Starting phenix.real_space_refine on Mon Sep 30 00:13:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q1z_13776/09_2024/7q1z_13776.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q1z_13776/09_2024/7q1z_13776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q1z_13776/09_2024/7q1z_13776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q1z_13776/09_2024/7q1z_13776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q1z_13776/09_2024/7q1z_13776.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q1z_13776/09_2024/7q1z_13776.cif" } resolution = 3.4 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 99 5.16 5 C 15087 2.51 5 N 3849 2.21 5 O 4659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23694 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "B" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "C" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 14.52, per 1000 atoms: 0.61 Number of scatterers: 23694 At special positions: 0 Unit cell: (136.85, 135.7, 171.35, 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 99 16.00 O 4659 8.00 N 3849 7.00 C 15087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=3, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.93 Conformation dependent library (CDL) restraints added in 2.7 seconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 44 sheets defined 26.5% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.381A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.697A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 501 through 501 No H-bonds generated for 'chain 'A' and resid 501 through 501' Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.598A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.589A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.123A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 945 removed outlier: 3.853A pdb=" N LEU A 945 " --> pdb=" O ALA A 942 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 942 through 945' Processing helix chain 'A' and resid 946 through 965 removed outlier: 3.688A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.417A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.109A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (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: 4.400A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.532A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.794A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 501 No H-bonds generated for 'chain 'B' and resid 501 through 501' Processing helix chain 'B' and resid 503 through 506 Processing helix chain 'B' and resid 737 through 744 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: 3.555A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.125A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 946 through 965 removed outlier: 3.716A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.223A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.066A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.447A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.636A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.346A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 501 No H-bonds generated for 'chain 'C' and resid 501 through 501' Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.565A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.523A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.102A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.670A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.458A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.109A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.679A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.564A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.679A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.157A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.768A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.139A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.410A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.823A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.025A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.901A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.782A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.432A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.856A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.719A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.853A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.210A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.908A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.192A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.526A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.445A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.525A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.053A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 removed outlier: 4.033A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.770A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.799A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.441A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.030A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.646A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.628A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.236A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.841A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.977A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.985A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.457A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.143A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.812A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.840A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.461A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.010A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 994 hydrogen bonds defined for protein. 2748 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: 11.45 Time building geometry restraints manager: 6.