Starting phenix.real_space_refine on Thu Aug 8 02:57:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tge_25880/08_2024/7tge_25880.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tge_25880/08_2024/7tge_25880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tge_25880/08_2024/7tge_25880.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tge_25880/08_2024/7tge_25880.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tge_25880/08_2024/7tge_25880.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tge_25880/08_2024/7tge_25880.cif" } resolution = 3.68 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= -0.002 sd= 0.139 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 93 5.16 5 C 13695 2.51 5 N 3504 2.21 5 O 4169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 21461 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8076 Classifications: {'peptide': 1030} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 50, 'TRANS': 979} Chain breaks: 7 Chain: "B" Number of atoms: 6562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 842, 6562 Classifications: {'peptide': 842} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 38, 'TRANS': 803} Chain breaks: 8 Chain: "C" Number of atoms: 6263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6263 Classifications: {'peptide': 805} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 767} Chain breaks: 10 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 11.68, per 1000 atoms: 0.54 Number of scatterers: 21461 At special positions: 0 Unit cell: (129.6, 132.84, 174.96, 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 93 16.00 O 4169 8.00 N 3504 7.00 C 13695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1201 " - " ASN A 61 " " NAG A1202 " - " ASN A 282 " " NAG A1203 " - " ASN A 331 " " NAG A1204 " - " ASN A 657 " " NAG A1205 " - " ASN A 709 " " NAG A1206 " - " ASN A 234 " " NAG B1201 " - " ASN B 61 " " NAG B1202 " - " ASN B 165 " " NAG B1203 " - " ASN B 282 " " NAG B1204 " - " ASN B 616 " " NAG B1205 " - " ASN B 709 " " NAG B1206 " - " ASN B1098 " " NAG B1207 " - " ASN B 122 " " NAG B1208 " - " ASN B1134 " " NAG C1201 " - " ASN C 61 " " NAG C1202 " - " ASN C 234 " " NAG C1203 " - " ASN C 616 " " NAG C1204 " - " ASN C 709 " " NAG C1205 " - " ASN C 801 " " NAG C1206 " - " ASN C1098 " " NAG C1207 " - " ASN C1134 " " NAG C1208 " - " ASN C 165 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 616 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN C 717 " Time building additional restraints: 8.38 Conformation dependent library (CDL) restraints added in 4.1 seconds 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5030 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 40 sheets defined 27.5% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.50 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.579A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 370 removed outlier: 4.052A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 370' Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.144A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.167A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 629 through 632 removed outlier: 3.835A pdb=" N THR A 632 " --> pdb=" O LEU A 629 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 629 through 632' Processing helix chain 'A' and resid 633 through 639 removed outlier: 3.565A pdb=" N GLY A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.634A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.699A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.627A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 removed outlier: 4.507A pdb=" N GLN A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.560A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.689A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.652A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 4.073A pdb=" N ASP A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 623 removed outlier: 3.953A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 634 through 638 removed outlier: 3.652A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 638' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.789A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.661A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.964A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.508A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.532A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.712A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.904A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.800A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 619 through 623 removed outlier: 3.535A pdb=" N VAL C 622 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.841A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.702A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.462A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.717A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 968 Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.887A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.105A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.920A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.481A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 226 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.021A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.140A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.867A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.592A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.548A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.123A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.784A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.807A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.335A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.383A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1098 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.950A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.103A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.143A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.963A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 543 removed outlier: 3.942A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.103A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.548A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1047 through 1048 removed outlier: 3.966A pdb=" N PHE B1103 " --> pdb=" O VAL B1096 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.582A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.150A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.774A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.264A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.889A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.570A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.998A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AD9, first strand: chain 'C' and resid 717 through 722 removed outlier: 6.410A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 717 through 722 removed outlier: 6.410A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.547A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.610A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1094 through 1097 897 hydrogen bonds defined for protein. 2496 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.58 Time building geometry restraints manager: 9.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6773 1.35 - 1.47: 5349 1.47 - 1.59: 9675 1.59 - 1.71: 0 1.71 - 1.83: 117 Bond restraints: 21914 Sorted by residual: bond pdb=" C THR B 630 " pdb=" N PRO B 631 " ideal model delta sigma weight residual 1.335 1.378 -0.043 8.70e-03 1.32e+04 2.46e+01 bond pdb=" N GLN B1106 " pdb=" CA GLN B1106 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N VAL B1094 " pdb=" CA VAL B1094 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.18e-02 7.18e+03 1.01e+01 bond pdb=" N VAL B1104 " pdb=" CA VAL B1104 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.20e-02 6.94e+03 9.38e+00 bond pdb=" N VAL B1096 " pdb=" CA VAL B1096 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.46e+00 ... (remaining 21909 not shown) Histogram of bond angle deviations from ideal: 98.25 - 105.44: 441 105.44 - 112.63: 11525 112.63 - 119.82: 7253 119.82 - 127.01: 10374 127.01 - 134.20: 197 Bond angle restraints: 29790 Sorted by residual: angle pdb=" C ILE B 834 " pdb=" N LYS B 835 " pdb=" CA LYS B 835 " ideal model delta sigma weight residual 121.54 131.85 -10.31 1.91e+00 2.74e-01 2.91e+01 angle pdb=" C PHE B 32 " pdb=" CA PHE B 32 " pdb=" CB PHE B 32 " ideal model delta sigma weight residual 116.54 110.39 6.15 1.15e+00 7.56e-01 2.86e+01 angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 122.08 128.65 -6.57 1.47e+00 4.63e-01 2.00e+01 angle pdb=" C ASN B 87 " pdb=" CA ASN B 87 " pdb=" CB ASN B 87 " ideal model delta sigma weight residual 115.79 110.48 5.31 1.19e+00 7.06e-01 1.99e+01 angle pdb=" N ASN B1098 " pdb=" CA ASN B1098 " pdb=" C ASN B1098 " ideal model delta sigma weight residual 112.92 107.58 5.34 1.23e+00 6.61e-01 1.89e+01 ... (remaining 29785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12464 17.93 - 35.85: 912 35.85 - 53.78: 155 53.78 - 71.70: 43 71.70 - 89.63: 24 Dihedral angle restraints: 13598 sinusoidal: 5811 harmonic: 7787 Sorted by residual: dihedral pdb=" CA CYS A1082 " pdb=" C CYS A1082 " pdb=" N HIS A1083 " pdb=" CA HIS A1083 " ideal model delta harmonic sigma weight residual 180.00 150.08 29.92 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -130.75 44.75 1 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" CA ASP B 985 " pdb=" C ASP B 985 " pdb=" N LYS B 986 " pdb=" CA LYS B 986 " ideal model delta harmonic sigma weight residual -180.00 -154.91 -25.09 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 13595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 3501 0.143 - 0.285: 39 0.285 - 0.428: 6 0.428 - 0.571: 1 0.571 - 0.714: 1 Chirality restraints: 3548 Sorted by residual: chirality pdb=" C1 NAG C1201 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1201 " pdb=" O5 NAG C1201 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" C1 NAG B1206 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1206 " pdb=" O5 NAG B1206 " both_signs ideal model delta sigma weight residual False -2.40 -2.92 0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" C2 NAG B1208 " pdb=" C1 NAG B1208 " pdb=" C3 NAG B1208 " pdb=" N2 NAG B1208 " both_signs ideal model delta sigma weight residual False -2.49 -2.14 -0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 3545 not shown) Planarity restraints: 3806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1098 " -0.027 2.00e-02 2.50e+03 2.86e-02 1.02e+01 pdb=" CG ASN B1098 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B1098 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B1098 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG B1206 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 633 " -0.018 2.00e-02 2.50e+03 1.98e-02 9.78e+00 pdb=" CG TRP A 633 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 633 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 633 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 633 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 633 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 633 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 633 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 633 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 633 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 294 " -0.043 5.00e-02 4.00e+02 6.52e-02 6.79e+00 pdb=" N PRO C 295 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " -0.036 5.00e-02 4.00e+02 ... (remaining 3803 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5194 2.80 - 3.32: 18596 3.32 - 3.85: 36361 3.85 - 4.37: 41084 4.37 - 4.90: 71700 Nonbonded interactions: 172935 Sorted by model distance: nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.270 3.040 nonbonded pdb=" O ALA B 879 " pdb=" OG1 THR B 883 " model vdw 2.294 3.040 nonbonded pdb=" OD1 ASN C 540 " pdb=" OG1 THR C 549 " model vdw 2.299 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.301 3.040 nonbonded pdb=" O LEU C 966 " pdb=" OG SER C 975 " model vdw 2.309 3.040 ... (remaining 172930 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 27 through 137 or resid 166 through 210 or resid 216 throu \ gh 623 or resid 638 through 677 or resid 689 through 827 or resid 854 through 11 \ 47 or resid 1201 through 1208)) selection = (chain 'C' and (resid 27 through 331 or resid 528 through 677 or resid 689 throu \ gh 1147 or resid 1201 through 1208)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 61.550 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.180 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:3.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21914 Z= 0.282 Angle : 0.761 12.213 29790 Z= 0.408 Chirality : 0.056 0.714 3548 Planarity : 0.006 0.065 3775 Dihedral : 13.344 89.626 8472 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.09 % Allowed : 0.51 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 2622 helix: -0.79 (0.17), residues: 632 sheet: 0.05 (0.24), residues: 468 loop : -1.19 (0.14), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 633 HIS 0.010 0.001 HIS A 519 PHE 0.040 0.002 PHE A 275 TYR 0.021 0.002 TYR A 904 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 633 TRP cc_start: 0.7392 (m-90) cc_final: 0.6961 (m-90) REVERT: B 740 MET cc_start: 0.8440 (tpp) cc_final: 0.8159 (tpt) REVERT: C 1029 MET cc_start: 0.7708 (tpp) cc_final: 0.7497 (tpp) outliers start: 2 outliers final: 0 residues processed: 60 average time/residue: 0.3569 time to fit residues: 35.8036 Evaluate side-chains 45 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 136 optimal weight: 0.0980 chunk 108 optimal weight: 0.9990 chunk 209 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 242 optimal weight: 4.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 913 GLN B 919 ASN B1011 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21914 Z= 0.208 Angle : 0.570 9.967 29790 Z= 0.298 Chirality : 0.046 0.588 3548 Planarity : 0.004 0.055 3775 Dihedral : 7.265 56.955 3679 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.13 % Allowed : 3.54 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.16), residues: 2622 helix: 0.67 (0.20), residues: 626 sheet: -0.13 (0.21), residues: 557 loop : -1.02 (0.15), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 633 HIS 0.007 0.001 HIS B1048 PHE 0.017 0.001 PHE C 275 TYR 0.022 0.001 TYR A1067 ARG 0.018 0.001 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 633 TRP cc_start: 0.7144 (m-90) cc_final: 0.6757 (m-90) REVERT: C 1029 MET cc_start: 0.7567 (tpp) cc_final: 0.7218 (tpp) outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 0.3289 time to fit residues: 27.5591 Evaluate side-chains 44 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 0.0980 chunk 75 optimal weight: 5.9990 chunk 201 optimal weight: 30.0000 chunk 165 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 242 optimal weight: 7.9990 chunk 262 optimal weight: 9.9990 chunk 216 optimal weight: 7.9990 chunk 240 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 194 optimal weight: 20.0000 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 580 GLN A 681 HIS ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21914 Z= 0.304 Angle : 0.616 9.691 29790 Z= 0.319 Chirality : 0.047 0.561 3548 Planarity : 0.004 0.056 3775 Dihedral : 7.098 57.146 3679 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.34 % Allowed : 5.85 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.16), residues: 2622 helix: 0.77 (0.20), residues: 631 sheet: -0.47 (0.21), residues: 546 loop : -1.10 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 633 HIS 0.007 0.001 HIS B1048 PHE 0.021 0.002 PHE B 318 TYR 0.030 0.002 TYR A 904 ARG 0.007 0.001 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 2.626 Fit side-chains revert: symmetry clash REVERT: A 633 TRP cc_start: 0.7397 (m-90) cc_final: 0.7184 (m-10) REVERT: B 740 MET cc_start: 0.8927 (tpp) cc_final: 0.8623 (tpp) outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 0.3096 time to fit residues: 27.5094 Evaluate side-chains 42 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 0.9990 chunk 182 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 163 optimal weight: 0.6980 chunk 243 optimal weight: 0.7980 chunk 258 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 231 optimal weight: 0.9980 chunk 69 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21914 Z= 0.120 Angle : 0.502 12.487 29790 Z= 0.258 Chirality : 0.044 0.539 3548 Planarity : 0.003 0.043 3775 Dihedral : 6.648 57.182 3679 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.56 % Allowed : 6.96 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.16), residues: 2622 helix: 1.49 (0.21), residues: 627 sheet: -0.27 (0.21), residues: 564 loop : -0.95 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 633 HIS 0.004 0.001 HIS B1048 PHE 0.019 0.001 PHE B 318 TYR 0.017 0.001 TYR A1067 ARG 0.005 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 2.467 Fit side-chains REVERT: A 633 TRP cc_start: 0.7199 (m-90) cc_final: 0.6691 (m-10) REVERT: A 1050 MET cc_start: 0.6675 (mtt) cc_final: 0.6436 (mtt) REVERT: B 740 MET cc_start: 0.8919 (tpp) cc_final: 0.8627 (tpp) outliers start: 13 outliers final: 5 residues processed: 57 average time/residue: 0.3053 time to fit residues: 31.1050 Evaluate side-chains 42 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 994 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 192 optimal weight: 30.0000 chunk 106 optimal weight: 7.9990 chunk 220 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 chunk 231 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 21914 Z= 0.394 Angle : 0.699 11.692 29790 Z= 0.357 Chirality : 0.048 0.350 3548 Planarity : 0.005 0.057 3775 Dihedral : 7.322 67.919 3679 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.02 % Allowed : 8.16 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.16), residues: 2622 helix: 0.65 (0.20), residues: 645 sheet: -0.71 (0.21), residues: 550 loop : -1.08 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 633 HIS 0.008 0.002 HIS B1048 PHE 0.032 0.002 PHE A 374 TYR 0.031 0.002 TYR C1067 ARG 0.004 0.001 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 42 time to evaluate : 2.460 Fit side-chains REVERT: B 740 MET cc_start: 0.8925 (tpp) cc_final: 0.8620 (tpp) REVERT: B 873 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.8147 (m-10) outliers start: 24 outliers final: 17 residues processed: 64 average time/residue: 0.3302 time to fit residues: 37.9580 Evaluate side-chains 54 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 36 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 963 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 10.0000 chunk 232 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 258 optimal weight: 0.7980 chunk 214 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN C 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2289 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: