Starting phenix.real_space_refine on Tue Mar 19 15:40:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iot_35623/03_2024/8iot_35623.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iot_35623/03_2024/8iot_35623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iot_35623/03_2024/8iot_35623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iot_35623/03_2024/8iot_35623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iot_35623/03_2024/8iot_35623.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iot_35623/03_2024/8iot_35623.pdb" } resolution = 2.51 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 15714 2.51 5 N 4041 2.21 5 O 4779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24642 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 7990 Classifications: {'peptide': 1021} Link IDs: {'PTRANS': 53, 'TRANS': 967} Chain breaks: 7 Chain: "B" Number of atoms: 7990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 7990 Classifications: {'peptide': 1021} Link IDs: {'PTRANS': 53, 'TRANS': 967} Chain breaks: 7 Chain: "C" Number of atoms: 7990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 7990 Classifications: {'peptide': 1021} Link IDs: {'PTRANS': 53, 'TRANS': 967} Chain breaks: 7 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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 15.97, per 1000 atoms: 0.65 Number of scatterers: 24642 At special positions: 0 Unit cell: (138.69, 137.685, 167.835, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4779 8.00 N 4041 7.00 C 15714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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=2.03 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=2.04 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 391 " - pdb=" SG CYS C 525 " 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=2.03 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=2.03 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=2.03 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B1134 " " NAG B1312 " - " ASN B 343 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C1134 " " NAG C1312 " - " ASN C 343 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B 801 " " NAG H 1 " - " ASN C 717 " " NAG I 1 " - " ASN C 801 " Time building additional restraints: 9.30 Conformation dependent library (CDL) restraints added in 4.4 seconds 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5748 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 42 sheets defined 24.0% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.511A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.814A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.797A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.831A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.792A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.121A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.548A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.849A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.914A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.512A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.815A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.797A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.831A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.792A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.122A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.547A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.849A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.915A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.511A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.814A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.797A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.831A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.793A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (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 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.122A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.548A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.849A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.914A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 5.973A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.749A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.012A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.612A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.308A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.749A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.016A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.050A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.834A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.559A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.455A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 25 through 28 removed outlier: 