Starting phenix.real_space_refine on Sun Jun 22 18:31:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uum_42590/06_2025/8uum_42590.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uum_42590/06_2025/8uum_42590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uum_42590/06_2025/8uum_42590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uum_42590/06_2025/8uum_42590.map" model { file = "/net/cci-nas-00/data/ceres_data/8uum_42590/06_2025/8uum_42590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uum_42590/06_2025/8uum_42590.cif" } resolution = 3.9 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= 0.016 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 116 5.16 5 C 16436 2.51 5 N 4252 2.21 5 O 4982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25786 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 8475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8475 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 57, 'TRANS': 1026} Chain breaks: 5 Chain: "A" Number of atoms: 8465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8465 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 57, 'TRANS': 1024} Chain breaks: 5 Chain: "B" Number of atoms: 8441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8441 Classifications: {'peptide': 1081} Link IDs: {'PTRANS': 57, 'TRANS': 1023} Chain breaks: 5 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} 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: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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 Time building chain proxies: 15.61, per 1000 atoms: 0.61 Number of scatterers: 25786 At special positions: 0 Unit cell: (146.08, 156.704, 200.971, 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 116 16.00 O 4982 8.00 N 4252 7.00 C 16436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " 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=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 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=2.04 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=1, symmetry=0 Links applied ALPHA1-4 " NAG D 1 " - " MAN D 2 " " NAG E 1 " - " MAN E 2 " " NAG F 1 " - " MAN F 2 " " NAG G 1 " - " MAN G 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 801 " " NAG A1305 " - " ASN A 61 " " NAG A1307 " - " ASN A 709 " " NAG B1302 " - " ASN B1134 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B 801 " " NAG B1309 " - " ASN B 61 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.08 Conformation dependent library (CDL) restraints added in 3.3 seconds 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6082 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 46 sheets defined 24.3% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.612A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.060A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.216A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.561A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.541A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.788A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 639 removed outlier: 3.983A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.600A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.546A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.700A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.525A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.592A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.615A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.640A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.744A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.590A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1149 removed outlier: 4.435A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.585A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 443' Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.169A pdb=" N GLU A 619 " --> pdb=" O ASN A 616 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 616 through 620' Processing helix chain 'A' and resid 634 through 638 removed outlier: 4.416A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.570A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.565A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) 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: 3.777A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.573A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.517A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.899A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.582A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (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 removed outlier: 3.998A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.593A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1149 removed outlier: 3.815A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (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 364 through 371 removed outlier: 4.159A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.601A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.436A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.537A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 438 through 443' 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: 3.548A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.516A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.947A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.691A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.543A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.571A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.678A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.786A 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 982 Processing helix chain 'B' and resid 988 through 1033 removed outlier: 4.198A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 3.772A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.434A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.834A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.226A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 142 through 143 removed outlier: 6.240A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.221A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.220A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.593A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.395A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.561A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.881A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'C' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.008A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.885A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N HIS A 69 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLY A 261 " --> pdb=" O HIS A 69 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.195A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.676A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 133 through 143 removed outlier: 8.746A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.609A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AC5, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.717A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.507A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.355A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.823A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.450A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.102A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.505A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.915A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.622A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.715A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.300A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.356A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.861A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AE1, first strand: chain 'B' and resid 318 through 319 removed outlier: 3.838A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AE3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.075A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.563A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.563A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'B' and resid 1120 through 1122 989 hydrogen bonds defined for protein. 2700 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: 12.00 Time building geometry restraints manager: 7.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7954 1.34 - 1.46: 6777 1.46 - 1.59: 11506 1.59 - 1.72: 0 1.72 - 1.85: 146 Bond restraints: 26383 Sorted by residual: bond pdb=" C LYS C 790 " pdb=" N THR C 791 " ideal model delta sigma weight residual 1.329 1.209 0.120 1.86e-02 2.89e+03 4.18e+01 bond pdb=" C VAL C 620 " pdb=" N PRO C 621 " ideal model delta sigma weight residual 1.335 1.415 -0.080 1.28e-02 6.10e+03 3.95e+01 bond pdb=" CA GLN B 965 " pdb=" C GLN B 965 " ideal model delta sigma weight residual 1.523 1.464 0.059 1.41e-02 5.03e+03 1.73e+01 bond pdb=" C5 MAN E 2 " pdb=" O5 MAN E 2 " ideal model delta sigma weight residual 1.418 1.473 -0.055 2.00e-02 2.50e+03 7.47e+00 bond pdb=" C ALA A 520 " pdb=" N PRO A 521 " ideal model delta sigma weight residual 1.332 1.366 -0.035 1.30e-02 5.92e+03 7.07e+00 ... (remaining 26378 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 34597 2.49 - 4.97: 1177 4.97 - 7.46: 113 7.46 - 9.94: 21 9.94 - 12.43: 6 Bond angle restraints: 35914 Sorted by residual: angle pdb=" C ARG C 102 " pdb=" N GLY C 103 " pdb=" CA GLY C 103 " ideal model delta sigma weight residual 122.18 117.47 4.71 6.90e-01 2.10e+00 4.67e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.40 -6.70 1.22e+00 6.72e-01 3.01e+01 angle pdb=" C PHE C 486 " pdb=" N ASN C 487 " pdb=" CA ASN C 487 " ideal model delta sigma weight residual 121.54 131.49 -9.95 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C VAL A 781 " pdb=" N PHE A 782 " pdb=" CA PHE A 782 " ideal model delta sigma weight residual 122.79 114.13 8.66 1.70e+00 3.46e-01 2.60e+01 angle pdb=" C LEU A 945 " pdb=" N GLY A 946 " pdb=" CA GLY A 946 " ideal model delta sigma weight residual 120.03 125.55 -5.52 1.12e+00 7.97e-01 2.43e+01 ... (remaining 35909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.80: 15190 23.80 - 47.60: 788 47.60 - 71.41: 98 71.41 - 95.21: 31 95.21 - 119.01: 22 Dihedral angle restraints: 16129 sinusoidal: 6677 harmonic: 9452 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 16.41 76.59 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CA CYS C 525 " pdb=" C CYS C 525 " pdb=" N GLY C 526 " pdb=" CA GLY C 526 " ideal model delta harmonic sigma weight residual 180.00 140.77 39.23 0 5.00e+00 4.00e-02 6.16e+01 dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual -180.00 -144.91 -35.09 0 5.00e+00 4.00e-02 4.93e+01 ... (remaining 16126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3571 0.089 - 0.178: 533 0.178 - 0.267: 26 0.267 - 0.356: 2 0.356 - 0.445: 3 Chirality restraints: 4135 Sorted by residual: chirality pdb=" CB ILE C1115 " pdb=" CA ILE C1115 " pdb=" CG1 ILE C1115 " pdb=" CG2 ILE C1115 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CB ILE A 332 " pdb=" CA ILE A 332 " pdb=" CG1 ILE A 332 " pdb=" CG2 ILE A 332 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 4132 not shown) Planarity restraints: 4628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 958 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C ALA A 958 " -0.058 2.00e-02 2.50e+03 pdb=" O ALA A 958 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU A 959 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 956 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C ALA A 956 " 0.056 2.00e-02 2.50e+03 pdb=" O ALA A 956 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A 957 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 956 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ALA B 956 " -0.055 2.00e-02 2.50e+03 pdb=" O ALA B 956 " 0.021 2.00e-02 2.50e+03 pdb=" N GLN B 957 " 0.019 2.00e-02 2.50e+03 ... (remaining 4625 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5452 2.77 - 3.30: 23277 3.30 - 3.84: 42243 3.84 - 4.37: 46355 4.37 - 4.90: 81472 Nonbonded interactions: 198799 Sorted by model distance: nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.241 3.040 nonbonded pdb=" O LEU A 296 " pdb=" OG1 THR A 299 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR B 307 " pdb=" OG1 THR B 602 " model vdw 2.254 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.260 3.040 nonbonded pdb=" OG SER B 735 " pdb=" OG1 THR B 859 " model vdw 2.267 3.040 ... (remaining 198794 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' and (resid 14 through 622 or resid 635 through 831 or resid 834 or re \ sid 852 through 1148 or resid 1302 through 1303)) selection = (chain 'B' and (resid 14 through 622 or resid 635 through 831 or resid 834 or re \ sid 852 through 1148 or resid 1303 through 1304)) selection = (chain 'C' and (resid 14 through 622 or resid 635 through 831 or resid 850 or re \ sid 852 through 1148 or resid 1302 through 1303)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 80.470 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: 1.080 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 61.180 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 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 : 0.008 0.123 26438 Z= 0.370 Angle : 1.046 12.429 36035 Z= 0.585 Chirality : 0.060 0.445 4135 Planarity : 0.007 0.073 4619 Dihedral : 14.963 119.012 9924 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.14 % Allowed : 0.81 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 3211 helix: -0.22 (0.19), residues: 674 sheet: -0.08 (0.19), residues: 684 loop : -1.99 (0.13), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 258 HIS 0.011 0.002 HIS C 655 PHE 0.049 0.003 PHE C 906 TYR 0.047 0.003 TYR C 421 ARG 0.012 0.001 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 9) link_NAG-ASN : angle 3.68320 ( 27) link_ALPHA1-4 : bond 0.00608 ( 4) link_ALPHA1-4 : angle 2.64464 ( 12) hydrogen bonds : bond 0.14548 ( 977) hydrogen bonds : angle 7.18361 ( 2700) SS BOND : bond 0.00592 ( 41) SS BOND : angle 1.84696 ( 82) covalent geometry : bond 0.00774 (26383) covalent geometry : angle 1.03819 (35914) Misc. bond : bond 0.00046 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 3.546 Fit side-chains REVERT: C 1050 MET cc_start: 0.8156 (ptp) cc_final: 0.7938 (ptp) REVERT: B 869 MET cc_start: 0.8941 (pmm) cc_final: 0.8577 (pmm) REVERT: B 947 LYS cc_start: 0.9066 (mppt) cc_final: 0.8401 (tppt) REVERT: B 1050 MET cc_start: 0.8234 (ptp) cc_final: 0.7910 (ptp) outliers start: 4 outliers final: 0 residues processed: 62 average time/residue: 0.4462 time to fit residues: 49.7164 Evaluate side-chains 44 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 10.0000 chunk 245 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 chunk 253 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 chunk 154 optimal weight: 30.0000 chunk 189 optimal weight: 0.8980 chunk 294 optimal weight: 9.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN C 901 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1011 GLN A 14 GLN A 188 ASN A 613 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN B 239 GLN B 616 ASN ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.046755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.031663 restraints weight = 202008.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.032742 restraints weight = 107816.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.033465 restraints weight = 71767.712| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26438 Z= 0.142 Angle : 0.599 9.213 36035 Z= 0.313 Chirality : 0.044 0.325 4135 Planarity : 0.005 0.062 4619 Dihedral : 9.770 101.237 4097 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.14 % Allowed : 5.32 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3211 helix: 0.94 (0.21), residues: 677 sheet: 0.00 (0.19), residues: 677 loop : -1.77 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 258 HIS 0.003 0.001 HIS A1083 PHE 0.014 0.001 PHE C 168 TYR 0.020 0.001 TYR B 313 ARG 0.004 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 9) link_NAG-ASN : angle 2.44954 ( 27) link_ALPHA1-4 : bond 0.00840 ( 4) link_ALPHA1-4 : angle 2.60956 ( 12) hydrogen bonds : bond 0.05053 ( 977) hydrogen bonds : angle 5.76273 ( 2700) SS BOND : bond 0.00276 ( 41) SS BOND : angle 0.96425 ( 82) covalent geometry : bond 0.00302 (26383) covalent geometry : angle 0.59225 (35914) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 3.260 Fit side-chains revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8584 (t80) cc_final: 0.8249 (t80) REVERT: C 1005 GLN cc_start: 0.9501 (mm-40) cc_final: 0.9284 (mm-40) REVERT: A 614 ASP cc_start: 0.8832 (m-30) cc_final: 0.8497 (t0) REVERT: A 900 MET cc_start: 0.9194 (mmp) cc_final: 0.8979 (mmt) REVERT: B 855 PHE cc_start: 0.8069 (p90) cc_final: 0.7859 (p90) outliers start: 4 outliers final: 1 residues processed: 59 average time/residue: 0.3293 time to fit residues: 36.6909 Evaluate side-chains 49 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 731 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 214 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 151 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 272 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 ASN C 613 GLN C 907 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.046950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.031960 restraints weight = 201677.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.033051 restraints weight = 107365.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.033776 restraints weight = 71180.011| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26438 Z= 0.134 Angle : 0.553 8.510 36035 Z= 0.286 Chirality : 0.043 0.278 4135 Planarity : 0.004 0.057 4619 Dihedral : 8.300 87.710 4097 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.49 % Allowed : 7.88 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3211 helix: 1.53 (0.21), residues: 672 sheet: -0.02 (0.19), residues: 678 loop : -1.61 (0.13), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 258 HIS 0.003 0.001 HIS B1083 PHE 0.013 0.001 PHE B 133 TYR 0.016 0.001 TYR B 369 ARG 0.003 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 9) link_NAG-ASN : angle 2.10231 ( 27) link_ALPHA1-4 : bond 0.01555 ( 4) link_ALPHA1-4 : angle 2.43970 ( 12) hydrogen bonds : bond 0.04390 ( 977) hydrogen bonds : angle 5.28524 ( 2700) SS BOND : bond 0.00258 ( 41) SS BOND : angle 0.82460 ( 82) covalent geometry : bond 0.00291 (26383) covalent geometry : angle 0.54735 (35914) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8568 (t80) cc_final: 0.8306 (t80) REVERT: C 223 LEU cc_start: 0.9081 (mt) cc_final: 0.8721 (tp) REVERT: C 955 ASN cc_start: 0.9132 (m-40) cc_final: 0.8699 (p0) REVERT: A 614 ASP cc_start: 0.8787 (m-30) cc_final: 0.8523 (t0) REVERT: A 773 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7617 (tm-30) REVERT: A 777 ASN cc_start: 0.8493 (m-40) cc_final: 0.8078 (m-40) outliers start: 14 outliers final: 5 residues processed: 65 average time/residue: 0.3147 time to fit residues: 38.7239 Evaluate side-chains 54 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 130 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 258 optimal weight: 20.0000 chunk 307 optimal weight: 4.9990 chunk 313 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 78 optimal weight: 0.9990 chunk 214 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 ASN C 613 GLN C 616 ASN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN A 146 HIS ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 271 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.046260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.031244 restraints weight = 209395.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.032303 restraints weight = 112391.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.033015 restraints weight = 74764.777| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 26438 Z= 0.215 Angle : 0.601 8.855 36035 Z= 0.308 Chirality : 0.043 0.268 4135 Planarity : 0.004 0.054 4619 Dihedral : 7.911 85.071 4097 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.60 % Allowed : 9.79 % Favored : 89.62 % 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: -0.81 (0.14), residues: 3211 helix: 1.54 (0.21), residues: 687 sheet: -0.12 (0.19), residues: 692 loop : -1.60 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 258 HIS 0.005 0.001 HIS B1083 PHE 0.015 0.001 PHE B 855 TYR 0.014 0.001 TYR B 313 ARG 0.006 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 9) link_NAG-ASN : angle 2.00213 ( 27) link_ALPHA1-4 : bond 0.01261 ( 4) link_ALPHA1-4 : angle 2.25513 ( 12) hydrogen bonds : bond 0.04483 ( 977) hydrogen bonds : angle 5.33422 ( 2700) SS BOND : bond 0.00311 ( 41) SS BOND : angle 0.90405 ( 82) covalent geometry : bond 0.00465 (26383) covalent geometry : angle 0.59610 (35914) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 2.810 Fit side-chains revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8620 (t80) cc_final: 0.8293 (t80) REVERT: C 613 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8258 (pp30) REVERT: C 869 MET cc_start: 0.9108 (mtt) cc_final: 0.8785 (ptp) REVERT: A 614 ASP cc_start: 0.8830 (m-30) cc_final: 0.8560 (t0) REVERT: A 900 MET cc_start: 0.9123 (mmm) cc_final: 0.8921 (mmt) outliers start: 17 outliers final: 7 residues processed: 62 average time/residue: 0.3005 time to fit residues: 35.2370 Evaluate side-chains 54 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 162 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 314 optimal weight: 0.4980 chunk 119 optimal weight: 6.9990 chunk 262 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 298 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 277 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 ASN C 613 GLN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.046192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.031207 restraints weight = 209410.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.032275 restraints weight = 112578.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.032979 restraints weight = 74850.517| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26438 Z= 0.190 Angle : 0.578 8.704 36035 Z= 0.297 Chirality : 0.043 0.258 4135 Planarity : 0.004 0.055 4619 Dihedral : 7.370 83.502 4097 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.84 % Allowed : 10.84 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3211 helix: 1.64 (0.21), residues: 687 sheet: -0.12 (0.19), residues: 693 loop : -1.60 (0.13), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 258 HIS 0.005 0.001 HIS C 655 PHE 0.015 0.001 PHE B 855 TYR 0.013 0.001 TYR C1067 ARG 0.005 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 9) link_NAG-ASN : angle 1.95556 ( 27) link_ALPHA1-4 : bond 0.01309 ( 4) link_ALPHA1-4 : angle 2.06632 ( 12) hydrogen bonds : bond 0.04405 ( 977) hydrogen bonds : angle 5.25927 ( 2700) SS BOND : bond 0.00310 ( 41) SS BOND : angle 1.03906 ( 82) covalent geometry : bond 0.00413 (26383) covalent geometry : angle 0.57283 (35914) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 3.258 Fit side-chains revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8619 (t80) cc_final: 0.8297 (t80) REVERT: A 614 ASP cc_start: 0.8827 (m-30) cc_final: 0.8578 (t0) REVERT: A 773 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7509 (tm-30) REVERT: A 777 ASN cc_start: 0.8607 (m-40) cc_final: 0.8273 (m-40) REVERT: A 900 MET cc_start: 0.9087 (mmm) cc_final: 0.8879 (mmt) REVERT: B 298 GLU cc_start: 0.9479 (tt0) cc_final: 0.9194 (mt-10) outliers start: 24 outliers final: 14 residues processed: 72 average time/residue: 0.3608 time to fit residues: 49.8317 Evaluate side-chains 62 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 250 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 49 optimal weight: 0.4980 chunk 156 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 chunk 245 optimal weight: 8.9990 chunk 237 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN C 709 ASN A 953 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** 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 = 0.3331 r_free = 0.3331 target = 0.046036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.031076 restraints weight = 206181.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.032139 restraints weight = 112483.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.032839 restraints weight = 75114.254| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26438 Z= 0.156 Angle : 0.549 9.603 36035 Z= 0.282 Chirality : 0.042 0.251 4135 Planarity : 0.004 0.052 4619 Dihedral : 6.740 80.334 4097 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.92 % Allowed : 11.65 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 3211 helix: 1.82 (0.21), residues: 683 sheet: -0.06 (0.19), residues: 660 loop : -1.56 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 258 HIS 0.004 0.001 HIS C 655 PHE 0.012 0.001 PHE B 133 TYR 0.013 0.001 TYR C1067 ARG 0.004 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 9) link_NAG-ASN : angle 1.90120 ( 27) link_ALPHA1-4 : bond 0.01076 ( 4) link_ALPHA1-4 : angle 2.09357 ( 12) hydrogen bonds : bond 0.04223 ( 977) hydrogen bonds : angle 5.10354 ( 2700) SS BOND : bond 0.00269 ( 41) SS BOND : angle 0.87371 ( 82) covalent geometry : bond 0.00342 (26383) covalent geometry : angle 0.54437 (35914) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 52 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 168 PHE cc_start: 0.8714 (t80) cc_final: 0.8398 (t80) REVERT: C 869 MET cc_start: 0.9153 (mtt) cc_final: 0.8893 (ptp) REVERT: A 614 ASP cc_start: 0.8842 (m-30) cc_final: 0.8630 (t0) REVERT: A 773 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7485 (tm-30) REVERT: A 777 ASN cc_start: 0.8504 (m-40) cc_final: 0.8047 (m-40) REVERT: B 298 GLU cc_start: 0.9511 (tt0) cc_final: 0.9222 (mt-10) outliers start: 26 outliers final: 17 residues processed: 73 average time/residue: 0.3138 time to fit residues: 41.8463 Evaluate side-chains 69 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 878 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 299 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 59 optimal weight: 0.0030 chunk 78 optimal weight: 1.9990 chunk 44 optimal weight: 0.0670 chunk 300 optimal weight: 3.9990 chunk 289 optimal weight: 0.0020 chunk 286 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.047304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.032317 restraints weight = 204093.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.033434 restraints weight = 108445.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.034175 restraints weight = 71558.575| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26438 Z= 0.093 Angle : 0.511 8.269 36035 Z= 0.262 Chirality : 0.042 0.247 4135 Planarity : 0.003 0.052 4619 Dihedral : 6.103 73.739 4097 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.84 % Allowed : 12.35 % Favored : 86.80 % 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: -0.40 (0.15), residues: 3211 helix: 2.20 (0.21), residues: 669 sheet: 0.08 (0.20), residues: 659 loop : -1.39 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 152 HIS 0.002 0.000 HIS A1048 PHE 0.013 0.001 PHE B 133 TYR 0.014 0.001 TYR C1067 ARG 0.002 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 9) link_NAG-ASN : angle 1.86295 ( 27) link_ALPHA1-4 : bond 0.01126 ( 4) link_ALPHA1-4 : angle 2.37893 ( 12) hydrogen bonds : bond 0.03822 ( 977) hydrogen bonds : angle 4.83812 ( 2700) SS BOND : bond 0.00264 ( 41) SS BOND : angle 0.70572 ( 82) covalent geometry : bond 0.00203 (26383) covalent geometry : angle 0.50637 (35914) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 666 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9067 (mp) REVERT: C 869 MET cc_start: 0.9155 (mtt) cc_final: 0.8830 (ptp) REVERT: A 773 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7470 (tm-30) REVERT: A 777 ASN cc_start: 0.8433 (m-40) cc_final: 0.7948 (m-40) REVERT: B 298 GLU cc_start: 0.9526 (tt0) cc_final: 0.9263 (mt-10) outliers start: 24 outliers final: 17 residues processed: 84 average time/residue: 0.4073 time to fit residues: 65.1834 Evaluate side-chains 72 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 4.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 52 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 310 optimal weight: 4.9990 chunk 320 optimal weight: 1.9990 chunk 269 optimal weight: 6.9990 chunk 313 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 308 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 292 optimal weight: 0.0670 chunk 304 optimal weight: 4.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.046622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.031655 restraints weight = 205986.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.032737 restraints weight = 109684.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.033467 restraints weight = 72972.767| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26438 Z= 0.142 Angle : 0.531 11.110 36035 Z= 0.272 Chirality : 0.042 0.241 4135 Planarity : 0.004 0.052 4619 Dihedral : 6.007 72.448 4097 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.99 % Allowed : 12.67 % Favored : 86.34 % 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: -0.38 (0.15), residues: 3211 helix: 2.21 (0.21), residues: 669 sheet: 0.10 (0.20), residues: 659 loop : -1.38 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 258 HIS 0.003 0.001 HIS B1083 PHE 0.026 0.001 PHE C 168 TYR 0.013 0.001 TYR C1067 ARG 0.005 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00173 ( 9) link_NAG-ASN : angle 1.80916 ( 27) link_ALPHA1-4 : bond 0.00788 ( 4) link_ALPHA1-4 : angle 2.21073 ( 12) hydrogen bonds : bond 0.03909 ( 977) hydrogen bonds : angle 4.88013 ( 2700) SS BOND : bond 0.00246 ( 41) SS BOND : angle 0.83398 ( 82) covalent geometry : bond 0.00315 (26383) covalent geometry : angle 0.52660 (35914) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6422 Ramachandran restraints generated. 3211 Oldfield, 0 Emsley, 3211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 54 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 666 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9134 (mp) REVERT: C 869 MET cc_start: 0.9143 (mtt) cc_final: 0.8830 (ptp) REVERT: A 697 MET cc_start: 0.9260 (tpp) cc_final: 0.9059 (mmm) REVERT: A 773 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 777 ASN cc_start: 0.8472 (m-40) cc_final: 0.7997 (m-40) REVERT: B 298 GLU cc_start: 0.9525 (tt0) cc_final: 0.9238 (mt-10) outliers start: 28 outliers final: 22 residues processed: 79 average time/residue: 0.3145 time to fit residues: 45.0143 Evaluate side-chains 76 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.0888 > 50: distance: 11 - 59: 26.871 distance: 14 - 56: 36.676 distance: 32 - 38: 34.838 distance: 38 - 39: 69.580 distance: 40 - 41: 39.959 distance: 40 - 42: 38.874 distance: 43 - 44: 40.939 distance: 43 - 46: 38.808 distance: 44 - 45: 40.385 distance: 44 - 51: 49.118 distance: 46 - 47: 70.024 distance: 47 - 48: 39.596 distance: 48 - 49: 39.356 distance: 49 - 50: 40.484 distance: 51 - 52: 31.059 distance: 52 - 53: 55.584 distance: 53 - 54: 41.247 distance: 53 - 56: 56.183 distance: 54 - 187: 33.290 distance: 56 - 57: 39.344 distance: 57 - 58: 68.304 distance: 57 - 60: 39.721 distance: 58 - 59: 58.612 distance: 60 - 61: 39.673 distance: 61 - 62: 39.763 distance: 62 - 64: 40.079 distance: 63 - 65: 39.289 distance: 64 - 65: 39.397 distance: 66 - 177: 32.089 distance: 67 - 68: 55.403 distance: 67 - 70: 56.116 distance: 68 - 77: 57.817 distance: 69 - 174: 34.752 distance: 70 - 71: 56.219 distance: 71 - 72: 40.882 distance: 72 - 74: 40.189 distance: 73 - 75: 40.111 distance: 74 - 76: 56.855 distance: 75 - 76: 39.452 distance: 77 - 78: 40.388 distance: 77 - 83: 55.251 distance: 78 - 79: 55.371 distance: 78 - 81: 56.884 distance: 79 - 80: 57.674 distance: 79 - 84: 68.919 distance: 81 - 82: 39.264 distance: 82 - 83: 55.713 distance: 84 - 85: 40.267 distance: 85 - 86: 39.215 distance: 85 - 88: 57.051 distance: 86 - 87: 39.558 distance: 86 - 95: 57.818 distance: 88 - 89: 39.493 distance: 90 - 91: 39.844 distance: 92 - 93: 39.407 distance: 92 - 94: 55.936 distance: 95 - 96: 39.357 distance: 96 - 97: 40.278 distance: 96 - 99: 39.192 distance: 97 - 104: 40.826 distance: 100 - 101: 40.983 distance: 101 - 102: 40.755 distance: 105 - 106: 40.593 distance: 106 - 107: 55.764 distance: 106 - 108: 41.232 distance: 108 - 140: 36.081 distance: 109 - 110: 40.011 distance: 110 - 115: 35.446 distance: 111 - 137: 33.862 distance: 112 - 113: 41.315 distance: 112 - 114: 38.711