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7489 1.35 - 1.47: 6158 1.47 - 1.59: 10428 1.59 - 1.72: 0 1.72 - 1.84: 123 Bond restraints: 24198 Sorted by residual: bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.42e+00 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.42e+00 bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.40e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 ... (remaining 24193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 31600 1.42 - 2.83: 1157 2.83 - 4.25: 125 4.25 - 5.66: 20 5.66 - 7.08: 11 Bond angle restraints: 32913 Sorted by residual: angle pdb=" C ASN A 87 " pdb=" CA ASN A 87 " pdb=" CB ASN A 87 " ideal model delta sigma weight residual 116.63 110.07 6.56 1.16e+00 7.43e-01 3.20e+01 angle pdb=" C ASN C 87 " pdb=" CA ASN C 87 " pdb=" CB ASN C 87 " ideal model delta sigma weight residual 117.23 110.15 7.08 1.36e+00 5.41e-01 2.71e+01 angle pdb=" C ASN B 87 " pdb=" CA ASN B 87 " pdb=" CB ASN B 87 " ideal model delta sigma weight residual 117.23 110.22 7.01 1.36e+00 5.41e-01 2.65e+01 angle pdb=" C PHE B 32 " pdb=" CA PHE B 32 " pdb=" CB PHE B 32 " ideal model delta sigma weight residual 117.23 110.23 7.00 1.36e+00 5.41e-01 2.65e+01 angle pdb=" C PHE C 32 " pdb=" CA PHE C 32 " pdb=" CB PHE C 32 " ideal model delta sigma weight residual 117.23 110.32 6.91 1.36e+00 5.41e-01 2.58e+01 ... (remaining 32908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 14159 17.91 - 35.82: 797 35.82 - 53.73: 184 53.73 - 71.64: 61 71.64 - 89.55: 27 Dihedral angle restraints: 15228 sinusoidal: 6738 harmonic: 8490 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.30 -86.30 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.29 -86.29 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.13 -86.13 1 1.00e+01 1.00e-02 8.95e+01 ... (remaining 15225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2695 0.040 - 0.079: 828 0.079 - 0.119: 379 0.119 - 0.159: 26 0.159 - 0.198: 4 Chirality restraints: 3932 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.84e-01 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.98e-01 ... (remaining 3929 not shown) Planarity restraints: 4196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 81 " -0.076 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO C 82 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO C 82 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 82 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 81 " -0.071 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO B 82 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 881 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C THR C 881 " -0.027 2.00e-02 2.50e+03 pdb=" O THR C 881 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE C 882 " 0.009 2.00e-02 2.50e+03 ... (remaining 4193 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 208 2.64 - 3.20: 20839 3.20 - 3.77: 34683 3.77 - 4.33: 49720 4.33 - 4.90: 82833 Nonbonded interactions: 188283 Sorted by model distance: nonbonded pdb=" OG1 THR A 393 " pdb=" OE2 GLU A 516 " model vdw 2.074 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" OD2 ASP C 53 " model vdw 2.229 3.040 nonbonded pdb=" NZ LYS C 557 " pdb=" OD2 ASP C 574 " model vdw 2.233 3.120 nonbonded pdb=" OG SER A 596 " pdb=" OE1 GLN A 613 " model vdw 2.236 3.040 ... (remaining 188278 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 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: 0.030 Extract box with map and model: 0.890 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 57.280 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3130 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24198 Z= 0.278 Angle : 0.607 7.081 32913 Z= 0.336 Chirality : 0.045 0.198 3932 Planarity : 0.004 0.113 4164 Dihedral : 12.724 89.552 9636 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.04 % Allowed : 0.31 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 2844 helix: 1.52 (0.20), residues: 723 sheet: 0.38 (0.19), residues: 645 loop : -0.08 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 886 HIS 0.004 0.001 HIS B 66 PHE 0.018 0.001 PHE B 817 TYR 0.018 0.001 TYR A 453 ARG 0.004 0.001 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 342 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 905 ARG cc_start: 0.2715 (mmt180) cc_final: 0.2190 (mtm180) REVERT: B 224 GLU cc_start: 0.5431 (pm20) cc_final: 0.4745 (mp0) REVERT: B 299 THR cc_start: 0.5027 (p) cc_final: 0.3047 (m) REVERT: B 358 ILE cc_start: 0.5281 (mt) cc_final: 0.4269 (mt) REVERT: B 394 ASN cc_start: 0.5133 (OUTLIER) cc_final: 0.4752 (m-40) REVERT: B 543 PHE cc_start: 0.4419 (m-80) cc_final: 0.2320 (m-10) REVERT: B 992 GLN cc_start: 0.3088 (mm-40) cc_final: 0.2712 (mm110) REVERT: C 281 GLU cc_start: 0.5233 (tp30) cc_final: 0.4937 (mm-30) REVERT: C 513 LEU cc_start: 0.5000 (mt) cc_final: 0.4738 (mt) REVERT: C 1018 ILE cc_start: 0.4296 (mm) cc_final: 0.4016 (tp) outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.3663 time to fit residues: 195.1983 Evaluate side-chains 266 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 0.5980 chunk 220 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 228 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 264 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 556 ASN A 655 HIS A 675 GLN A 764 ASN A 955 ASN B 134 GLN B 394 ASN B 613 GLN B 675 GLN B 901 GLN B 925 ASN B 949 GLN B1023 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 196 ASN C 394 ASN C 501 ASN C 613 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C1088 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4809 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.251 24198 Z= 0.453 Angle : 1.010 24.854 32913 Z= 0.504 Chirality : 0.064 1.506 3932 Planarity : 0.007 0.093 4164 Dihedral : 7.375 58.505 4424 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.34 % Favored : 96.62 % Rotamer: Outliers : 1.88 % Allowed : 6.38 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 2844 helix: 0.25 (0.18), residues: 726 sheet: 0.19 (0.21), residues: 576 loop : -0.69 (0.14), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B1102 HIS 0.008 0.002 HIS B1048 PHE 0.044 0.004 PHE A 543 TYR 0.036 0.003 TYR B 380 ARG 0.012 0.001 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 414 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ILE cc_start: 0.5229 (OUTLIER) cc_final: 0.4969 (pt) REVERT: A 312 ILE cc_start: 0.4575 (OUTLIER) cc_final: 0.4287 (tt) REVERT: A 327 VAL cc_start: 0.5889 (t) cc_final: 0.5386 (p) REVERT: A 516 GLU cc_start: 0.5639 (pp20) cc_final: 0.5325 (mp0) REVERT: A 764 ASN cc_start: 0.6631 (m110) cc_final: 0.6417 (m110) REVERT: A 970 PHE cc_start: 0.6396 (m-80) cc_final: 0.5146 (m-10) REVERT: A 988 GLU cc_start: 0.6664 (pm20) cc_final: 0.6307 (pm20) REVERT: A 1000 ARG cc_start: 0.6691 (mtt180) cc_final: 0.6038 (mtt-85) REVERT: A 1067 TYR cc_start: 0.6241 (t80) cc_final: 0.5937 (t80) REVERT: B 121 ASN cc_start: 0.5688 (OUTLIER) cc_final: 0.4992 (p0) REVERT: B 194 PHE cc_start: 0.5977 (m-80) cc_final: 0.4968 (m-10) REVERT: B 224 GLU cc_start: 0.5749 (pm20) cc_final: 0.5389 (mp0) REVERT: B 543 PHE cc_start: 0.5251 (m-80) cc_final: 0.4784 (m-10) REVERT: B 900 MET cc_start: 0.4197 (mmt) cc_final: 0.3868 (mmp) REVERT: B 979 ASP cc_start: 0.6216 (m-30) cc_final: 0.5953 (m-30) REVERT: B 1000 ARG cc_start: 0.6043 (mpt180) cc_final: 0.4734 (mpt-90) REVERT: C 196 ASN cc_start: 0.6022 (m110) cc_final: 0.5803 (m-40) REVERT: C 239 GLN cc_start: 0.6069 (tp-100) cc_final: 0.5811 (tp40) REVERT: C 595 VAL cc_start: 0.6959 (OUTLIER) cc_final: 0.6745 (p) REVERT: C 763 LEU cc_start: 0.6432 (mt) cc_final: 0.6042 (mt) REVERT: C 768 THR cc_start: 0.6919 (m) cc_final: 0.5766 (p) REVERT: C 867 ASP cc_start: 0.6495 (m-30) cc_final: 0.6274 (m-30) REVERT: C 963 VAL cc_start: 0.6359 (t) cc_final: 0.5497 (p) REVERT: C 1006 THR cc_start: 0.6897 (m) cc_final: 0.6649 (p) REVERT: C 1008 VAL cc_start: 0.6014 (t) cc_final: 0.4768 (m) REVERT: C 1010 GLN cc_start: 0.6370 (mm-40) cc_final: 0.6160 (mm-40) REVERT: C 1013 ILE cc_start: 0.5863 (mt) cc_final: 0.5475 (mt) REVERT: C 1029 MET cc_start: 0.6328 (tmm) cc_final: 0.6065 (tmm) outliers start: 48 outliers final: 19 residues processed: 437 average time/residue: 0.3618 time to fit residues: 243.4621 Evaluate side-chains 355 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 332 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 605 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 0.0470 chunk 82 optimal weight: 0.9980 chunk 219 optimal weight: 0.9990 chunk 179 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 264 optimal weight: 1.9990 chunk 285 optimal weight: 0.5980 chunk 235 optimal weight: 1.9990 chunk 262 optimal weight: 0.0770 chunk 90 optimal weight: 0.4980 chunk 212 optimal weight: 0.8980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 901 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN A1119 ASN B 115 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B 992 GLN C 196 ASN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN C 607 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5265 moved from start: 0.5838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 24198 Z= 0.259 Angle : 0.676 12.666 32913 Z= 0.348 Chirality : 0.048 0.439 3932 Planarity : 0.005 0.057 4164 Dihedral : 6.124 57.099 4422 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.70 % Allowed : 10.13 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 2844 helix: 1.03 (0.20), residues: 735 sheet: 0.13 (0.20), residues: 591 loop : -0.63 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 64 HIS 0.009 0.001 HIS C1088 PHE 0.027 0.002 PHE B 306 TYR 0.022 0.002 TYR B1067 ARG 0.014 0.001 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 402 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 VAL cc_start: 0.6180 (t) cc_final: 0.5882 (p) REVERT: A 565 PHE cc_start: 0.5670 (OUTLIER) cc_final: 0.5460 (m-80) REVERT: A 664 ILE cc_start: 0.6395 (tp) cc_final: 0.6110 (tt) REVERT: A 762 GLN cc_start: 0.6285 (tp-100) cc_final: 0.5099 (tm-30) REVERT: A 869 MET cc_start: 0.6978 (ttp) cc_final: 0.6750 (ttm) REVERT: A 1000 ARG cc_start: 0.7077 (mtt180) cc_final: 0.6603 (mtt180) REVERT: A 1048 HIS cc_start: 0.5720 (t70) cc_final: 0.5510 (t-90) REVERT: A 1067 TYR cc_start: 0.6627 (t80) cc_final: 0.6108 (t80) REVERT: A 1120 THR cc_start: 0.4337 (p) cc_final: 0.4097 (t) REVERT: B 130 VAL cc_start: 0.8073 (t) cc_final: 0.7817 (t) REVERT: B 319 ARG cc_start: 0.6007 (ttm-80) cc_final: 0.4539 (ttm-80) REVERT: B 428 ASP cc_start: 0.5743 (t0) cc_final: 0.5451 (t0) REVERT: B 543 PHE cc_start: 0.5586 (m-80) cc_final: 0.4832 (m-10) REVERT: B 900 MET cc_start: 0.4677 (mmt) cc_final: 0.4328 (mmp) REVERT: B 906 PHE cc_start: 0.4363 (m-80) cc_final: 0.3260 (m-10) REVERT: B 1000 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.5707 (mmm-85) REVERT: B 1095 PHE cc_start: 0.4980 (m-80) cc_final: 0.4691 (m-10) REVERT: C 115 GLN cc_start: 0.4243 (mp10) cc_final: 0.3799 (tt0) REVERT: C 316 SER cc_start: 0.7146 (t) cc_final: 0.6785 (m) REVERT: C 365 TYR cc_start: 0.7093 (m-80) cc_final: 0.6746 (m-80) REVERT: C 1006 THR cc_start: 0.7320 (m) cc_final: 0.6984 (p) REVERT: C 1008 VAL cc_start: 0.6802 (t) cc_final: 0.5502 (m) REVERT: C 1029 MET cc_start: 0.6790 (tmm) cc_final: 0.6518 (tpp) outliers start: 69 outliers final: 37 residues processed: 432 average time/residue: 0.3292 time to fit residues: 227.5570 Evaluate side-chains 387 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 348 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 0.0670 chunk 199 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 chunk 126 optimal weight: 0.1980 chunk 177 optimal weight: 0.6980 chunk 265 optimal weight: 1.9990 chunk 281 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 251 optimal weight: 0.0270 chunk 75 optimal weight: 0.9990 overall best weight: 0.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 762 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5485 moved from start: 0.6640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 24198 Z= 0.190 Angle : 0.599 12.570 32913 Z= 0.309 Chirality : 0.045 0.338 3932 Planarity : 0.004 0.047 4164 Dihedral : 5.738 58.349 4422 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.62 % Allowed : 12.87 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.12 (0.15), residues: 2844 helix: 1.28 (0.20), residues: 735 sheet: 0.29 (0.20), residues: 612 loop : -0.60 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C1102 HIS 0.010 0.001 HIS B1048 PHE 0.023 0.002 PHE B 201 TYR 0.022 0.001 TYR B1067 ARG 0.009 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 384 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.5663 (p90) cc_final: 0.5434 (p90) REVERT: A 327 VAL cc_start: 0.6334 (t) cc_final: 0.6048 (p) REVERT: A 354 ASN cc_start: 0.7612 (t0) cc_final: 0.7367 (t0) REVERT: A 869 MET cc_start: 0.7211 (ttp) cc_final: 0.6853 (ttm) REVERT: A 934 ILE cc_start: 0.7066 (mm) cc_final: 0.6753 (mt) REVERT: A 1089 PHE cc_start: 0.6732 (m-80) cc_final: 0.5730 (m-80) REVERT: A 1120 THR cc_start: 0.4620 (p) cc_final: 0.4378 (t) REVERT: B 319 ARG cc_start: 0.6551 (ttm-80) cc_final: 0.5858 (ttm-80) REVERT: B 428 ASP cc_start: 0.5826 (t0) cc_final: 0.5516 (t0) REVERT: B 873 TYR cc_start: 0.6978 (m-10) cc_final: 0.6704 (m-80) REVERT: B 900 MET cc_start: 0.4956 (mmt) cc_final: 0.4622 (mmp) REVERT: B 906 PHE cc_start: 0.4675 (m-10) cc_final: 0.3661 (m-10) REVERT: B 1000 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6238 (mmm-85) REVERT: C 52 GLN cc_start: 0.6334 (mm-40) cc_final: 0.6101 (mm-40) REVERT: C 115 GLN cc_start: 0.4308 (mp10) cc_final: 0.3913 (tt0) REVERT: C 191 GLU cc_start: 0.6271 (mt-10) cc_final: 0.5523 (mt-10) REVERT: C 765 ARG cc_start: 0.5966 (tpp80) cc_final: 0.5671 (tpp80) REVERT: C 984 LEU cc_start: 0.6724 (mt) cc_final: 0.6468 (mm) REVERT: C 1006 THR cc_start: 0.7484 (m) cc_final: 0.7276 (p) REVERT: C 1102 TRP cc_start: 0.5294 (m100) cc_final: 0.5023 (m100) outliers start: 67 outliers final: 41 residues processed: 413 average time/residue: 0.3757 time to fit residues: 245.6103 Evaluate side-chains 410 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 368 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 209 optimal weight: 0.0470 chunk 116 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 252 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 207 HIS A 764 ASN A 901 GLN A1005 GLN A1048 HIS A1054 GLN A1064 HIS ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 603 ASN C 607 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 1.0095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 24198 Z= 0.362 Angle : 0.819 14.970 32913 Z= 0.436 Chirality : 0.052 0.327 3932 Planarity : 0.006 0.074 4164 Dihedral : 5.921 55.518 4422 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.52 % Favored : 96.45 % Rotamer: Outliers : 3.60 % Allowed : 13.81 % Favored : 82.59 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.46 (0.15), residues: 2844 helix: 0.60 (0.19), residues: 732 sheet: 0.17 (0.20), residues: 615 loop : -0.95 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 64 HIS 0.009 0.002 HIS C1088 PHE 0.048 0.003 PHE B 201 TYR 0.032 0.002 TYR B 204 ARG 0.017 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 567 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.7003 (m-80) REVERT: A 192 PHE cc_start: 0.7565 (m-80) cc_final: 0.7321 (m-10) REVERT: A 224 GLU cc_start: 0.7128 (pm20) cc_final: 0.6831 (mp0) REVERT: A 236 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7922 (m) REVERT: A 433 VAL cc_start: 0.7695 (t) cc_final: 0.7263 (m) REVERT: A 537 LYS cc_start: 0.7951 (mtmm) cc_final: 0.7696 (mtpp) REVERT: A 578 ASP cc_start: 0.6952 (t0) cc_final: 0.6650 (t0) REVERT: A 599 THR cc_start: 0.6921 (t) cc_final: 0.6648 (t) REVERT: A 673 SER cc_start: 0.8547 (p) cc_final: 0.8287 (t) REVERT: A 697 MET cc_start: 0.5750 (ppp) cc_final: 0.4973 (ptm) REVERT: A 714 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7749 (mt) REVERT: A 726 ILE cc_start: 0.8309 (mp) cc_final: 0.8107 (mp) REVERT: A 729 VAL cc_start: 0.8143 (t) cc_final: 0.7251 (p) REVERT: A 752 LEU cc_start: 0.8811 (tp) cc_final: 0.8527 (tt) REVERT: A 765 ARG cc_start: 0.7243 (ttm-80) cc_final: 0.6995 (ttm-80) REVERT: A 780 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7341 (tm-30) REVERT: A 868 GLU cc_start: 0.6773 (mp0) cc_final: 0.6553 (mp0) REVERT: A 990 GLU cc_start: 0.7331 (tm-30) cc_final: 0.7087 (tm-30) REVERT: A 1023 ASN cc_start: 0.7953 (t0) cc_final: 0.7425 (m-40) REVERT: A 1065 VAL cc_start: 0.7276 (OUTLIER) cc_final: 0.6182 (m) REVERT: A 1072 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7117 (pp20) REVERT: B 224 GLU cc_start: 0.7275 (mp0) cc_final: 0.6161 (tp30) REVERT: B 240 THR cc_start: 0.7502 (m) cc_final: 0.7184 (t) REVERT: B 278 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6841 (ttmt) REVERT: B 305 SER cc_start: 0.8420 (t) cc_final: 0.8064 (p) REVERT: B 514 SER cc_start: 0.8249 (t) cc_final: 0.7612 (p) REVERT: B 574 ASP cc_start: 0.6782 (t70) cc_final: 0.6530 (t0) REVERT: B 735 SER cc_start: 0.8707 (p) cc_final: 0.8259 (t) REVERT: B 740 MET cc_start: 0.6522 (ppp) cc_final: 0.6322 (ppp) REVERT: B 765 ARG cc_start: 0.6828 (ttm110) cc_final: 0.6610 (ttm110) REVERT: B 788 ILE cc_start: 0.6439 (OUTLIER) cc_final: 0.6180 (mm) REVERT: B 790 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7532 (ptmm) REVERT: B 900 MET cc_start: 0.6427 (mmt) cc_final: 0.6205 (mmm) REVERT: B 990 GLU cc_start: 0.7146 (tt0) cc_final: 0.6923 (tt0) REVERT: B 1000 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8193 (mmt90) REVERT: B 1014 ARG cc_start: 0.7753 (ttp80) cc_final: 0.7454 (ttp-110) REVERT: B 1029 MET cc_start: 0.7586 (tpt) cc_final: 0.7374 (tpp) REVERT: B 1030 SER cc_start: 0.7473 (m) cc_final: 0.7202 (p) REVERT: B 1079 PRO cc_start: 0.7926 (Cg_endo) cc_final: 0.7718 (Cg_exo) REVERT: B 1096 VAL cc_start: 0.7714 (p) cc_final: 0.7500 (t) REVERT: C 238 PHE cc_start: 0.6700 (OUTLIER) cc_final: 0.6091 (p90) REVERT: C 279 TYR cc_start: 0.7674 (m-80) cc_final: 0.7468 (m-10) REVERT: C 307 THR cc_start: 0.8723 (m) cc_final: 0.8308 (p) REVERT: C 365 TYR cc_start: 0.7452 (m-80) cc_final: 0.7181 (m-80) REVERT: C 537 LYS cc_start: 0.7843 (ttpt) cc_final: 0.7554 (ttmm) REVERT: C 599 THR cc_start: 0.8352 (t) cc_final: 0.8096 (t) REVERT: C 756 TYR cc_start: 0.8236 (m-80) cc_final: 0.7676 (m-80) REVERT: C 994 ASP cc_start: 0.7397 (m-30) cc_final: 0.7088 (m-30) REVERT: C 1002 GLN cc_start: 0.7669 (tp40) cc_final: 0.7306 (tp40) outliers start: 92 outliers final: 38 residues processed: 618 average time/residue: 0.3465 time to fit residues: 339.4265 Evaluate side-chains 528 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 480 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 0.2980 chunk 253 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 281 optimal weight: 0.5980 chunk 233 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 93 optimal weight: 0.0970 chunk 147 optimal weight: 0.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 872 GLN A 926 GLN A1002 GLN A1119 ASN B 115 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN B 949 GLN B 957 GLN B1005 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 901 GLN C 914 ASN C1005 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 1.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24198 Z= 0.226 Angle : 0.647 12.767 32913 Z= 0.335 Chirality : 0.047 0.302 3932 Planarity : 0.005 0.055 4164 Dihedral : 5.571 56.616 4422 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.56 % Allowed : 17.14 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 2844 helix: 1.23 (0.20), residues: 720 sheet: 0.20 (0.20), residues: 630 loop : -0.77 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.008 0.001 HIS A1088 PHE 0.030 0.002 PHE C 194 TYR 0.022 0.002 TYR A1067 ARG 0.011 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 485 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6700 (tp40) cc_final: 0.6451 (tp40) REVERT: A 105 ILE cc_start: 0.7327 (OUTLIER) cc_final: 0.7111 (mt) REVERT: A 192 PHE cc_start: 0.7782 (m-80) cc_final: 0.7553 (m-10) REVERT: A 224 GLU cc_start: 0.7098 (pm20) cc_final: 0.6775 (mp0) REVERT: A 236 THR cc_start: 0.8074 (t) cc_final: 0.7777 (m) REVERT: A 298 GLU cc_start: 0.6391 (tp30) cc_final: 0.6051 (tp30) REVERT: A 599 THR cc_start: 0.6952 (t) cc_final: 0.6680 (t) REVERT: A 608 VAL cc_start: 0.7232 (t) cc_final: 0.6928 (p) REVERT: A 673 SER cc_start: 0.8562 (p) cc_final: 0.8303 (t) REVERT: A 714 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7481 (mt) REVERT: A 729 VAL cc_start: 0.8229 (t) cc_final: 0.7934 (m) REVERT: A 755 GLN cc_start: 0.7846 (tt0) cc_final: 0.7613 (mt0) REVERT: A 900 MET cc_start: 0.7593 (mmt) cc_final: 0.7132 (mmp) REVERT: A 960 ASN cc_start: 0.7616 (t0) cc_final: 0.6996 (t0) REVERT: A 987 PRO cc_start: 0.8658 (Cg_exo) cc_final: 0.8442 (Cg_endo) REVERT: A 988 GLU cc_start: 0.7715 (mp0) cc_final: 0.7515 (mp0) REVERT: A 1002 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: A 1008 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8329 (t) REVERT: A 1014 ARG cc_start: 0.7676 (tpp80) cc_final: 0.7222 (ttm110) REVERT: A 1023 ASN cc_start: 0.7820 (t0) cc_final: 0.7493 (m-40) REVERT: B 271 GLN cc_start: 0.6879 (mp10) cc_final: 0.6559 (mp10) REVERT: B 278 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6808 (ttmt) REVERT: B 305 SER cc_start: 0.8434 (t) cc_final: 0.8160 (p) REVERT: B 357 ARG cc_start: 0.6447 (mpt180) cc_final: 0.6197 (mpt180) REVERT: B 428 ASP cc_start: 0.6376 (t0) cc_final: 0.6044 (t0) REVERT: B 514 SER cc_start: 0.8160 (t) cc_final: 0.7683 (p) REVERT: B 515 PHE cc_start: 0.7471 (m-10) cc_final: 0.7271 (m-80) REVERT: B 529 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7255 (ptmm) REVERT: B 535 LYS cc_start: 0.8359 (ptpp) cc_final: 0.8083 (mtpt) REVERT: B 644 GLN cc_start: 0.6318 (mm-40) cc_final: 0.5943 (mm-40) REVERT: B 726 ILE cc_start: 0.8049 (mm) cc_final: 0.7791 (mm) REVERT: B 735 SER cc_start: 0.8802 (p) cc_final: 0.8512 (t) REVERT: B 740 MET cc_start: 0.6800 (ppp) cc_final: 0.6377 (ppp) REVERT: B 765 ARG cc_start: 0.7150 (ttm110) cc_final: 0.6909 (ttm110) REVERT: B 973 ILE cc_start: 0.8354 (tp) cc_final: 0.7909 (pt) REVERT: B 1000 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7793 (mtt90) REVERT: B 1005 GLN cc_start: 0.7388 (mt0) cc_final: 0.7147 (mt0) REVERT: B 1030 SER cc_start: 0.7621 (m) cc_final: 0.7363 (p) REVERT: B 1096 VAL cc_start: 0.7877 (p) cc_final: 0.7582 (t) REVERT: C 53 ASP cc_start: 0.6078 (t70) cc_final: 0.5442 (t70) REVERT: C 238 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.6096 (p90) REVERT: C 279 TYR cc_start: 0.7546 (m-80) cc_final: 0.7285 (m-10) REVERT: C 307 THR cc_start: 0.8690 (m) cc_final: 0.8284 (p) REVERT: C 365 TYR cc_start: 0.7347 (m-80) cc_final: 0.6804 (m-80) REVERT: C 515 PHE cc_start: 0.7969 (m-10) cc_final: 0.7682 (m-80) REVERT: C 537 LYS cc_start: 0.7739 (ttpt) cc_final: 0.7450 (ttmm) REVERT: C 573 THR cc_start: 0.7156 (m) cc_final: 0.6900 (p) REVERT: C 657 ASN cc_start: 0.6916 (m-40) cc_final: 0.6582 (m-40) REVERT: C 764 ASN cc_start: 0.7890 (t0) cc_final: 0.7567 (m-40) REVERT: C 959 LEU cc_start: 0.8107 (mt) cc_final: 0.7889 (mt) REVERT: C 990 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6890 (mm-30) REVERT: C 994 ASP cc_start: 0.7410 (m-30) cc_final: 0.7201 (m-30) REVERT: C 1002 GLN cc_start: 0.7749 (tp40) cc_final: 0.7368 (tp40) REVERT: C 1027 THR cc_start: 0.7975 (m) cc_final: 0.7768 (m) outliers start: 91 outliers final: 55 residues processed: 538 average time/residue: 0.3413 time to fit residues: 288.8183 Evaluate side-chains 503 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 440 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 160 optimal weight: 0.0070 chunk 205 optimal weight: 3.9990 chunk 159 optimal weight: 0.0870 chunk 237 optimal weight: 0.6980 chunk 157 optimal weight: 0.7980 chunk 280 optimal weight: 0.9990 chunk 175 optimal weight: 0.5980 chunk 170 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 764 ASN A1058 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 GLN B1002 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 658 ASN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 1.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 24198 Z= 0.250 Angle : 0.650 11.338 32913 Z= 0.338 Chirality : 0.047 0.268 3932 Planarity : 0.005 0.056 4164 Dihedral : 5.457 54.713 4422 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.01 % Allowed : 18.90 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.15 (0.15), residues: 2844 helix: 1.20 (0.20), residues: 729 sheet: 0.09 (0.20), residues: 660 loop : -0.85 (0.15), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS B1064 PHE 0.023 0.002 PHE A 168 TYR 0.025 0.001 TYR A1067 ARG 0.007 0.001 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 502 time to evaluate : 2.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6890 (tp40) cc_final: 0.6629 (tp40) REVERT: A 105 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7231 (mt) REVERT: A 236 THR cc_start: 0.8237 (t) cc_final: 0.7966 (m) REVERT: A 608 VAL cc_start: 0.7589 (t) cc_final: 0.7296 (p) REVERT: A 646 ARG cc_start: 0.7029 (mmp80) cc_final: 0.6556 (mmp80) REVERT: A 650 LEU cc_start: 0.7662 (mp) cc_final: 0.7280 (mt) REVERT: A 673 SER cc_start: 0.8466 (p) cc_final: 0.8193 (p) REVERT: A 773 GLU cc_start: 0.7461 (tp30) cc_final: 0.7042 (tp30) REVERT: A 900 MET cc_start: 0.7848 (mmt) cc_final: 0.7536 (mmp) REVERT: A 933 LYS cc_start: 0.7308 (mttt) cc_final: 0.7076 (mtmm) REVERT: A 957 GLN cc_start: 0.6984 (mm110) cc_final: 0.6710 (mm110) REVERT: A 976 VAL cc_start: 0.8422 (t) cc_final: 0.8117 (m) REVERT: A 981 LEU cc_start: 0.8666 (mm) cc_final: 0.8352 (mp) REVERT: A 987 PRO cc_start: 0.8686 (Cg_exo) cc_final: 0.8376 (Cg_endo) REVERT: A 988 GLU cc_start: 0.7658 (mp0) cc_final: 0.7310 (mp0) REVERT: A 1008 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8333 (t) REVERT: B 49 HIS cc_start: 0.7486 (t70) cc_final: 0.7245 (t-90) REVERT: B 278 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.6893 (ttmt) REVERT: B 305 SER cc_start: 0.8597 (t) cc_final: 0.8233 (p) REVERT: B 357 ARG cc_start: 0.6594 (mpt180) cc_final: 0.6355 (mpt180) REVERT: B 364 ASP cc_start: 0.6031 (t0) cc_final: 0.5596 (t0) REVERT: B 382 VAL cc_start: 0.8302 (t) cc_final: 0.7869 (p) REVERT: B 514 SER cc_start: 0.8248 (t) cc_final: 0.7709 (p) REVERT: B 515 PHE cc_start: 0.7751 (m-10) cc_final: 0.7510 (m-80) REVERT: B 726 ILE cc_start: 0.8199 (mm) cc_final: 0.7960 (mm) REVERT: B 1000 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7984 (mtt90) REVERT: B 1030 SER cc_start: 0.8079 (m) cc_final: 0.7825 (p) REVERT: C 53 ASP cc_start: 0.6227 (t70) cc_final: 0.5607 (t70) REVERT: C 59 PHE cc_start: 0.7298 (m-80) cc_final: 0.6861 (m-80) REVERT: C 195 LYS cc_start: 0.7648 (ptpp) cc_final: 0.7324 (ptmt) REVERT: C 202 LYS cc_start: 0.6754 (tptt) cc_final: 0.6514 (mtmt) REVERT: C 238 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6123 (p90) REVERT: C 275 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.8033 (t80) REVERT: C 279 TYR cc_start: 0.7615 (m-80) cc_final: 0.7369 (m-10) REVERT: C 305 SER cc_start: 0.8786 (t) cc_final: 0.8482 (m) REVERT: C 356 LYS cc_start: 0.7980 (ttmt) cc_final: 0.7743 (ttmt) REVERT: C 358 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7566 (mt) REVERT: C 365 TYR cc_start: 0.7595 (m-80) cc_final: 0.7246 (m-80) REVERT: C 516 GLU cc_start: 0.6217 (tm-30) cc_final: 0.5954 (tm-30) REVERT: C 657 ASN cc_start: 0.6996 (m-40) cc_final: 0.6705 (m-40) REVERT: C 759 PHE cc_start: 0.8123 (m-10) cc_final: 0.7870 (m-80) REVERT: C 990 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6975 (mm-30) REVERT: C 994 ASP cc_start: 0.7417 (m-30) cc_final: 0.7216 (m-30) REVERT: C 1002 GLN cc_start: 0.7683 (tp40) cc_final: 0.7329 (tp40) REVERT: C 1072 GLU cc_start: 0.7258 (pm20) cc_final: 0.6998 (pm20) outliers start: 77 outliers final: 49 residues processed: 544 average time/residue: 0.3507 time to fit residues: 302.3031 Evaluate side-chains 517 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 461 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 167 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 0.0020 chunk 54 optimal weight: 0.9990 chunk 178 optimal weight: 0.8980 chunk 191 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 26 optimal weight: 0.0770 chunk 220 optimal weight: 3.9990 overall best weight: 0.4946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 969 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 314 GLN C 658 ASN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 1.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 24198 Z= 0.259 Angle : 0.700 20.234 32913 Z= 0.359 Chirality : 0.049 0.865 3932 Planarity : 0.005 0.086 4164 Dihedral : 5.633 53.272 4422 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.09 % Allowed : 19.87 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.15 (0.15), residues: 2844 helix: 1.24 (0.20), residues: 729 sheet: 0.05 (0.19), residues: 690 loop : -0.87 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1102 HIS 0.006 0.001 HIS B1064 PHE 0.032 0.002 PHE A 192 TYR 0.028 0.002 TYR C 660 ARG 0.013 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 531 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7022 (tp40) cc_final: 0.6815 (tp40) REVERT: A 565 PHE cc_start: 0.7218 (m-80) cc_final: 0.6991 (m-80) REVERT: A 693 ILE cc_start: 0.8014 (pt) cc_final: 0.7808 (pt) REVERT: A 823 PHE cc_start: 0.7608 (m-80) cc_final: 0.7393 (m-80) REVERT: A 887 THR cc_start: 0.8150 (m) cc_final: 0.7945 (p) REVERT: A 900 MET cc_start: 0.7905 (mmt) cc_final: 0.7688 (mmp) REVERT: A 933 LYS cc_start: 0.7607 (mttt) cc_final: 0.7320 (mtmm) REVERT: A 957 GLN cc_start: 0.7135 (mm110) cc_final: 0.6866 (mm110) REVERT: A 976 VAL cc_start: 0.8536 (t) cc_final: 0.8183 (m) REVERT: A 981 LEU cc_start: 0.8710 (mm) cc_final: 0.8413 (mp) REVERT: A 987 PRO cc_start: 0.8771 (Cg_exo) cc_final: 0.8537 (Cg_endo) REVERT: A 1005 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7252 (mt0) REVERT: A 1008 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8397 (t) REVERT: A 1072 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6674 (pt0) REVERT: A 1104 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8069 (p) REVERT: B 55 PHE cc_start: 0.7156 (m-80) cc_final: 0.6371 (m-80) REVERT: B 118 LEU cc_start: 0.7228 (tp) cc_final: 0.6741 (mt) REVERT: B 276 LEU cc_start: 0.7269 (tt) cc_final: 0.7038 (tp) REVERT: B 278 LYS cc_start: 0.7284 (OUTLIER) cc_final: 0.6770 (ttmt) REVERT: B 357 ARG cc_start: 0.6630 (mpt180) cc_final: 0.6352 (mpt180) REVERT: B 364 ASP cc_start: 0.6388 (t0) cc_final: 0.6016 (t0) REVERT: B 382 VAL cc_start: 0.8480 (t) cc_final: 0.8208 (p) REVERT: B 514 SER cc_start: 0.8305 (t) cc_final: 0.7726 (p) REVERT: B 584 ILE cc_start: 0.7927 (mm) cc_final: 0.7548 (mm) REVERT: B 699 LEU cc_start: 0.8403 (mt) cc_final: 0.8153 (mp) REVERT: B 726 ILE cc_start: 0.8262 (mm) cc_final: 0.7956 (mm) REVERT: B 765 ARG cc_start: 0.7305 (ttm110) cc_final: 0.6952 (ttm110) REVERT: B 1000 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7832 (mtt90) REVERT: B 1002 GLN cc_start: 0.7530 (tm-30) cc_final: 0.7247 (tm-30) REVERT: B 1017 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6928 (tm-30) REVERT: B 1136 THR cc_start: 0.7521 (p) cc_final: 0.6064 (m) REVERT: C 53 ASP cc_start: 0.5939 (t70) cc_final: 0.5416 (t70) REVERT: C 113 LYS cc_start: 0.6969 (tptp) cc_final: 0.6767 (tptp) REVERT: C 195 LYS cc_start: 0.7729 (ptpp) cc_final: 0.7279 (ptmt) REVERT: C 203 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7565 (mt) REVERT: C 238 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.6028 (p90) REVERT: C 240 THR cc_start: 0.8085 (m) cc_final: 0.7441 (t) REVERT: C 279 TYR cc_start: 0.7715 (m-80) cc_final: 0.7378 (m-10) REVERT: C 305 SER cc_start: 0.8862 (t) cc_final: 0.8498 (m) REVERT: C 320 VAL cc_start: 0.8255 (t) cc_final: 0.7882 (m) REVERT: C 358 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7654 (mt) REVERT: C 365 TYR cc_start: 0.7640 (m-80) cc_final: 0.7166 (m-80) REVERT: C 573 THR cc_start: 0.7559 (m) cc_final: 0.7197 (p) REVERT: C 583 GLU cc_start: 0.7112 (pm20) cc_final: 0.6773 (pm20) REVERT: C 654 GLU cc_start: 0.6981 (tp30) cc_final: 0.6753 (tp30) REVERT: C 656 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7896 (t) REVERT: C 657 ASN cc_start: 0.6780 (m-40) cc_final: 0.6509 (m-40) REVERT: C 699 LEU cc_start: 0.8810 (mt) cc_final: 0.8515 (mt) REVERT: C 979 ASP cc_start: 0.7246 (m-30) cc_final: 0.7045 (m-30) REVERT: C 990 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6918 (mm-30) REVERT: C 994 ASP cc_start: 0.7401 (m-30) cc_final: 0.7177 (m-30) REVERT: C 1002 GLN cc_start: 0.7688 (tp40) cc_final: 0.7265 (tp40) REVERT: C 1031 GLU cc_start: 0.7595 (tt0) cc_final: 0.7213 (mt-10) REVERT: C 1133 VAL cc_start: 0.8678 (p) cc_final: 0.8297 (m) outliers start: 79 outliers final: 47 residues processed: 574 average time/residue: 0.3626 time to fit residues: 325.9322 Evaluate side-chains 545 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 488 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 0.7980 chunk 268 optimal weight: 0.6980 chunk 245 optimal weight: 0.9980 chunk 261 optimal weight: 0.6980 chunk 157 optimal weight: 0.4980 chunk 113 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 236 optimal weight: 0.9980 chunk 247 optimal weight: 1.9990 chunk 260 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 317 ASN A 394 ASN A 613 GLN A1005 GLN A1119 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1023 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 314 GLN C 658 ASN C 777 ASN C 804 GLN C1125 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 1.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 24198 Z= 0.326 Angle : 0.744 13.102 32913 Z= 0.391 Chirality : 0.049 0.225 3932 Planarity : 0.005 0.063 4164 Dihedral : 6.040 55.472 4422 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.09 % Allowed : 21.24 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 2844 helix: 0.92 (0.20), residues: 729 sheet: 0.15 (0.20), residues: 621 loop : -0.91 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 436 HIS 0.010 0.001 HIS B 655 PHE 0.055 0.002 PHE B 759 TYR 0.030 0.002 TYR A1067 ARG 0.009 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 552 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7166 (tp40) cc_final: 0.6882 (tp40) REVERT: A 117 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8196 (pp) REVERT: A 281 GLU cc_start: 0.6860 (tp30) cc_final: 0.6459 (tp30) REVERT: A 429 PHE cc_start: 0.7620 (t80) cc_final: 0.7295 (t80) REVERT: A 587 ILE cc_start: 0.8392 (mt) cc_final: 0.8041 (mt) REVERT: A 693 ILE cc_start: 0.8437 (pt) cc_final: 0.8188 (pt) REVERT: A 752 LEU cc_start: 0.8673 (tt) cc_final: 0.8348 (tp) REVERT: A 933 LYS cc_start: 0.7827 (mttt) cc_final: 0.7495 (mtmm) REVERT: A 949 GLN cc_start: 0.6778 (tp40) cc_final: 0.6564 (tp40) REVERT: A 976 VAL cc_start: 0.8672 (t) cc_final: 0.8262 (m) REVERT: A 981 LEU cc_start: 0.8686 (mm) cc_final: 0.8438 (mp) REVERT: A 987 PRO cc_start: 0.8839 (Cg_exo) cc_final: 0.8596 (Cg_endo) REVERT: A 1002 GLN cc_start: 0.7702 (tm-30) cc_final: 0.7475 (tm-30) REVERT: A 1045 LYS cc_start: 0.8120 (tttm) cc_final: 0.7860 (mtpp) REVERT: B 55 PHE cc_start: 0.7332 (m-80) cc_final: 0.6808 (m-80) REVERT: B 276 LEU cc_start: 0.7589 (tt) cc_final: 0.7291 (tp) REVERT: B 278 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6939 (ttmt) REVERT: B 281 GLU cc_start: 0.5896 (tp30) cc_final: 0.5462 (tp30) REVERT: B 357 ARG cc_start: 0.6740 (mpt180) cc_final: 0.6458 (mpt180) REVERT: B 364 ASP cc_start: 0.7046 (t0) cc_final: 0.6620 (t0) REVERT: B 365 TYR cc_start: 0.7545 (m-80) cc_final: 0.7106 (m-80) REVERT: B 377 PHE cc_start: 0.7372 (t80) cc_final: 0.7121 (t80) REVERT: B 382 VAL cc_start: 0.8514 (t) cc_final: 0.8245 (p) REVERT: B 428 ASP cc_start: 0.6579 (t0) cc_final: 0.6268 (p0) REVERT: B 514 SER cc_start: 0.8291 (t) cc_final: 0.7661 (p) REVERT: B 529 LYS cc_start: 0.7701 (ptmm) cc_final: 0.7490 (ptmm) REVERT: B 549 THR cc_start: 0.8235 (t) cc_final: 0.7753 (p) REVERT: B 567 ARG cc_start: 0.7600 (tpp80) cc_final: 0.7284 (ttm-80) REVERT: B 584 ILE cc_start: 0.8090 (mm) cc_final: 0.7796 (mm) REVERT: B 651 ILE cc_start: 0.8422 (mm) cc_final: 0.8139 (mm) REVERT: B 699 LEU cc_start: 0.8710 (mt) cc_final: 0.8488 (mp) REVERT: B 707 TYR cc_start: 0.8070 (t80) cc_final: 0.7684 (t80) REVERT: B 726 ILE cc_start: 0.8422 (mm) cc_final: 0.8008 (mm) REVERT: B 765 ARG cc_start: 0.7302 (ttm110) cc_final: 0.6908 (ttm110) REVERT: B 780 GLU cc_start: 0.7053 (pp20) cc_final: 0.6728 (pp20) REVERT: B 872 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7741 (mm-40) REVERT: B 900 MET cc_start: 0.7382 (mmm) cc_final: 0.7159 (mpp) REVERT: B 954 GLN cc_start: 0.6554 (mt0) cc_final: 0.6330 (mt0) REVERT: B 1000 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8049 (mtt90) REVERT: B 1111 GLU cc_start: 0.6789 (tt0) cc_final: 0.6571 (tt0) REVERT: B 1125 ASN cc_start: 0.7604 (m-40) cc_final: 0.7270 (m-40) REVERT: C 53 ASP cc_start: 0.6022 (t70) cc_final: 0.5697 (t70) REVERT: C 195 LYS cc_start: 0.7813 (ptpp) cc_final: 0.7491 (ptmt) REVERT: C 240 THR cc_start: 0.8101 (m) cc_final: 0.7579 (t) REVERT: C 305 SER cc_start: 0.8940 (t) cc_final: 0.8586 (m) REVERT: C 320 VAL cc_start: 0.8549 (t) cc_final: 0.8174 (m) REVERT: C 329 PHE cc_start: 0.7734 (m-80) cc_final: 0.7324 (m-10) REVERT: C 529 LYS cc_start: 0.7892 (mmtt) cc_final: 0.7514 (mmtt) REVERT: C 551 VAL cc_start: 0.8597 (m) cc_final: 0.8376 (p) REVERT: C 564 GLN cc_start: 0.6940 (mm110) cc_final: 0.6706 (mm110) REVERT: C 573 THR cc_start: 0.7671 (m) cc_final: 0.7224 (p) REVERT: C 587 ILE cc_start: 0.8388 (pt) cc_final: 0.8139 (pt) REVERT: C 610 VAL cc_start: 0.8577 (t) cc_final: 0.8355 (t) REVERT: C 654 GLU cc_start: 0.7035 (tp30) cc_final: 0.6706 (tp30) REVERT: C 900 MET cc_start: 0.7752 (mtt) cc_final: 0.7513 (mtp) REVERT: C 990 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6505 (mm-30) REVERT: C 994 ASP cc_start: 0.7334 (m-30) cc_final: 0.7128 (m-30) REVERT: C 1002 GLN cc_start: 0.7695 (tp40) cc_final: 0.7274 (tp40) REVERT: C 1133 VAL cc_start: 0.8793 (p) cc_final: 0.8479 (m) outliers start: 79 outliers final: 56 residues processed: 596 average time/residue: 0.3553 time to fit residues: 327.8904 Evaluate side-chains 587 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 528 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 0.9990 chunk 276 optimal weight: 0.5980 chunk 168 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 289 optimal weight: 0.8980 chunk 266 optimal weight: 0.3980 chunk 230 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 178 optimal weight: 0.1980 chunk 141 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B1002 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 314 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1125 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 1.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 24198 Z= 0.296 Angle : 0.708 12.297 32913 Z= 0.370 Chirality : 0.048 0.232 3932 Planarity : 0.005 0.059 4164 Dihedral : 5.785 53.405 4422 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.39 % Allowed : 22.65 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.24 (0.15), residues: 2844 helix: 1.09 (0.20), residues: 729 sheet: 0.11 (0.20), residues: 651 loop : -0.92 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.010 0.001 HIS A1083 PHE 0.031 0.002 PHE B 797 TYR 0.030 0.002 TYR A1067 ARG 0.006 0.001 ARG B 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 532 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7241 (tp40) cc_final: 0.6915 (tp40) REVERT: A 117 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8165 (pp) REVERT: A 198 ASP cc_start: 0.7422 (p0) cc_final: 0.7187 (p0) REVERT: A 281 GLU cc_start: 0.6904 (tp30) cc_final: 0.6474 (tp30) REVERT: A 309 GLU cc_start: 0.6677 (tm-30) cc_final: 0.6419 (tm-30) REVERT: A 329 PHE cc_start: 0.7475 (m-80) cc_final: 0.7161 (m-80) REVERT: A 378 LYS cc_start: 0.7736 (mttt) cc_final: 0.7379 (mttm) REVERT: A 429 PHE cc_start: 0.7694 (t80) cc_final: 0.7356 (t80) REVERT: A 587 ILE cc_start: 0.8412 (mt) cc_final: 0.8071 (mt) REVERT: A 651 ILE cc_start: 0.8438 (mp) cc_final: 0.8203 (mt) REVERT: A 693 ILE cc_start: 0.8453 (pt) cc_final: 0.8200 (pt) REVERT: A 931 ILE cc_start: 0.8209 (mm) cc_final: 0.7896 (mm) REVERT: A 933 LYS cc_start: 0.7872 (mttt) cc_final: 0.7517 (mtmm) REVERT: A 976 VAL cc_start: 0.8677 (t) cc_final: 0.8256 (m) REVERT: A 981 LEU cc_start: 0.8580 (mm) cc_final: 0.8378 (mp) REVERT: A 987 PRO cc_start: 0.8741 (Cg_exo) cc_final: 0.8505 (Cg_endo) REVERT: A 1014 ARG cc_start: 0.8017 (tpp80) cc_final: 0.7690 (ttm170) REVERT: A 1045 LYS cc_start: 0.8104 (tttm) cc_final: 0.7889 (mtpp) REVERT: A 1050 MET cc_start: 0.8046 (ptp) cc_final: 0.7778 (ptp) REVERT: B 55 PHE cc_start: 0.7333 (m-80) cc_final: 0.6827 (m-80) REVERT: B 276 LEU cc_start: 0.7613 (tt) cc_final: 0.7307 (tp) REVERT: B 278 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.7008 (ttmt) REVERT: B 357 ARG cc_start: 0.6744 (mpt180) cc_final: 0.6450 (mpt180) REVERT: B 365 TYR cc_start: 0.7644 (m-80) cc_final: 0.7081 (m-80) REVERT: B 377 PHE cc_start: 0.7507 (t80) cc_final: 0.7222 (t80) REVERT: B 382 VAL cc_start: 0.8554 (t) cc_final: 0.8058 (p) REVERT: B 428 ASP cc_start: 0.6631 (t0) cc_final: 0.6322 (p0) REVERT: B 514 SER cc_start: 0.8306 (t) cc_final: 0.7689 (p) REVERT: B 529 LYS cc_start: 0.7823 (ptmm) cc_final: 0.7606 (ptmm) REVERT: B 549 THR cc_start: 0.8200 (t) cc_final: 0.7765 (p) REVERT: B 567 ARG cc_start: 0.7657 (tpp80) cc_final: 0.7337 (ttm-80) REVERT: B 651 ILE cc_start: 0.8448 (mm) cc_final: 0.8177 (mm) REVERT: B 654 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7100 (tm-30) REVERT: B 699 LEU cc_start: 0.8737 (mt) cc_final: 0.8497 (mp) REVERT: B 765 ARG cc_start: 0.7233 (ttm110) cc_final: 0.6825 (ttm110) REVERT: B 872 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7803 (mm-40) REVERT: B 954 GLN cc_start: 0.6505 (mt0) cc_final: 0.6202 (mt0) REVERT: B 1000 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8054 (mtt90) REVERT: C 195 LYS cc_start: 0.7815 (ptpp) cc_final: 0.7548 (ptmt) REVERT: C 240 THR cc_start: 0.8091 (m) cc_final: 0.7577 (t) REVERT: C 305 SER cc_start: 0.8913 (t) cc_final: 0.8575 (m) REVERT: C 320 VAL cc_start: 0.8584 (t) cc_final: 0.8176 (m) REVERT: C 396 TYR cc_start: 0.6553 (m-10) cc_final: 0.6351 (m-10) REVERT: C 551 VAL cc_start: 0.8564 (m) cc_final: 0.8356 (p) REVERT: C 564 GLN cc_start: 0.6982 (mm110) cc_final: 0.6759 (mm110) REVERT: C 573 THR cc_start: 0.7678 (m) cc_final: 0.7294 (p) REVERT: C 587 ILE cc_start: 0.8376 (pt) cc_final: 0.8143 (pt) REVERT: C 610 VAL cc_start: 0.8595 (t) cc_final: 0.8360 (t) REVERT: C 654 GLU cc_start: 0.7028 (tp30) cc_final: 0.6694 (tp30) REVERT: C 657 ASN cc_start: 0.6712 (m-40) cc_final: 0.6464 (m-40) REVERT: C 710 ASN cc_start: 0.7604 (t0) cc_final: 0.7383 (t0) REVERT: C 779 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7776 (tm-30) REVERT: C 784 GLN cc_start: 0.7438 (tt0) cc_final: 0.7233 (tt0) REVERT: C 900 MET cc_start: 0.7791 (mtt) cc_final: 0.7523 (mtp) REVERT: C 990 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6441 (mm-30) REVERT: C 1002 GLN cc_start: 0.7509 (tp40) cc_final: 0.7231 (tp40) REVERT: C 1031 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7278 (mt-10) REVERT: C 1041 ASP cc_start: 0.7013 (m-30) cc_final: 0.6808 (m-30) REVERT: C 1077 THR cc_start: 0.8299 (t) cc_final: 0.8072 (m) REVERT: C 1133 VAL cc_start: 0.8804 (p) cc_final: 0.8562 (m) outliers start: 61 outliers final: 44 residues processed: 563 average time/residue: 0.3915 time to fit residues: 335.4162 Evaluate side-chains 560 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 513 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 0.0670 chunk 245 optimal weight: 0.3980 chunk 70 optimal weight: 0.0980 chunk 212 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 231 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 237 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1002 GLN B1005 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 314 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.161728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.129046 restraints weight = 36218.755| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.05 r_work: 0.3417 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 1.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 24198 Z= 0.231 Angle : 0.679 10.651 32913 Z= 0.354 Chirality : 0.047 0.221 3932 Planarity : 0.005 0.060 4164 Dihedral : 5.554 53.375 4422 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.96 % Allowed : 23.83 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.15 (0.16), residues: 2844 helix: 1.21 (0.20), residues: 729 sheet: 0.08 (0.20), residues: 681 loop : -0.86 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.008 0.001 HIS A1048 PHE 0.044 0.002 PHE B 168 TYR 0.027 0.001 TYR B 200 ARG 0.010 0.001 ARG A 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6281.79 seconds wall clock time: 112 minutes 20.04 seconds (6740.04 seconds total)