5.973A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.749A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.012A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.612A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.308A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.015A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.050A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.834A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.559A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 787 through 789 removed outlier: 5.462A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 25 through 28 removed outlier: 5.973A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.012A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.612A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.307A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.015A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.049A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.835A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.558A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1121 Processing sheet with id=AE6, first strand: chain 'C' and resid 1094 through 1097 934 hydrogen bonds defined for protein. 2559 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: 9.98 Time building geometry restraints manager: 9.96 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: 7747 1.34 - 1.46: 6250 1.46 - 1.59: 11068 1.59 - 1.71: 0 1.71 - 1.83: 135 Bond restraints: 25200 Sorted by residual: bond pdb=" C1 NAG A1307 " pdb=" O5 NAG A1307 " ideal model delta sigma weight residual 1.406 1.527 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.527 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.527 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 25195 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.13: 789 107.13 - 113.84: 14177 113.84 - 120.55: 9276 120.55 - 127.26: 9815 127.26 - 133.97: 227 Bond angle restraints: 34284 Sorted by residual: angle pdb=" C VAL A 656 " pdb=" N ASN A 657 " pdb=" CA ASN A 657 " ideal model delta sigma weight residual 120.38 128.09 -7.71 1.46e+00 4.69e-01 2.79e+01 angle pdb=" C VAL B 656 " pdb=" N ASN B 657 " pdb=" CA ASN B 657 " ideal model delta sigma weight residual 120.38 128.06 -7.68 1.46e+00 4.69e-01 2.77e+01 angle pdb=" C VAL C 656 " pdb=" N ASN C 657 " pdb=" CA ASN C 657 " ideal model delta sigma weight residual 120.38 128.06 -7.68 1.46e+00 4.69e-01 2.77e+01 angle pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " pdb=" C5 NAG C1307 " ideal model delta sigma weight residual 113.21 125.00 -11.79 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " pdb=" C5 NAG B1307 " ideal model delta sigma weight residual 113.21 124.95 -11.74 3.00e+00 1.11e-01 1.53e+01 ... (remaining 34279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 14630 17.44 - 34.88: 846 34.88 - 52.32: 121 52.32 - 69.76: 42 69.76 - 87.20: 15 Dihedral angle restraints: 15654 sinusoidal: 6729 harmonic: 8925 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -132.98 46.98 1 1.00e+01 1.00e-02 3.05e+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 -132.95 46.95 1 1.00e+01 1.00e-02 3.05e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -132.94 46.94 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 15651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 3923 0.112 - 0.223: 102 0.223 - 0.335: 1 0.335 - 0.446: 3 0.446 - 0.558: 3 Chirality restraints: 4032 Sorted by residual: chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.96 0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 657 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.96 0.56 2.00e-01 2.50e+01 7.73e+00 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.96 0.56 2.00e-01 2.50e+01 7.72e+00 ... (remaining 4029 not shown) Planarity restraints: 4404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 657 " 0.010 2.00e-02 2.50e+03 5.57e-02 3.88e+01 pdb=" CG ASN C 657 " -0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN C 657 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN C 657 " -0.059 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " 0.011 2.00e-02 2.50e+03 5.57e-02 3.87e+01 pdb=" CG ASN B 657 " -0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " -0.059 2.00e-02 2.50e+03 pdb=" C1 NAG B1307 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 657 " 0.010 2.00e-02 2.50e+03 5.55e-02 3.85e+01 pdb=" CG ASN A 657 " -0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN A 657 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN A 657 " -0.059 2.00e-02 2.50e+03 pdb=" C1 NAG A1307 " 0.054 2.00e-02 2.50e+03 ... (remaining 4401 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 744 2.72 - 3.26: 23526 3.26 - 3.81: 36985 3.81 - 4.35: 46103 4.35 - 4.90: 81084 Nonbonded interactions: 188442 Sorted by model distance: nonbonded pdb=" OG SER C 735 " pdb=" OG1 THR C 859 " model vdw 2.169 2.440 nonbonded pdb=" OG SER A 735 " pdb=" OG1 THR A 859 " model vdw 2.169 2.440 nonbonded pdb=" OG SER B 735 " pdb=" OG1 THR B 859 " model vdw 2.169 2.440 nonbonded pdb=" O PRO B 230 " pdb=" NH1 ARG C 357 " model vdw 2.200 2.520 nonbonded pdb=" O PRO A 230 " pdb=" NH1 ARG B 357 " model vdw 2.206 2.520 ... (remaining 188437 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.820 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: 13.400 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 68.190 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.200 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:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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 0.121 25200 Z= 0.236 Angle : 0.566 11.787 34284 Z= 0.297 Chirality : 0.049 0.558 4032 Planarity : 0.004 0.039 4362 Dihedral : 11.070 87.200 9789 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.21 (0.15), residues: 3015 helix: 2.59 (0.22), residues: 609 sheet: 0.87 (0.20), residues: 669 loop : -1.13 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 64 HIS 0.002 0.000 HIS B 339 PHE 0.020 0.001 PHE C 906 TYR 0.016 0.001 TYR A 655 ARG 0.003 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 3.021 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: A 140 PHE cc_start: 0.7672 (p90) cc_final: 0.7417 (p90) REVERT: A 160 TYR cc_start: 0.8098 (p90) cc_final: 0.7818 (p90) REVERT: A 902 MET cc_start: 0.9289 (tpt) cc_final: 0.9039 (tpt) REVERT: A 955 ASN cc_start: 0.8130 (m-40) cc_final: 0.7915 (t0) REVERT: A 987 PRO cc_start: 0.8103 (Cg_endo) cc_final: 0.7559 (Cg_exo) REVERT: B 140 PHE cc_start: 0.7659 (p90) cc_final: 0.7401 (p90) REVERT: B 160 TYR cc_start: 0.8226 (p90) cc_final: 0.7939 (p90) REVERT: B 955 ASN cc_start: 0.8126 (m-40) cc_final: 0.7894 (t0) REVERT: B 987 PRO cc_start: 0.7942 (Cg_endo) cc_final: 0.7372 (Cg_exo) REVERT: C 140 PHE cc_start: 0.7582 (p90) cc_final: 0.7230 (p90) REVERT: C 160 TYR cc_start: 0.8241 (p90) cc_final: 0.7964 (p90) REVERT: C 560 LEU cc_start: 0.8913 (mt) cc_final: 0.8618 (mp) REVERT: C 955 ASN cc_start: 0.8113 (m-40) cc_final: 0.7880 (t0) REVERT: C 987 PRO cc_start: 0.8086 (Cg_endo) cc_final: 0.7663 (Cg_exo) outliers start: 0 outliers final: 2 residues processed: 337 average time/residue: 0.8940 time to fit residues: 369.8810 Evaluate side-chains 193 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain C residue 368 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.7980 chunk 231 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 145 optimal weight: 0.0870 chunk 178 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 339 HIS A 448 ASN A 755 GLN B 207 HIS B 339 HIS B 394 ASN B 448 ASN C 339 HIS C 755 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25200 Z= 0.170 Angle : 0.554 10.865 34284 Z= 0.284 Chirality : 0.046 0.371 4032 Planarity : 0.004 0.053 4362 Dihedral : 7.427 58.721 4291 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.30 % Allowed : 6.67 % Favored : 92.02 % 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: 0.42 (0.15), residues: 3015 helix: 2.33 (0.21), residues: 666 sheet: 1.12 (0.19), residues: 735 loop : -1.08 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 436 HIS 0.006 0.001 HIS B 207 PHE 0.027 0.001 PHE A 429 TYR 0.025 0.001 TYR B 453 ARG 0.004 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 206 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7639 (p90) cc_final: 0.7283 (p90) REVERT: A 160 TYR cc_start: 0.8237 (p90) cc_final: 0.7782 (p90) REVERT: A 168 PHE cc_start: 0.7868 (t80) cc_final: 0.7588 (t80) REVERT: A 902 MET cc_start: 0.9258 (tpt) cc_final: 0.9007 (tpt) REVERT: A 955 ASN cc_start: 0.8129 (m-40) cc_final: 0.7922 (t0) REVERT: B 140 PHE cc_start: 0.7761 (p90) cc_final: 0.7530 (p90) REVERT: B 160 TYR cc_start: 0.8387 (p90) cc_final: 0.7731 (p90) REVERT: B 753 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8471 (tp) REVERT: B 955 ASN cc_start: 0.8160 (m-40) cc_final: 0.7937 (t0) REVERT: C 140 PHE cc_start: 0.7745 (p90) cc_final: 0.7293 (p90) REVERT: C 160 TYR cc_start: 0.8279 (p90) cc_final: 0.7684 (p90) REVERT: C 560 LEU cc_start: 0.8942 (mt) cc_final: 0.8645 (mp) REVERT: C 955 ASN cc_start: 0.8144 (m-40) cc_final: 0.7930 (t0) outliers start: 35 outliers final: 14 residues processed: 221 average time/residue: 0.8553 time to fit residues: 234.4553 Evaluate side-chains 189 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 174 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 278 optimal weight: 0.4980 chunk 300 optimal weight: 0.9980 chunk 247 optimal weight: 20.0000 chunk 276 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 223 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 339 HIS B 207 HIS B 339 HIS B 394 ASN C 339 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25200 Z= 0.163 Angle : 0.525 7.832 34284 Z= 0.271 Chirality : 0.045 0.357 4032 Planarity : 0.004 0.052 4362 Dihedral : 7.057 59.969 4291 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.60 % Allowed : 7.61 % Favored : 90.79 % 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: 0.43 (0.15), residues: 3015 helix: 2.27 (0.21), residues: 669 sheet: 1.16 (0.19), residues: 738 loop : -1.06 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 436 HIS 0.010 0.001 HIS A 207 PHE 0.024 0.001 PHE B 133 TYR 0.020 0.001 TYR C 453 ARG 0.008 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 186 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.8316 (p90) cc_final: 0.7579 (p90) REVERT: A 753 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8523 (tp) REVERT: A 955 ASN cc_start: 0.8131 (m-40) cc_final: 0.7927 (t0) REVERT: B 160 TYR cc_start: 0.8295 (p90) cc_final: 0.7675 (p90) REVERT: B 176 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7902 (mm) REVERT: B 753 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8450 (tp) REVERT: B 955 ASN cc_start: 0.8146 (m-40) cc_final: 0.7936 (t0) REVERT: C 140 PHE cc_start: 0.7999 (p90) cc_final: 0.7681 (p90) REVERT: C 160 TYR cc_start: 0.8197 (p90) cc_final: 0.7602 (p90) REVERT: C 379 CYS cc_start: 0.5986 (m) cc_final: 0.5668 (m) REVERT: C 955 ASN cc_start: 0.8115 (m-40) cc_final: 0.7893 (t0) outliers start: 43 outliers final: 14 residues processed: 208 average time/residue: 0.7838 time to fit residues: 207.1508 Evaluate side-chains 190 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 173 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 2.9990 chunk 209 optimal weight: 0.6980 chunk 144 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 186 optimal weight: 4.9990 chunk 279 optimal weight: 0.6980 chunk 295 optimal weight: 2.9990 chunk 145 optimal weight: 20.0000 chunk 264 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 339 HIS B 207 HIS B 339 HIS B 394 ASN B 613 GLN C 207 HIS C 339 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25200 Z= 0.279 Angle : 0.584 6.572 34284 Z= 0.309 Chirality : 0.048 0.397 4032 Planarity : 0.004 0.047 4362 Dihedral : 6.807 58.722 4291 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.57 % Allowed : 9.77 % Favored : 88.67 % 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: 0.26 (0.15), residues: 3015 helix: 2.07 (0.21), residues: 669 sheet: 1.05 (0.19), residues: 738 loop : -1.14 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 436 HIS 0.011 0.001 HIS A 207 PHE 0.029 0.002 PHE C 906 TYR 0.021 0.002 TYR A1067 ARG 0.013 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 182 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.8130 (p90) cc_final: 0.7468 (p90) REVERT: A 753 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8505 (tp) REVERT: B 160 TYR cc_start: 0.8311 (p90) cc_final: 0.7636 (p90) REVERT: B 176 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7947 (mm) REVERT: B 753 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8344 (tp) REVERT: B 904 TYR cc_start: 0.8310 (m-10) cc_final: 0.8002 (m-10) REVERT: C 140 PHE cc_start: 0.7986 (p90) cc_final: 0.7682 (p90) REVERT: C 160 TYR cc_start: 0.8205 (p90) cc_final: 0.7706 (p90) REVERT: C 176 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7792 (mm) REVERT: C 955 ASN cc_start: 0.8165 (m-40) cc_final: 0.7925 (t0) outliers start: 42 outliers final: 22 residues processed: 202 average time/residue: 0.7821 time to fit residues: 200.0074 Evaluate side-chains 198 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 172 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 753 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 6.9990 chunk 167 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 220 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 265 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 339 HIS A 613 GLN B 207 HIS B 339 HIS B 613 GLN C 207 HIS C 339 HIS C 613 GLN C1010 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 25200 Z= 0.356 Angle : 0.618 7.601 34284 Z= 0.328 Chirality : 0.049 0.428 4032 Planarity : 0.005 0.050 4362 Dihedral : 6.914 58.393 4291 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.83 % Allowed : 10.33 % Favored : 87.84 % 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: 0.07 (0.15), residues: 3015 helix: 1.72 (0.20), residues: 690 sheet: 0.92 (0.19), residues: 741 loop : -1.20 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 436 HIS 0.011 0.002 HIS A 207 PHE 0.020 0.002 PHE B 133 TYR 0.021 0.002 TYR A1067 ARG 0.012 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 187 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.8149 (p90) cc_final: 0.7300 (p90) REVERT: A 1107 ARG cc_start: 0.8210 (mmt90) cc_final: 0.7743 (mmt-90) REVERT: B 160 TYR cc_start: 0.8255 (p90) cc_final: 0.7626 (p90) REVERT: B 168 PHE cc_start: 0.7976 (t80) cc_final: 0.7739 (t80) REVERT: B 176 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7704 (mm) REVERT: B 753 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8494 (tp) REVERT: C 140 PHE cc_start: 0.8020 (p90) cc_final: 0.7546 (p90) REVERT: C 160 TYR cc_start: 0.8229 (p90) cc_final: 0.7616 (p90) REVERT: C 176 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8181 (mm) REVERT: C 904 TYR cc_start: 0.8641 (m-10) cc_final: 0.8354 (m-10) REVERT: C 955 ASN cc_start: 0.8149 (m-40) cc_final: 0.7922 (t0) outliers start: 49 outliers final: 23 residues processed: 213 average time/residue: 0.7859 time to fit residues: 212.8531 Evaluate side-chains 190 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 1.9990 chunk 266 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 173 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 296 optimal weight: 0.9990 chunk 245 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 339 HIS A 613 GLN A1002 GLN A1088 HIS B 207 HIS B 339 HIS B 394 ASN B 613 GLN B1002 GLN B1088 HIS C 207 HIS C 339 HIS C 613 GLN C1088 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25200 Z= 0.165 Angle : 0.531 8.325 34284 Z= 0.280 Chirality : 0.046 0.389 4032 Planarity : 0.004 0.037 4362 Dihedral : 6.624 59.632 4291 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.45 % Allowed : 11.52 % Favored : 87.02 % 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: 0.27 (0.15), residues: 3015 helix: 1.94 (0.21), residues: 687 sheet: 1.08 (0.19), residues: 738 loop : -1.12 (0.14), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 436 HIS 0.011 0.001 HIS A 207 PHE 0.025 0.001 PHE C 429 TYR 0.015 0.001 TYR B1067 ARG 0.004 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 172 time to evaluate : 2.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8669 (m-80) cc_final: 0.8463 (m-80) REVERT: A 160 TYR cc_start: 0.8125 (p90) cc_final: 0.7185 (p90) REVERT: A 1107 ARG cc_start: 0.8140 (mmt90) cc_final: 0.7929 (tpp80) REVERT: B 160 TYR cc_start: 0.8211 (p90) cc_final: 0.7461 (p90) REVERT: B 176 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7971 (mm) REVERT: C 140 PHE cc_start: 0.7978 (p90) cc_final: 0.7448 (p90) REVERT: C 160 TYR cc_start: 0.8197 (p90) cc_final: 0.7241 (p90) REVERT: C 176 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7923 (mm) REVERT: C 955 ASN cc_start: 0.8109 (m-40) cc_final: 0.7861 (t0) outliers start: 39 outliers final: 22 residues processed: 191 average time/residue: 0.8009 time to fit residues: 193.8818 Evaluate side-chains 184 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 249 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 136 optimal weight: 0.0070 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 207 HIS B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B1002 GLN C 207 HIS C 339 HIS C 613 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25200 Z= 0.268 Angle : 0.569 7.952 34284 Z= 0.302 Chirality : 0.047 0.414 4032 Planarity : 0.004 0.039 4362 Dihedral : 6.629 59.920 4291 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.72 % Allowed : 11.63 % Favored : 86.65 % 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: 0.19 (0.15), residues: 3015 helix: 1.88 (0.21), residues: 687 sheet: 0.99 (0.19), residues: 741 loop : -1.15 (0.14), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 436 HIS 0.011 0.001 HIS C 207 PHE 0.031 0.002 PHE B 429 TYR 0.022 0.001 TYR B 904 ARG 0.005 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 165 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.8134 (p90) cc_final: 0.7424 (p90) REVERT: B 160 TYR cc_start: 0.8260 (p90) cc_final: 0.7621 (p90) REVERT: B 176 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7913 (mm) REVERT: C 140 PHE cc_start: 0.7996 (p90) cc_final: 0.7382 (p90) REVERT: C 160 TYR cc_start: 0.8201 (p90) cc_final: 0.7608 (p90) REVERT: C 176 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7998 (mm) REVERT: C 955 ASN cc_start: 0.8119 (m-40) cc_final: 0.7878 (t0) REVERT: C 1107 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7242 (mpp-170) outliers start: 46 outliers final: 30 residues processed: 195 average time/residue: 0.8081 time to fit residues: 199.1366 Evaluate side-chains 192 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 159 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 187 optimal weight: 0.0670 chunk 200 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 231 optimal weight: 7.9990 chunk 268 optimal weight: 3.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 207 HIS B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B1002 GLN C 207 HIS ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25200 Z= 0.235 Angle : 0.558 8.389 34284 Z= 0.296 Chirality : 0.047 0.412 4032 Planarity : 0.004 0.039 4362 Dihedral : 6.610 59.500 4291 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.53 % Allowed : 11.97 % Favored : 86.50 % 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: 0.21 (0.15), residues: 3015 helix: 1.92 (0.21), residues: 684 sheet: 1.02 (0.19), residues: 726 loop : -1.13 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 436 HIS 0.012 0.001 HIS C 207 PHE 0.027 0.001 PHE C 429 TYR 0.019 0.001 TYR B 904 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 165 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.8118 (p90) cc_final: 0.7211 (p90) REVERT: B 160 TYR cc_start: 0.8250 (p90) cc_final: 0.7486 (p90) REVERT: B 176 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7872 (mm) REVERT: C 140 PHE cc_start: 0.7988 (p90) cc_final: 0.7377 (p90) REVERT: C 160 TYR cc_start: 0.8217 (p90) cc_final: 0.7515 (p90) REVERT: C 955 ASN cc_start: 0.8109 (m-40) cc_final: 0.7868 (t0) REVERT: C 1107 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7222 (mpp-170) outliers start: 41 outliers final: 23 residues processed: 192 average time/residue: 0.7695 time to fit residues: 188.6770 Evaluate side-chains 186 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 161 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 0.9980 chunk 257 optimal weight: 5.9990 chunk 274 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 259 optimal weight: 3.9990 chunk 273 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B1002 GLN C 207 HIS ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25200 Z= 0.230 Angle : 0.561 8.546 34284 Z= 0.296 Chirality : 0.047 0.415 4032 Planarity : 0.004 0.040 4362 Dihedral : 6.587 59.003 4291 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.27 % Allowed : 12.42 % Favored : 86.32 % 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: 0.22 (0.15), residues: 3015 helix: 1.92 (0.21), residues: 684 sheet: 1.02 (0.19), residues: 726 loop : -1.12 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 436 HIS 0.011 0.001 HIS C 207 PHE 0.036 0.002 PHE B 429 TYR 0.034 0.001 TYR C 453 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.8124 (p90) cc_final: 0.7417 (p90) REVERT: B 160 TYR cc_start: 0.8240 (p90) cc_final: 0.7535 (p90) REVERT: C 140 PHE cc_start: 0.8003 (p90) cc_final: 0.7351 (p90) REVERT: C 160 TYR cc_start: 0.8221 (p90) cc_final: 0.7563 (p90) REVERT: C 955 ASN cc_start: 0.8111 (m-40) cc_final: 0.7870 (t0) REVERT: C 1107 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7203 (mpp-170) outliers start: 34 outliers final: 26 residues processed: 185 average time/residue: 0.8114 time to fit residues: 191.7205 Evaluate side-chains 187 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.3980 chunk 177 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 chunk 280 optimal weight: 0.6980 chunk 242 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 207 HIS B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 207 HIS ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25200 Z= 0.165 Angle : 0.533 8.952 34284 Z= 0.279 Chirality : 0.046 0.395 4032 Planarity : 0.004 0.039 4362 Dihedral : 6.459 58.910 4291 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.08 % Allowed : 12.64 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3015 helix: 2.17 (0.21), residues: 660 sheet: 1.13 (0.19), residues: 723 loop : -1.07 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 436 HIS 0.011 0.001 HIS C 207 PHE 0.025 0.001 PHE C 429 TYR 0.029 0.001 TYR C 453 ARG 0.004 0.000 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 165 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.8104 (p90) cc_final: 0.7224 (p90) REVERT: B 160 TYR cc_start: 0.8227 (p90) cc_final: 0.7525 (p90) REVERT: B 421 TYR cc_start: 0.7634 (m-80) cc_final: 0.6999 (m-80) REVERT: C 140 PHE cc_start: 0.7995 (p90) cc_final: 0.7334 (p90) REVERT: C 160 TYR cc_start: 0.8176 (p90) cc_final: 0.7539 (p90) REVERT: C 955 ASN cc_start: 0.8084 (m-40) cc_final: 0.7845 (t0) outliers start: 29 outliers final: 21 residues processed: 180 average time/residue: 0.7917 time to fit residues: 181.5280 Evaluate side-chains 179 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 223 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 243 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 213 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B1002 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.127366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.069566 restraints weight = 43308.138| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.10 r_work: 0.2746 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25200 Z= 0.272 Angle : 0.575 8.799 34284 Z= 0.304 Chirality : 0.048 0.422 4032 Planarity : 0.004 0.038 4362 Dihedral : 6.551 58.861 4289 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.97 % Allowed : 13.01 % Favored : 86.02 % 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: 0.23 (0.15), residues: 3015 helix: 2.00 (0.21), residues: 678 sheet: 1.03 (0.19), residues: 723 loop : -1.15 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 436 HIS 0.010 0.001 HIS C 207 PHE 0.032 0.002 PHE B 429 TYR 0.029 0.001 TYR C 453 ARG 0.004 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6886.83 seconds wall clock time: 123 minutes 41.70 seconds (7421.70 seconds total)