 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 4 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 209 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 215 optimal weight: 20.0000 chunk 230 optimal weight: 20.0000 chunk 167 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 655 HIS ** D 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1058 HIS ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5555 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 28299 Z= 0.346 Angle : 0.708 12.929 38489 Z= 0.378 Chirality : 0.049 0.348 4353 Planarity : 0.005 0.078 4992 Dihedral : 5.614 28.676 3812 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 3.38 % Allowed : 14.99 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.13), residues: 3498 helix: -0.94 (0.20), residues: 609 sheet: -0.63 (0.19), residues: 761 loop : -2.01 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C1102 HIS 0.007 0.001 HIS D 655 PHE 0.025 0.002 PHE C 888 TYR 0.041 0.002 TYR D1047 ARG 0.014 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 308 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 214 ARG cc_start: 0.2241 (OUTLIER) cc_final: 0.1965 (ptp90) REVERT: C 658 ASN cc_start: 0.6909 (p0) cc_final: 0.3625 (p0) REVERT: C 720 ILE cc_start: 0.8389 (mm) cc_final: 0.8161 (mt) REVERT: C 790 LYS cc_start: 0.7640 (mttt) cc_final: 0.7309 (mmmt) REVERT: C 901 GLN cc_start: 0.5426 (OUTLIER) cc_final: 0.3383 (mt0) REVERT: C 949 GLN cc_start: 0.6504 (OUTLIER) cc_final: 0.6272 (mm110) REVERT: C 1045 LYS cc_start: 0.7593 (mmmt) cc_final: 0.7264 (mmmt) REVERT: A 297 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8117 (t) REVERT: A 789 TYR cc_start: 0.6135 (OUTLIER) cc_final: 0.5389 (m-80) REVERT: A 802 PHE cc_start: 0.7005 (m-10) cc_final: 0.6729 (m-80) REVERT: A 815 ARG cc_start: 0.5828 (ptt-90) cc_final: 0.4091 (mtm180) REVERT: A 909 ILE cc_start: 0.2005 (OUTLIER) cc_final: 0.1415 (mp) REVERT: A 950 ASN cc_start: 0.6348 (p0) cc_final: 0.5905 (p0) REVERT: D 224 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6694 (pm20) REVERT: D 740 MET cc_start: 0.5500 (tpp) cc_final: 0.4844 (tpp) REVERT: D 904 TYR cc_start: 0.4718 (OUTLIER) cc_final: 0.2773 (t80) REVERT: D 1089 PHE cc_start: 0.0426 (m-10) cc_final: -0.0146 (m-10) outliers start: 104 outliers final: 79 residues processed: 376 average time/residue: 0.3999 time to fit residues: 244.8460 Evaluate side-chains 383 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 296 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 733 LYS Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 904 TYR Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 975 SER Chi-restraints excluded: chain D residue 1032 CYS Chi-restraints excluded: chain D residue 1116 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 4 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 307 optimal weight: 6.9990 chunk 324 optimal weight: 0.0270 chunk 295 optimal weight: 1.9990 chunk 315 optimal weight: 9.9990 chunk 189 optimal weight: 1.9990 chunk 137 optimal weight: 30.0000 chunk 247 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 284 optimal weight: 4.9990 chunk 298 optimal weight: 0.8980 chunk 314 optimal weight: 8.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 207 HIS ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5421 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 28299 Z= 0.217 Angle : 0.641 15.958 38489 Z= 0.336 Chirality : 0.046 0.306 4353 Planarity : 0.005 0.076 4992 Dihedral : 5.318 25.065 3812 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.98 % Favored : 93.00 % Rotamer: Outliers : 2.76 % Allowed : 15.84 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.14), residues: 3498 helix: -0.74 (0.20), residues: 608 sheet: -0.54 (0.19), residues: 762 loop : -1.86 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.009 0.001 HIS A1048 PHE 0.024 0.001 PHE C 888 TYR 0.023 0.002 TYR A 741 ARG 0.008 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 317 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 720 ILE cc_start: 0.8233 (mm) cc_final: 0.7928 (mt) REVERT: C 790 LYS cc_start: 0.7564 (mttt) cc_final: 0.7205 (mmmt) REVERT: C 901 GLN cc_start: 0.5073 (OUTLIER) cc_final: 0.3724 (tt0) REVERT: C 902 MET cc_start: 0.5889 (mmp) cc_final: 0.2997 (ttp) REVERT: C 1045 LYS cc_start: 0.7665 (mmmt) cc_final: 0.7387 (mmmt) REVERT: A 297 SER cc_start: 0.8563 (OUTLIER) cc_final: 0.8125 (t) REVERT: A 789 TYR cc_start: 0.6042 (OUTLIER) cc_final: 0.5054 (m-80) REVERT: A 802 PHE cc_start: 0.6909 (m-10) cc_final: 0.6627 (m-80) REVERT: A 815 ARG cc_start: 0.5667 (ptt-90) cc_final: 0.3960 (mtm180) REVERT: D 224 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6612 (pm20) REVERT: D 620 VAL cc_start: 0.4208 (OUTLIER) cc_final: 0.3986 (m) REVERT: D 703 ASN cc_start: 0.7784 (t0) cc_final: 0.7237 (t0) REVERT: D 740 MET cc_start: 0.5396 (tpp) cc_final: 0.4874 (tpp) REVERT: D 904 TYR cc_start: 0.4562 (OUTLIER) cc_final: 0.2499 (t80) REVERT: D 1089 PHE cc_start: 0.0400 (m-10) cc_final: -0.0133 (m-10) REVERT: D 1109 PHE cc_start: 0.3535 (t80) cc_final: 0.3185 (t80) REVERT: K 4 MET cc_start: -0.0819 (ptp) cc_final: -0.1734 (ppp) outliers start: 85 outliers final: 71 residues processed: 375 average time/residue: 0.3755 time to fit residues: 226.9421 Evaluate side-chains 379 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 302 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 733 LYS Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 786 LYS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 904 TYR Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 975 SER Chi-restraints excluded: chain D residue 1032 CYS Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 4 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 207 optimal weight: 9.9990 chunk 333 optimal weight: 40.0000 chunk 203 optimal weight: 7.9990 chunk 158 optimal weight: 0.5980 chunk 231 optimal weight: 7.9990 chunk 349 optimal weight: 6.9990 chunk 321 optimal weight: 0.7980 chunk 278 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 215 optimal weight: 30.0000 chunk 170 optimal weight: 0.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 HIS ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 28299 Z= 0.266 Angle : 0.670 25.645 38489 Z= 0.350 Chirality : 0.047 0.326 4353 Planarity : 0.005 0.077 4992 Dihedral : 5.356 26.701 3812 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.52 % Favored : 91.45 % Rotamer: Outliers : 2.60 % Allowed : 16.07 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.14), residues: 3498 helix: -0.75 (0.20), residues: 607 sheet: -0.52 (0.19), residues: 753 loop : -1.88 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.006 0.001 HIS C1048 PHE 0.029 0.002 PHE D 275 TYR 0.029 0.002 TYR D1047 ARG 0.010 0.001 ARG C 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 299 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.4822 (tpp) cc_final: 0.4121 (ttt) REVERT: C 790 LYS cc_start: 0.7568 (mttt) cc_final: 0.7231 (mmmt) REVERT: C 901 GLN cc_start: 0.5016 (OUTLIER) cc_final: 0.3644 (tt0) REVERT: C 902 MET cc_start: 0.5687 (mmp) cc_final: 0.3078 (ttt) REVERT: C 1045 LYS cc_start: 0.7608 (mmmt) cc_final: 0.7276 (mmmt) REVERT: C 1050 MET cc_start: 0.6158 (ptp) cc_final: 0.5846 (ptm) REVERT: A 297 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8112 (t) REVERT: A 789 TYR cc_start: 0.6162 (OUTLIER) cc_final: 0.5264 (m-80) REVERT: A 802 PHE cc_start: 0.7028 (m-10) cc_final: 0.6695 (m-80) REVERT: A 815 ARG cc_start: 0.5771 (ptt-90) cc_final: 0.4059 (mtm180) REVERT: A 909 ILE cc_start: 0.1459 (OUTLIER) cc_final: 0.0854 (mp) REVERT: D 224 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6693 (pm20) REVERT: D 620 VAL cc_start: 0.4237 (OUTLIER) cc_final: 0.4002 (m) REVERT: D 740 MET cc_start: 0.5508 (tpp) cc_final: 0.4982 (tpp) REVERT: D 904 TYR cc_start: 0.4634 (OUTLIER) cc_final: 0.2578 (t80) REVERT: D 1089 PHE cc_start: 0.0380 (m-10) cc_final: -0.0121 (m-10) REVERT: D 1109 PHE cc_start: 0.3564 (t80) cc_final: 0.3299 (t80) REVERT: K 4 MET cc_start: -0.0702 (ptp) cc_final: -0.1663 (ppp) outliers start: 80 outliers final: 69 residues processed: 351 average time/residue: 0.3999 time to fit residues: 225.9061 Evaluate side-chains 370 residues out of total 3087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 294 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 733 LYS Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 904 TYR Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 975 SER Chi-restraints excluded: chain D residue 1032 CYS Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 4 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 221 optimal weight: 0.8980 chunk 296 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 256 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 278 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 51 optimal weight: 0.0980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 953 ASN C1002 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 HIS D 422 ASN ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.260990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.226349 restraints weight = 49203.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.223941 restraints weight = 63321.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.225439 restraints weight = 52372.140| |-----------------------------------------------------------------------------| r_work (final): 0.4576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5323 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 28299 Z= 0.199 Angle : 0.634 26.265 38489 Z= 0.328 Chirality : 0.046 0.284 4353 Planarity : 0.004 0.074 4992 Dihedral : 5.151 24.042 3812 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.69 % Favored : 93.28 % Rotamer: Outliers : 2.50 % Allowed : 16.39 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.14), residues: 3498 helix: -0.70 (0.20), residues: 625 sheet: -0.50 (0.19), residues: 753 loop : -1.78 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 436 HIS 0.007 0.001 HIS A1048 PHE 0.025 0.001 PHE C 888 TYR 0.022 0.001 TYR A 741 ARG 0.012 0.000 ARG A 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5661.01 seconds wall clock time: 104 minutes 3.23 seconds (6243.23 seconds total)