Starting phenix.real_space_refine on Sun Jan 26 12:40:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zp1_11333/01_2025/6zp1_11333.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zp1_11333/01_2025/6zp1_11333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zp1_11333/01_2025/6zp1_11333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zp1_11333/01_2025/6zp1_11333.map" model { file = "/net/cci-nas-00/data/ceres_data/6zp1_11333/01_2025/6zp1_11333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zp1_11333/01_2025/6zp1_11333.cif" } resolution = 3.3 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= 0.005 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 15708 2.51 5 N 4029 2.21 5 O 4860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 24705 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7941 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 49, 'TRANS': 967} Chain breaks: 7 Chain: "B" Number of atoms: 7941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7941 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 49, 'TRANS': 967} Chain breaks: 7 Chain: "C" Number of atoms: 7941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7941 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 49, '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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 13.81, per 1000 atoms: 0.56 Number of scatterers: 24705 At special positions: 0 Unit cell: (133.686, 145.357, 162.333, 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 4860 8.00 N 4029 7.00 C 15708 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 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=2.04 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=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 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=2.04 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=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1316 " - " ASN A1074 " " NAG A1321 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 709 " " NAG B1316 " - " ASN B1074 " " NAG B1321 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 657 " " NAG C1311 " - " ASN C 709 " " NAG C1316 " - " ASN C1074 " " NAG C1321 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Time building additional restraints: 6.27 Conformation dependent library (CDL) restraints added in 3.0 seconds 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 48 sheets defined 24.9% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.061A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.555A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.255A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.723A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.740A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.259A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.257A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.498A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.061A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.555A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.254A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.723A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.740A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.259A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.256A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.499A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.061A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.556A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.255A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.722A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.740A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.259A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.256A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.499A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.744A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.007A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.518A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.339A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.692A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.773A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.433A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.686A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.021A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.543A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.478A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.745A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.007A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.518A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.339A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.691A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.773A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.687A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.021A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.477A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.745A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.518A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.338A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.691A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.774A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.687A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.021A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.478A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1047 hydrogen bonds defined for protein. 2898 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: 12.57 Time building geometry restraints manager: 7.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 6274 1.33 - 1.47: 8002 1.47 - 1.60: 10831 1.60 - 1.74: 6 1.74 - 1.87: 129 Bond restraints: 25242 Sorted by residual: bond pdb=" CG1 ILE B 896 " pdb=" CD1 ILE B 896 " ideal model delta sigma weight residual 1.513 1.371 0.142 3.90e-02 6.57e+02 1.32e+01 bond pdb=" CG1 ILE C 896 " pdb=" CD1 ILE C 896 " ideal model delta sigma weight residual 1.513 1.371 0.142 3.90e-02 6.57e+02 1.32e+01 bond pdb=" CG1 ILE A 896 " pdb=" CD1 ILE A 896 " ideal model delta sigma weight residual 1.513 1.372 0.141 3.90e-02 6.57e+02 1.31e+01 bond pdb=" CA PHE B 106 " pdb=" CB PHE B 106 " ideal model delta sigma weight residual 1.533 1.591 -0.058 1.90e-02 2.77e+03 9.28e+00 bond pdb=" CG GLU B 990 " pdb=" CD GLU B 990 " ideal model delta sigma weight residual 1.516 1.440 0.076 2.50e-02 1.60e+03 9.27e+00 ... (remaining 25237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 33665 3.92 - 7.84: 609 7.84 - 11.76: 55 11.76 - 15.68: 0 15.68 - 19.60: 3 Bond angle restraints: 34332 Sorted by residual: angle pdb=" CA GLU C 990 " pdb=" CB GLU C 990 " pdb=" CG GLU C 990 " ideal model delta sigma weight residual 114.10 133.70 -19.60 2.00e+00 2.50e-01 9.60e+01 angle pdb=" CA GLU B 990 " pdb=" CB GLU B 990 " pdb=" CG GLU B 990 " ideal model delta sigma weight residual 114.10 133.67 -19.57 2.00e+00 2.50e-01 9.57e+01 angle pdb=" CA GLU A 990 " pdb=" CB GLU A 990 " pdb=" CG GLU A 990 " ideal model delta sigma weight residual 114.10 133.66 -19.56 2.00e+00 2.50e-01 9.57e+01 angle pdb=" C PHE A 429 " pdb=" CA PHE A 429 " pdb=" CB PHE A 429 " ideal model delta sigma weight residual 109.84 120.10 -10.26 1.50e+00 4.44e-01 4.68e+01 angle pdb=" C PHE C 429 " pdb=" CA PHE C 429 " pdb=" CB PHE C 429 " ideal model delta sigma weight residual 109.84 120.05 -10.21 1.50e+00 4.44e-01 4.64e+01 ... (remaining 34327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 14750 17.48 - 34.96: 757 34.96 - 52.45: 231 52.45 - 69.93: 81 69.93 - 87.41: 27 Dihedral angle restraints: 15846 sinusoidal: 6975 harmonic: 8871 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 173.60 -80.60 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 173.59 -80.59 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 173.54 -80.54 1 1.00e+01 1.00e-02 8.02e+01 ... (remaining 15843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 3699 0.121 - 0.242: 348 0.242 - 0.363: 15 0.363 - 0.484: 15 0.484 - 0.605: 3 Chirality restraints: 4080 Sorted by residual: chirality pdb=" CG LEU A 277 " pdb=" CB LEU A 277 " pdb=" CD1 LEU A 277 " pdb=" CD2 LEU A 277 " both_signs ideal model delta sigma weight residual False -2.59 -1.98 -0.60 2.00e-01 2.50e+01 9.15e+00 chirality pdb=" CG LEU C 277 " pdb=" CB LEU C 277 " pdb=" CD1 LEU C 277 " pdb=" CD2 LEU C 277 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.60 2.00e-01 2.50e+01 9.01e+00 chirality pdb=" CG LEU B 277 " pdb=" CB LEU B 277 " pdb=" CD1 LEU B 277 " pdb=" CD2 LEU B 277 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.60 2.00e-01 2.50e+01 8.99e+00 ... (remaining 4077 not shown) Planarity restraints: 4416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 986 " 0.040 2.00e-02 2.50e+03 7.79e-02 6.07e+01 pdb=" C PRO A 986 " -0.135 2.00e-02 2.50e+03 pdb=" O PRO A 986 " 0.048 2.00e-02 2.50e+03 pdb=" N PRO A 987 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 986 " -0.040 2.00e-02 2.50e+03 7.77e-02 6.04e+01 pdb=" C PRO C 986 " 0.135 2.00e-02 2.50e+03 pdb=" O PRO C 986 " -0.048 2.00e-02 2.50e+03 pdb=" N PRO C 987 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 986 " -0.040 2.00e-02 2.50e+03 7.76e-02 6.02e+01 pdb=" C PRO B 986 " 0.134 2.00e-02 2.50e+03 pdb=" O PRO B 986 " -0.048 2.00e-02 2.50e+03 pdb=" N PRO B 987 " -0.047 2.00e-02 2.50e+03 ... (remaining 4413 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2533 2.74 - 3.28: 24214 3.28 - 3.82: 40020 3.82 - 4.36: 48929 4.36 - 4.90: 83428 Nonbonded interactions: 199124 Sorted by model distance: nonbonded pdb=" OG SER A 813 " pdb=" OE2 GLU A 868 " model vdw 2.197 3.040 nonbonded pdb=" OG SER C 813 " pdb=" OE2 GLU C 868 " model vdw 2.197 3.040 nonbonded pdb=" OG SER B 813 " pdb=" OE2 GLU B 868 " model vdw 2.197 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.205 3.040 ... (remaining 199119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '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' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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=0.00 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.810 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 57.810 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 : 0.011 0.142 25242 Z= 0.681 Angle : 1.287 19.597 34332 Z= 0.739 Chirality : 0.078 0.605 4080 Planarity : 0.008 0.086 4368 Dihedral : 12.573 87.411 10017 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.60 % Favored : 96.10 % Rotamer: Outliers : 0.34 % Allowed : 0.68 % Favored : 98.99 % Cbeta Deviations : 0.32 % 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: 0.13 (0.14), residues: 3003 helix: 0.66 (0.19), residues: 615 sheet: 0.91 (0.19), residues: 654 loop : -0.42 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP B 353 HIS 0.016 0.003 HIS C 519 PHE 0.126 0.006 PHE C 490 TYR 0.099 0.006 TYR B 495 ARG 0.030 0.002 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 248 time to evaluate : 2.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.9170 (tp) cc_final: 0.8942 (tt) REVERT: A 238 PHE cc_start: 0.7015 (p90) cc_final: 0.6763 (p90) REVERT: A 351 TYR cc_start: 0.8222 (p90) cc_final: 0.7786 (p90) REVERT: A 353 TRP cc_start: 0.8180 (p-90) cc_final: 0.7476 (p-90) REVERT: B 351 TYR cc_start: 0.8108 (p90) cc_final: 0.7706 (p90) REVERT: B 353 TRP cc_start: 0.8309 (p-90) cc_final: 0.7471 (p-90) REVERT: B 378 LYS cc_start: 0.8212 (tmmt) cc_final: 0.7596 (tmtt) REVERT: C 64 TRP cc_start: 0.7984 (t60) cc_final: 0.7630 (t60) REVERT: C 351 TYR cc_start: 0.8119 (p90) cc_final: 0.7727 (p90) REVERT: C 378 LYS cc_start: 0.8162 (tmmt) cc_final: 0.7722 (tmtt) outliers start: 9 outliers final: 3 residues processed: 249 average time/residue: 0.3379 time to fit residues: 140.3867 Evaluate side-chains 190 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 187 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 990 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 0.9980 chunk 229 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 237 optimal weight: 50.0000 chunk 91 optimal weight: 0.9980 chunk 144 optimal weight: 20.0000 chunk 176 optimal weight: 0.8980 chunk 275 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 66 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.135017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.082091 restraints weight = 48904.864| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.15 r_work: 0.2851 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25242 Z= 0.206 Angle : 0.646 8.865 34332 Z= 0.338 Chirality : 0.049 0.370 4080 Planarity : 0.004 0.057 4368 Dihedral : 7.834 58.126 4590 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.73 % Favored : 98.17 % Rotamer: Outliers : 0.60 % Allowed : 4.40 % Favored : 95.00 % 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: 0.28 (0.14), residues: 3003 helix: 1.75 (0.20), residues: 651 sheet: 0.49 (0.19), residues: 666 loop : -0.55 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 104 HIS 0.004 0.001 HIS A 207 PHE 0.033 0.002 PHE B 429 TYR 0.023 0.002 TYR C 380 ARG 0.005 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 246 time to evaluate : 2.591 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: A 238 PHE cc_start: 0.6797 (p90) cc_final: 0.6459 (p90) REVERT: A 351 TYR cc_start: 0.8388 (p90) cc_final: 0.8082 (p90) REVERT: A 400 PHE cc_start: 0.9111 (p90) cc_final: 0.8860 (p90) REVERT: A 429 PHE cc_start: 0.8635 (t80) cc_final: 0.7997 (t80) REVERT: B 104 TRP cc_start: 0.7509 (m-90) cc_final: 0.7225 (m-90) REVERT: B 351 TYR cc_start: 0.8250 (p90) cc_final: 0.7977 (p90) REVERT: B 568 ASP cc_start: 0.8189 (t70) cc_final: 0.7853 (p0) REVERT: B 979 ASP cc_start: 0.8937 (t0) cc_final: 0.8723 (t0) REVERT: C 351 TYR cc_start: 0.8312 (p90) cc_final: 0.8003 (p90) REVERT: C 429 PHE cc_start: 0.8591 (t80) cc_final: 0.8372 (t80) REVERT: C 568 ASP cc_start: 0.8246 (t70) cc_final: 0.8046 (p0) REVERT: C 574 ASP cc_start: 0.8061 (t0) cc_final: 0.7826 (t0) REVERT: C 1138 TYR cc_start: 0.8580 (t80) cc_final: 0.8283 (m-10) outliers start: 16 outliers final: 6 residues processed: 250 average time/residue: 0.3192 time to fit residues: 133.5037 Evaluate side-chains 190 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 184 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 156 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 164 optimal weight: 0.6980 chunk 237 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 282 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 291 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1005 GLN C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.131650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.078059 restraints weight = 48591.959| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.99 r_work: 0.2763 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 25242 Z= 0.383 Angle : 0.647 9.357 34332 Z= 0.332 Chirality : 0.049 0.336 4080 Planarity : 0.004 0.048 4368 Dihedral : 7.063 59.566 4584 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.47 % Rotamer: Outliers : 1.16 % Allowed : 7.44 % Favored : 91.39 % 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: 0.18 (0.15), residues: 3003 helix: 1.74 (0.21), residues: 648 sheet: 0.16 (0.18), residues: 708 loop : -0.53 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 104 HIS 0.005 0.001 HIS A1064 PHE 0.030 0.002 PHE A 515 TYR 0.020 0.002 TYR B1138 ARG 0.005 0.001 ARG C1014 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 3.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8448 (p90) cc_final: 0.8146 (p90) REVERT: A 400 PHE cc_start: 0.9100 (p90) cc_final: 0.8652 (p90) REVERT: A 429 PHE cc_start: 0.8719 (t80) cc_final: 0.8289 (t80) REVERT: A 515 PHE cc_start: 0.8277 (m-80) cc_final: 0.8046 (m-80) REVERT: A 1138 TYR cc_start: 0.8286 (m-10) cc_final: 0.8007 (t80) REVERT: B 104 TRP cc_start: 0.7768 (m-90) cc_final: 0.7558 (m-90) REVERT: B 351 TYR cc_start: 0.8248 (p90) cc_final: 0.8019 (p90) REVERT: B 436 TRP cc_start: 0.8570 (p90) cc_final: 0.8024 (p90) REVERT: B 568 ASP cc_start: 0.8445 (t70) cc_final: 0.8204 (p0) REVERT: B 979 ASP cc_start: 0.9084 (t0) cc_final: 0.8810 (t0) REVERT: C 351 TYR cc_start: 0.8421 (p90) cc_final: 0.8145 (p90) REVERT: C 429 PHE cc_start: 0.8775 (t80) cc_final: 0.8547 (t80) REVERT: C 568 ASP cc_start: 0.8510 (t70) cc_final: 0.8250 (p0) REVERT: C 990 GLU cc_start: 0.8486 (pm20) cc_final: 0.8107 (pm20) outliers start: 31 outliers final: 15 residues processed: 220 average time/residue: 0.3297 time to fit residues: 120.9205 Evaluate side-chains 189 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 127 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 264 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 chunk 171 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 149 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 126 optimal weight: 0.0470 overall best weight: 2.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN B 487 ASN B 957 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.133018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.079555 restraints weight = 48644.314| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.27 r_work: 0.2767 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25242 Z= 0.259 Angle : 0.586 9.393 34332 Z= 0.302 Chirality : 0.047 0.323 4080 Planarity : 0.004 0.042 4368 Dihedral : 6.611 59.486 4581 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.01 % Allowed : 8.94 % Favored : 90.04 % 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: 0.17 (0.15), residues: 3003 helix: 1.73 (0.21), residues: 651 sheet: 0.18 (0.19), residues: 666 loop : -0.55 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 104 HIS 0.004 0.001 HIS A1048 PHE 0.024 0.001 PHE A 133 TYR 0.021 0.001 TYR C1138 ARG 0.003 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7632 (m-90) cc_final: 0.7332 (m-90) REVERT: A 238 PHE cc_start: 0.7185 (p90) cc_final: 0.6719 (p90) REVERT: A 351 TYR cc_start: 0.8412 (p90) cc_final: 0.8151 (p90) REVERT: A 429 PHE cc_start: 0.8659 (t80) cc_final: 0.8182 (t80) REVERT: B 351 TYR cc_start: 0.8297 (p90) cc_final: 0.8079 (p90) REVERT: B 436 TRP cc_start: 0.8518 (p90) cc_final: 0.8004 (p90) REVERT: B 979 ASP cc_start: 0.8933 (t0) cc_final: 0.8700 (t0) REVERT: B 990 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: C 351 TYR cc_start: 0.8414 (p90) cc_final: 0.8190 (p90) REVERT: C 429 PHE cc_start: 0.8704 (t80) cc_final: 0.8418 (t80) outliers start: 27 outliers final: 9 residues processed: 209 average time/residue: 0.3211 time to fit residues: 112.6395 Evaluate side-chains 190 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 265 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 chunk 280 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 268 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 275 optimal weight: 0.5980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 196 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 196 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.131216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.077245 restraints weight = 49060.554| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.27 r_work: 0.2717 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 25242 Z= 0.408 Angle : 0.625 9.455 34332 Z= 0.322 Chirality : 0.048 0.319 4080 Planarity : 0.004 0.039 4368 Dihedral : 6.352 55.175 4581 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.28 % Allowed : 9.36 % Favored : 89.36 % 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: 0.06 (0.15), residues: 3003 helix: 1.74 (0.21), residues: 633 sheet: 0.14 (0.18), residues: 684 loop : -0.66 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 353 HIS 0.006 0.001 HIS A1048 PHE 0.023 0.002 PHE C 515 TYR 0.022 0.001 TYR B1138 ARG 0.004 0.000 ARG C1014 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7145 (p90) cc_final: 0.6679 (p90) REVERT: A 351 TYR cc_start: 0.8522 (p90) cc_final: 0.8260 (p90) REVERT: A 429 PHE cc_start: 0.8755 (t80) cc_final: 0.8345 (t80) REVERT: A 495 TYR cc_start: 0.6403 (m-80) cc_final: 0.6079 (m-80) REVERT: B 351 TYR cc_start: 0.8386 (p90) cc_final: 0.8170 (p90) REVERT: B 436 TRP cc_start: 0.8482 (p90) cc_final: 0.7938 (p90) REVERT: B 964 LYS cc_start: 0.9249 (mmmm) cc_final: 0.8881 (ttmm) REVERT: B 979 ASP cc_start: 0.9007 (t70) cc_final: 0.8741 (t0) REVERT: C 351 TYR cc_start: 0.8447 (p90) cc_final: 0.8211 (p90) REVERT: C 429 PHE cc_start: 0.8743 (t80) cc_final: 0.8438 (t80) outliers start: 34 outliers final: 19 residues processed: 200 average time/residue: 0.3215 time to fit residues: 109.0810 Evaluate side-chains 188 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 118 optimal weight: 0.0670 chunk 212 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 250 optimal weight: 10.0000 chunk 208 optimal weight: 20.0000 chunk 246 optimal weight: 8.9990 chunk 286 optimal weight: 0.8980 chunk 280 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 10 optimal weight: 40.0000 chunk 172 optimal weight: 6.9990 overall best weight: 1.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.132376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.078502 restraints weight = 48613.930| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.07 r_work: 0.2769 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 25242 Z= 0.245 Angle : 0.587 10.806 34332 Z= 0.303 Chirality : 0.047 0.312 4080 Planarity : 0.004 0.037 4368 Dihedral : 5.999 55.402 4581 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.35 % Allowed : 9.85 % Favored : 88.80 % 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: 0.09 (0.15), residues: 3003 helix: 1.87 (0.21), residues: 633 sheet: 0.20 (0.18), residues: 681 loop : -0.70 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 104 HIS 0.003 0.001 HIS A1048 PHE 0.021 0.001 PHE C 515 TYR 0.024 0.001 TYR C1138 ARG 0.003 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7141 (p90) cc_final: 0.6639 (p90) REVERT: A 351 TYR cc_start: 0.8504 (p90) cc_final: 0.8266 (p90) REVERT: A 429 PHE cc_start: 0.8724 (t80) cc_final: 0.8299 (t80) REVERT: A 964 LYS cc_start: 0.9156 (mmmm) cc_final: 0.8693 (mttp) REVERT: B 52 GLN cc_start: 0.9066 (tt0) cc_final: 0.8587 (tm-30) REVERT: B 436 TRP cc_start: 0.8502 (p90) cc_final: 0.7946 (p90) REVERT: B 979 ASP cc_start: 0.8974 (t70) cc_final: 0.8692 (t0) REVERT: C 351 TYR cc_start: 0.8441 (p90) cc_final: 0.8222 (p90) REVERT: C 429 PHE cc_start: 0.8734 (t80) cc_final: 0.8399 (t80) REVERT: C 436 TRP cc_start: 0.8680 (p90) cc_final: 0.8278 (p90) REVERT: C 990 GLU cc_start: 0.8272 (pm20) cc_final: 0.7905 (pm20) outliers start: 36 outliers final: 19 residues processed: 209 average time/residue: 0.2710 time to fit residues: 95.4022 Evaluate side-chains 188 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 59 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 295 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 211 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 204 optimal weight: 7.9990 chunk 279 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: