Starting phenix.real_space_refine on Fri Jun 20 01:21:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y45_33601/06_2025/7y45_33601.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y45_33601/06_2025/7y45_33601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y45_33601/06_2025/7y45_33601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y45_33601/06_2025/7y45_33601.map" model { file = "/net/cci-nas-00/data/ceres_data/7y45_33601/06_2025/7y45_33601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y45_33601/06_2025/7y45_33601.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 6 8.98 5 P 26 5.49 5 S 118 5.16 5 C 14656 2.51 5 N 3516 2.21 5 O 4316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22638 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "A" Number of atoms: 7683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7683 Classifications: {'peptide': 993} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 949} Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2399 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 278} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "H" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "E" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 557 Unusual residues: {' K': 3, 'CLR': 2, 'PCW': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Restraints were copied for chains: G, K, N, L, C, D, M Time building chain proxies: 23.95, per 1000 atoms: 1.06 Number of scatterers: 22638 At special positions: 0 Unit cell: (183.996, 220.58, 100.068, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 6 19.00 S 118 16.00 P 26 15.00 O 4316 8.00 N 3516 7.00 C 14656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA H 3 " - " MAN H 6 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 6 " BETA1-2 " MAN H 4 " - " NAG H 5 " " MAN L 4 " - " NAG L 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " BETA1-6 " NAG F 1 " - " FUC F 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 5 " " NAG K 1 " - " FUC K 6 " " NAG M 1 " - " FUC M 5 " NAG-ASN " NAG F 1 " - " ASN D 114 " " NAG H 1 " - " ASN D 159 " " NAG I 1 " - " ASN D 194 " " NAG J 1 " - " ASN D 267 " " NAG K 1 " - " ASN B 114 " " NAG L 1 " - " ASN B 159 " " NAG M 1 " - " ASN B 194 " " NAG N 1 " - " ASN B 267 " Time building additional restraints: 6.83 Conformation dependent library (CDL) restraints added in 2.6 seconds 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4912 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 20 sheets defined 49.7% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'C' and resid 47 through 56 removed outlier: 3.625A pdb=" N HIS C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN C 53 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 76 Processing helix chain 'C' and resid 87 through 96 removed outlier: 4.121A pdb=" N LYS C 91 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 122 Processing helix chain 'C' and resid 127 through 151 removed outlier: 3.602A pdb=" N CYS C 145 " --> pdb=" O ILE C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 163 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 215 through 220 Processing helix chain 'C' and resid 261 through 264 removed outlier: 3.586A pdb=" N ARG C 264 " --> pdb=" O THR C 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 261 through 264' Processing helix chain 'C' and resid 265 through 277 Processing helix chain 'C' and resid 282 through 313 removed outlier: 3.567A pdb=" N PHE C 291 " --> pdb=" O GLU C 287 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 332 removed outlier: 3.972A pdb=" N ILE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 Processing helix chain 'C' and resid 362 through 367 removed outlier: 3.573A pdb=" N LEU C 367 " --> pdb=" O ALA C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 428 removed outlier: 3.692A pdb=" N SER C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 466 through 473 Processing helix chain 'C' and resid 510 through 516 Processing helix chain 'C' and resid 531 through 548 Processing helix chain 'C' and resid 598 through 610 Processing helix chain 'C' and resid 620 through 632 removed outlier: 4.013A pdb=" N ALA C 626 " --> pdb=" O ILE C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 648 Processing helix chain 'C' and resid 656 through 660 removed outlier: 3.687A pdb=" N ALA C 660 " --> pdb=" O PRO C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 672 Processing helix chain 'C' and resid 674 through 685 Processing helix chain 'C' and resid 694 through 708 removed outlier: 4.025A pdb=" N LYS C 698 " --> pdb=" O SER C 694 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU C 699 " --> pdb=" O PRO C 695 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE C 700 " --> pdb=" O GLN C 696 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG C 707 " --> pdb=" O GLU C 703 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN C 708 " --> pdb=" O GLY C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 728 removed outlier: 3.687A pdb=" N LYS C 727 " --> pdb=" O PRO C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 746 Processing helix chain 'C' and resid 755 through 782 removed outlier: 3.819A pdb=" N VAL C 759 " --> pdb=" O PHE C 755 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 772 " --> pdb=" O ILE C 768 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER C 782 " --> pdb=" O TYR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 796 Proline residue: C 789 - end of helix Processing helix chain 'C' and resid 803 through 812 removed outlier: 3.556A pdb=" N ILE C 807 " --> pdb=" O GLY C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 822 Processing helix chain 'C' and resid 823 through 825 No H-bonds generated for 'chain 'C' and resid 823 through 825' Processing helix chain 'C' and resid 846 through 854 removed outlier: 3.928A pdb=" N ILE C 850 " --> pdb=" O ASN C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 877 Processing helix chain 'C' and resid 879 through 884 removed outlier: 4.258A pdb=" N ILE C 884 " --> pdb=" O PRO C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 907 through 939 removed outlier: 4.045A pdb=" N ALA C 932 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR C 939 " --> pdb=" O ILE C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 948 Processing helix chain 'C' and resid 951 through 971 removed outlier: 3.554A pdb=" N ILE C 955 " --> pdb=" O ASN C 951 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 965 " --> pdb=" O GLU C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 990 removed outlier: 3.768A pdb=" N PHE C 989 " --> pdb=" O SER C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1012 removed outlier: 3.557A pdb=" N PHE C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C1008 " --> pdb=" O MET C1004 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C1009 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ARG C1010 " --> pdb=" O ARG C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1022 Processing helix chain 'D' and resid 14 through 18 Processing helix chain 'D' and resid 29 through 61 removed outlier: 3.749A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 removed outlier: 3.506A pdb=" N SER D 98 " --> pdb=" O ASN D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 99 through 111 removed outlier: 3.761A pdb=" N SER D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 removed outlier: 3.956A pdb=" N ALA D 204 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 225 removed outlier: 4.406A pdb=" N LYS D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 221 through 225' Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.745A pdb=" N TYR D 237 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'D' and resid 248 through 253 removed outlier: 4.176A pdb=" N LEU D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 13 Processing helix chain 'E' and resid 15 through 40 Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.625A pdb=" N HIS A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN A 53 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 87 through 96 removed outlier: 4.121A pdb=" N LYS A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 122 Processing helix chain 'A' and resid 127 through 151 removed outlier: 3.602A pdb=" N CYS A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 261 through 264 removed outlier: 3.585A pdb=" N ARG A 264 " --> pdb=" O THR A 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 264' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 282 through 313 removed outlier: 3.567A pdb=" N PHE A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 292 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 332 removed outlier: 3.972A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 Processing helix chain 'A' and resid 362 through 367 removed outlier: 3.572A pdb=" N LEU A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 428 removed outlier: 3.692A pdb=" N SER A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 531 through 548 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 620 through 632 removed outlier: 4.013A pdb=" N ALA A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 648 Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.688A pdb=" N ALA A 660 " --> pdb=" O PRO A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 694 through 708 removed outlier: 4.023A pdb=" N LYS A 698 " --> pdb=" O SER A 694 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 699 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE A 700 " --> pdb=" O GLN A 696 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN A 708 " --> pdb=" O GLY A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 728 removed outlier: 3.687A pdb=" N LYS A 727 " --> pdb=" O PRO A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 746 Processing helix chain 'A' and resid 755 through 782 removed outlier: 3.820A pdb=" N VAL A 759 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 772 " --> pdb=" O ILE A 768 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 796 Proline residue: A 789 - end of helix Processing helix chain 'A' and resid 803 through 812 removed outlier: 3.557A pdb=" N ILE A 807 " --> pdb=" O GLY A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 822 Processing helix chain 'A' and resid 823 through 825 No H-bonds generated for 'chain 'A' and resid 823 through 825' Processing helix chain 'A' and resid 846 through 854 removed outlier: 3.929A pdb=" N ILE A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 877 Processing helix chain 'A' and resid 879 through 884 removed outlier: 4.257A pdb=" N ILE A 884 " --> pdb=" O PRO A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 907 through 939 removed outlier: 4.046A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR A 939 " --> pdb=" O ILE A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 948 Processing helix chain 'A' and resid 951 through 971 removed outlier: 3.554A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 965 " --> pdb=" O GLU A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 990 removed outlier: 3.768A pdb=" N PHE A 989 " --> pdb=" O SER A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.557A pdb=" N PHE A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG A1010 " --> pdb=" O ARG A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1022 Processing helix chain 'B' and resid 14 through 18 Processing helix chain 'B' and resid 29 through 61 removed outlier: 3.750A pdb=" N LEU B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 98 removed outlier: 3.507A pdb=" N SER B 98 " --> pdb=" O ASN B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 95 through 98' Processing helix chain 'B' and resid 99 through 111 removed outlier: 3.761A pdb=" N SER B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.956A pdb=" N ALA B 204 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 4.405A pdb=" N LYS B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 225' Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.746A pdb=" N TYR B 237 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 248 through 253 removed outlier: 4.176A pdb=" N LEU B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 13 Processing helix chain 'G' and resid 15 through 40 Processing sheet with id=AA1, first strand: chain 'C' and resid 177 through 181 removed outlier: 12.081A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N CYS C 249 " --> pdb=" O ASP C 214 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP C 214 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU C 251 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N THR C 253 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLY C 210 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ARG C 255 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ALA C 208 " --> pdb=" O ARG C 255 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL C 257 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE C 206 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL C 259 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ARG C 204 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 177 through 181 removed outlier: 12.081A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N CYS C 249 " --> pdb=" O ASP C 214 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP C 214 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU C 251 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N THR C 253 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLY C 210 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ARG C 255 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ALA C 208 " --> pdb=" O ARG C 255 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL C 257 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE C 206 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL C 259 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ARG C 204 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 356 through 358 removed outlier: 6.300A pdb=" N VAL C 712 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL C 732 " --> pdb=" O VAL C 712 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL C 714 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR C 372 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N THR C 715 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N CYS C 374 " --> pdb=" O THR C 715 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER C 375 " --> pdb=" O ILE C 614 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL C 613 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N PHE C 690 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N MET C 615 " --> pdb=" O PHE C 690 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 390 through 392 Processing sheet with id=AA5, first strand: chain 'C' and resid 432 through 433 removed outlier: 3.845A pdb=" N VAL C 432 " --> pdb=" O ALA C 448 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 476 through 480 removed outlier: 6.400A pdb=" N LYS C 476 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU C 494 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR C 503 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N HIS C 557 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N PHE C 585 " --> pdb=" O HIS C 557 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ALA C 559 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N LEU C 583 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE C 585 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE C 521 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N GLY C 587 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 11.543A pdb=" N LEU C 523 " --> pdb=" O GLY C 587 " (cutoff:3.500A) removed outlier: 17.072A pdb=" N MET C 589 " --> pdb=" O LEU C 523 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 898 through 899 Processing sheet with id=AA8, first strand: chain 'D' and resid 78 through 80 removed outlier: 3.514A pdb=" N THR D 266 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU D 268 " --> pdb=" O ILE D 226 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ILE D 226 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 88 through 91 Processing sheet with id=AB1, first strand: chain 'D' and resid 124 through 125 Processing sheet with id=AB2, first strand: chain 'A' and resid 177 through 181 removed outlier: 12.081A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N CYS A 249 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP A 214 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 251 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N THR A 253 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLY A 210 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ARG A 255 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ALA A 208 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N VAL A 257 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE A 206 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL A 259 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ARG A 204 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 177 through 181 removed outlier: 12.081A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N CYS A 249 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP A 214 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 251 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N THR A 253 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLY A 210 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ARG A 255 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ALA A 208 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N VAL A 257 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE A 206 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL A 259 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ARG A 204 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 356 through 358 removed outlier: 6.301A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR A 372 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N THR A 715 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N CYS A 374 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 375 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 390 through 392 Processing sheet with id=AB6, first strand: chain 'A' and resid 432 through 433 removed outlier: 3.845A pdb=" N VAL A 432 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 476 through 480 removed outlier: 6.400A pdb=" N LYS A 476 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU A 494 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR A 503 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N HIS A 557 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE A 585 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ALA A 559 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N LEU A 583 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE A 585 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 521 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N GLY A 587 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 11.543A pdb=" N LEU A 523 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 17.072A pdb=" N MET A 589 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 898 through 899 Processing sheet with id=AB9, first strand: chain 'B' and resid 78 through 80 removed outlier: 3.514A pdb=" N THR B 266 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU B 268 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ILE B 226 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 88 through 91 Processing sheet with id=AC2, first strand: chain 'B' and resid 124 through 125 1005 hydrogen bonds defined for protein. 2925 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: 8.86 Time building geometry restraints manager: 7.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6815 1.34 - 1.46: 5034 1.46 - 1.59: 10961 1.59 - 1.71: 76 1.71 - 1.83: 172 Bond restraints: 23058 Sorted by residual: bond pdb=" C39 PCW G 102 " pdb=" C40 PCW G 102 " ideal model delta sigma weight residual 1.333 1.543 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C39 PCW E 102 " pdb=" C40 PCW E 102 " ideal model delta sigma weight residual 1.333 1.542 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C19 PCW A1108 " pdb=" C20 PCW A1108 " ideal model delta sigma weight residual 1.333 1.540 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C19 PCW C1108 " pdb=" C20 PCW C1108 " ideal model delta sigma weight residual 1.333 1.539 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C19 PCW E 102 " pdb=" C20 PCW E 102 " ideal model delta sigma weight residual 1.333 1.537 -0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 23053 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 28596 2.49 - 4.99: 1950 4.99 - 7.48: 416 7.48 - 9.98: 119 9.98 - 12.47: 21 Bond angle restraints: 31102 Sorted by residual: angle pdb=" C PRO A 84 " pdb=" N THR A 85 " pdb=" CA THR A 85 " ideal model delta sigma weight residual 123.03 111.77 11.26 1.79e+00 3.12e-01 3.95e+01 angle pdb=" C PRO C 84 " pdb=" N THR C 85 " pdb=" CA THR C 85 " ideal model delta sigma weight residual 123.03 111.79 11.24 1.79e+00 3.12e-01 3.95e+01 angle pdb=" C SER A 310 " pdb=" N LEU A 311 " pdb=" CA LEU A 311 " ideal model delta sigma weight residual 122.06 111.41 10.65 1.86e+00 2.89e-01 3.28e+01 angle pdb=" C SER C 310 " pdb=" N LEU C 311 " pdb=" CA LEU C 311 " ideal model delta sigma weight residual 122.06 111.49 10.57 1.86e+00 2.89e-01 3.23e+01 angle pdb=" N ILE A 592 " pdb=" CA ILE A 592 " pdb=" C ILE A 592 " ideal model delta sigma weight residual 108.53 116.71 -8.18 1.45e+00 4.76e-01 3.18e+01 ... (remaining 31097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.86: 13604 27.86 - 55.71: 1087 55.71 - 83.57: 161 83.57 - 111.42: 58 111.42 - 139.28: 38 Dihedral angle restraints: 14948 sinusoidal: 7292 harmonic: 7656 Sorted by residual: dihedral pdb=" C33 PCW A1113 " pdb=" C31 PCW A1113 " pdb=" C32 PCW A1113 " pdb=" O2 PCW A1113 " ideal model delta sinusoidal sigma weight residual 191.83 52.55 139.28 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" C33 PCW C1113 " pdb=" C31 PCW C1113 " pdb=" C32 PCW C1113 " pdb=" O2 PCW C1113 " ideal model delta sinusoidal sigma weight residual 191.83 52.68 139.15 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" C33 PCW C1111 " pdb=" C31 PCW C1111 " pdb=" C32 PCW C1111 " pdb=" O2 PCW C1111 " ideal model delta sinusoidal sigma weight residual -168.17 -29.87 -138.30 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 14945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2810 0.075 - 0.150: 591 0.150 - 0.225: 64 0.225 - 0.300: 29 0.300 - 0.375: 20 Chirality restraints: 3514 Sorted by residual: chirality pdb=" C1 FUC I 5 " pdb=" O6 NAG I 1 " pdb=" C2 FUC I 5 " pdb=" O5 FUC I 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.84e+01 chirality pdb=" C1 FUC M 5 " pdb=" O6 NAG M 1 " pdb=" C2 FUC M 5 " pdb=" O5 FUC M 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.77e+01 chirality pdb=" C1 FUC K 6 " pdb=" O6 NAG K 1 " pdb=" C2 FUC K 6 " pdb=" O5 FUC K 6 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.13e+01 ... (remaining 3511 not shown) Planarity restraints: 3816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 122 " 0.090 5.00e-02 4.00e+02 1.41e-01 3.19e+01 pdb=" N PRO B 123 " -0.244 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 122 " -0.090 5.00e-02 4.00e+02 1.41e-01 3.18e+01 pdb=" N PRO D 123 " 0.244 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 594 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO A 595 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO A 595 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 595 " 0.055 5.00e-02 4.00e+02 ... (remaining 3813 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.65: 435 2.65 - 3.27: 22810 3.27 - 3.89: 40910 3.89 - 4.52: 55022 4.52 - 5.14: 89394 Nonbonded interactions: 208571 Sorted by model distance: nonbonded pdb=" SG CYS B 160 " pdb=" SG CYS B 176 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS D 160 " pdb=" SG CYS D 176 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS B 215 " pdb=" SG CYS B 278 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS D 215 " pdb=" SG CYS D 278 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS D 127 " pdb=" SG CYS D 150 " model vdw 2.035 3.760 ... (remaining 208566 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: 0.11 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'I' selection = chain 'M' } 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: 1.320 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: 1.050 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 63.110 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.110 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.210 23096 Z= 0.550 Angle : 1.500 17.574 31216 Z= 0.752 Chirality : 0.068 0.375 3514 Planarity : 0.009 0.141 3808 Dihedral : 20.374 139.275 10036 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.68 % Allowed : 9.99 % Favored : 89.33 % Rotamer: Outliers : 11.22 % Allowed : 10.11 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -3.83 (0.14), residues: 2642 helix: -2.21 (0.12), residues: 1160 sheet: -2.75 (0.29), residues: 254 loop : -2.77 (0.15), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 156 HIS 0.008 0.002 HIS A 919 PHE 0.030 0.003 PHE A 923 TYR 0.035 0.002 TYR B 206 ARG 0.009 0.001 ARG B 137 Details of bonding type rmsd link_NAG-ASN : bond 0.01600 ( 8) link_NAG-ASN : angle 3.86327 ( 24) link_ALPHA1-6 : bond 0.00746 ( 4) link_ALPHA1-6 : angle 1.23909 ( 12) link_BETA1-2 : bond 0.00528 ( 2) link_BETA1-2 : angle 5.41267 ( 6) link_BETA1-4 : bond 0.00863 ( 14) link_BETA1-4 : angle 6.17097 ( 42) link_ALPHA1-3 : bond 0.00771 ( 6) link_ALPHA1-3 : angle 3.12893 ( 18) hydrogen bonds : bond 0.17918 ( 983) hydrogen bonds : angle 7.38773 ( 2925) link_BETA1-6 : bond 0.00251 ( 4) link_BETA1-6 : angle 1.25254 ( 12) covalent geometry : bond 0.01089 (23058) covalent geometry : angle 1.47751 (31102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 254 poor density : 322 time to evaluate : 2.451 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: C 161 PHE cc_start: 0.7830 (m-80) cc_final: 0.7529 (m-80) REVERT: C 173 ARG cc_start: 0.3216 (mtt180) cc_final: 0.2361 (ptt180) REVERT: C 324 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8862 (tp) REVERT: C 488 TYR cc_start: 0.4527 (OUTLIER) cc_final: 0.4257 (p90) REVERT: C 493 HIS cc_start: 0.4768 (OUTLIER) cc_final: 0.4154 (m-70) REVERT: C 698 LYS cc_start: 0.4825 (OUTLIER) cc_final: 0.4233 (tttt) REVERT: C 816 MET cc_start: 0.8081 (mmm) cc_final: 0.7605 (mmm) REVERT: C 949 MET cc_start: 0.8455 (mmm) cc_final: 0.8084 (mtp) REVERT: C 975 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7915 (p0) REVERT: D 106 MET cc_start: 0.8232 (mmm) cc_final: 0.7969 (mmm) REVERT: D 142 ASP cc_start: 0.7018 (t0) cc_final: 0.6781 (t0) REVERT: D 154 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8009 (ttt180) REVERT: D 272 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7230 (ttm) REVERT: D 305 SER cc_start: 0.7577 (t) cc_final: 0.7301 (p) REVERT: A 173 ARG cc_start: 0.3246 (mtt180) cc_final: 0.2491 (ptt180) REVERT: A 185 VAL cc_start: 0.7489 (t) cc_final: 0.7261 (p) REVERT: A 488 TYR cc_start: 0.4507 (OUTLIER) cc_final: 0.4249 (p90) REVERT: A 493 HIS cc_start: 0.5462 (OUTLIER) cc_final: 0.4356 (m-70) REVERT: A 615 MET cc_start: 0.5860 (ttm) cc_final: 0.5467 (ttp) REVERT: A 708 GLN cc_start: 0.6476 (OUTLIER) cc_final: 0.6262 (mt0) REVERT: A 816 MET cc_start: 0.8225 (mmm) cc_final: 0.7806 (mmm) REVERT: A 846 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7547 (p0) REVERT: A 975 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7687 (p0) REVERT: B 23 LYS cc_start: 0.8326 (mttt) cc_final: 0.8003 (mmtp) REVERT: B 73 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7553 (p) REVERT: B 106 MET cc_start: 0.8454 (mmm) cc_final: 0.8187 (mmm) REVERT: B 142 ASP cc_start: 0.7097 (t0) cc_final: 0.6751 (t0) REVERT: B 154 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8106 (ttt180) REVERT: B 156 TRP cc_start: 0.8513 (OUTLIER) cc_final: 0.8253 (m-10) REVERT: B 272 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7550 (ttm) outliers start: 254 outliers final: 40 residues processed: 516 average time/residue: 0.4263 time to fit residues: 320.3818 Evaluate side-chains 201 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 145 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 698 LYS Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 952 LYS Chi-restraints excluded: chain C residue 975 ASP Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 272 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.9980 chunk 200 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 134 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 206 optimal weight: 0.7980 chunk 80 optimal weight: 0.0040 chunk 125 optimal weight: 2.9990 chunk 154 optimal weight: 40.0000 chunk 239 optimal weight: 1.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN C 209 HIS C 434 GLN C 474 ASN C 483 ASN C 486 ASN ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 HIS ** C 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 696 GLN C 720 ASN C 744 GLN C 904 GLN C1019 GLN D 258 GLN A 118 GLN A 129 ASN A 209 HIS A 383 GLN A 434 GLN A 474 ASN A 483 ASN A 486 ASN A 540 ASN A 557 HIS ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN A 720 ASN A 744 GLN A 904 GLN A1019 GLN B 56 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.148698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.104386 restraints weight = 41262.831| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.08 r_work: 0.3136 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23096 Z= 0.155 Angle : 0.720 10.337 31216 Z= 0.352 Chirality : 0.047 0.437 3514 Planarity : 0.006 0.074 3808 Dihedral : 17.592 136.892 5189 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.62 % Allowed : 13.16 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.15), residues: 2642 helix: -0.04 (0.15), residues: 1214 sheet: -1.92 (0.30), residues: 262 loop : -1.73 (0.16), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 89 HIS 0.008 0.002 HIS A 620 PHE 0.024 0.002 PHE C 393 TYR 0.016 0.001 TYR C 488 ARG 0.008 0.001 ARG C 889 Details of bonding type rmsd link_NAG-ASN : bond 0.00705 ( 8) link_NAG-ASN : angle 2.32235 ( 24) link_ALPHA1-6 : bond 0.00768 ( 4) link_ALPHA1-6 : angle 2.18892 ( 12) link_BETA1-2 : bond 0.00670 ( 2) link_BETA1-2 : angle 4.88757 ( 6) link_BETA1-4 : bond 0.01040 ( 14) link_BETA1-4 : angle 3.84808 ( 42) link_ALPHA1-3 : bond 0.00958 ( 6) link_ALPHA1-3 : angle 3.78814 ( 18) hydrogen bonds : bond 0.06186 ( 983) hydrogen bonds : angle 5.12905 ( 2925) link_BETA1-6 : bond 0.00607 ( 4) link_BETA1-6 : angle 1.53976 ( 12) covalent geometry : bond 0.00332 (23058) covalent geometry : angle 0.69317 (31102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 179 time to evaluate : 2.672 Fit side-chains revert: symmetry clash REVERT: C 153 LYS cc_start: 0.7720 (mmmt) cc_final: 0.7209 (mmmm) REVERT: C 164 MET cc_start: 0.7697 (mmp) cc_final: 0.7403 (ttm) REVERT: C 173 ARG cc_start: 0.3145 (mtt180) cc_final: 0.2299 (ptt180) REVERT: C 218 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6340 (pp) REVERT: C 267 MET cc_start: 0.6053 (ppp) cc_final: 0.5559 (ppp) REVERT: C 324 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9008 (tp) REVERT: C 493 HIS cc_start: 0.4174 (OUTLIER) cc_final: 0.3212 (m-70) REVERT: C 816 MET cc_start: 0.8378 (mmm) cc_final: 0.8041 (mmm) REVERT: C 952 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7622 (mptt) REVERT: D 14 LYS cc_start: 0.7230 (tptt) cc_final: 0.6575 (mmpt) REVERT: D 106 MET cc_start: 0.8657 (mmm) cc_final: 0.8436 (mmm) REVERT: D 142 ASP cc_start: 0.7637 (t0) cc_final: 0.7242 (t0) REVERT: A 41 MET cc_start: 0.5814 (ppp) cc_final: 0.5333 (ptm) REVERT: A 42 ASP cc_start: 0.4855 (OUTLIER) cc_final: 0.4629 (t70) REVERT: A 153 LYS cc_start: 0.7605 (mmmt) cc_final: 0.7086 (mmmm) REVERT: A 164 MET cc_start: 0.7796 (mmp) cc_final: 0.7440 (ttm) REVERT: A 173 ARG cc_start: 0.3385 (mtt180) cc_final: 0.2674 (ptt180) REVERT: A 267 MET cc_start: 0.6137 (ppp) cc_final: 0.5691 (ppp) REVERT: A 396 GLN cc_start: 0.6568 (tp40) cc_final: 0.5879 (mt0) REVERT: A 493 HIS cc_start: 0.4101 (OUTLIER) cc_final: 0.3071 (m-70) REVERT: A 534 MET cc_start: 0.2777 (mtp) cc_final: 0.2511 (mmm) REVERT: B 23 LYS cc_start: 0.8647 (mttt) cc_final: 0.8098 (mmtm) REVERT: B 106 MET cc_start: 0.8725 (mmm) cc_final: 0.8497 (mmm) REVERT: B 201 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8478 (pm20) REVERT: B 203 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7454 (mp10) outliers start: 82 outliers final: 40 residues processed: 255 average time/residue: 0.3700 time to fit residues: 144.2771 Evaluate side-chains 191 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 698 LYS Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 804 THR Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 952 LYS Chi-restraints excluded: chain C residue 986 SER Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 203 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 121 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 151 optimal weight: 40.0000 chunk 65 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 398 HIS C 489 GLN ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 708 GLN D 56 GLN A 638 ASN B 258 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.144053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.098667 restraints weight = 40745.588| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.79 r_work: 0.2970 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23096 Z= 0.166 Angle : 0.650 9.238 31216 Z= 0.318 Chirality : 0.046 0.424 3514 Planarity : 0.005 0.064 3808 Dihedral : 16.182 132.902 5118 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.87 % Allowed : 13.56 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 2642 helix: 0.85 (0.15), residues: 1232 sheet: -1.46 (0.30), residues: 262 loop : -1.19 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 890 HIS 0.008 0.001 HIS C 557 PHE 0.024 0.002 PHE A 433 TYR 0.020 0.002 TYR B 248 ARG 0.013 0.001 ARG A 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00802 ( 8) link_NAG-ASN : angle 1.76951 ( 24) link_ALPHA1-6 : bond 0.00844 ( 4) link_ALPHA1-6 : angle 1.58112 ( 12) link_BETA1-2 : bond 0.00754 ( 2) link_BETA1-2 : angle 4.37554 ( 6) link_BETA1-4 : bond 0.00798 ( 14) link_BETA1-4 : angle 3.48924 ( 42) link_ALPHA1-3 : bond 0.01095 ( 6) link_ALPHA1-3 : angle 3.12642 ( 18) hydrogen bonds : bond 0.05961 ( 983) hydrogen bonds : angle 4.56423 ( 2925) link_BETA1-6 : bond 0.00378 ( 4) link_BETA1-6 : angle 1.57784 ( 12) covalent geometry : bond 0.00389 (23058) covalent geometry : angle 0.62749 (31102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 151 time to evaluate : 2.567 Fit side-chains revert: symmetry clash REVERT: C 173 ARG cc_start: 0.3088 (mtt180) cc_final: 0.2325 (ptt180) REVERT: C 816 MET cc_start: 0.8493 (mmm) cc_final: 0.8075 (mmm) REVERT: D 14 LYS cc_start: 0.7458 (tptt) cc_final: 0.6611 (mmtm) REVERT: D 106 MET cc_start: 0.8732 (mmm) cc_final: 0.8419 (mmm) REVERT: D 142 ASP cc_start: 0.8067 (t0) cc_final: 0.7696 (t0) REVERT: A 41 MET cc_start: 0.5620 (ppp) cc_final: 0.5382 (ptm) REVERT: A 173 ARG cc_start: 0.3386 (mtt180) cc_final: 0.2617 (ptt180) REVERT: B 23 LYS cc_start: 0.8681 (mttt) cc_final: 0.8024 (mmtm) REVERT: B 106 MET cc_start: 0.8823 (mmm) cc_final: 0.8518 (mmm) REVERT: B 201 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8576 (pm20) REVERT: B 203 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7749 (mp10) REVERT: G 7 ASP cc_start: 0.8002 (t0) cc_final: 0.7598 (t0) outliers start: 65 outliers final: 39 residues processed: 210 average time/residue: 0.3601 time to fit residues: 117.8346 Evaluate side-chains 177 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 986 SER Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 203 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 1 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 154 optimal weight: 40.0000 chunk 14 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 246 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN A 708 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.144791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.100031 restraints weight = 41244.650| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.20 r_work: 0.3013 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23096 Z= 0.118 Angle : 0.580 8.634 31216 Z= 0.279 Chirality : 0.044 0.437 3514 Planarity : 0.005 0.060 3808 Dihedral : 15.290 128.216 5086 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.47 % Allowed : 14.36 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.03 (0.16), residues: 2642 helix: 1.21 (0.15), residues: 1244 sheet: -1.00 (0.28), residues: 296 loop : -1.03 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 89 HIS 0.007 0.001 HIS C 557 PHE 0.021 0.001 PHE C 393 TYR 0.014 0.001 TYR C 869 ARG 0.010 0.000 ARG A 889 Details of bonding type rmsd link_NAG-ASN : bond 0.00642 ( 8) link_NAG-ASN : angle 1.61681 ( 24) link_ALPHA1-6 : bond 0.00827 ( 4) link_ALPHA1-6 : angle 1.76396 ( 12) link_BETA1-2 : bond 0.00578 ( 2) link_BETA1-2 : angle 4.50607 ( 6) link_BETA1-4 : bond 0.00638 ( 14) link_BETA1-4 : angle 3.20167 ( 42) link_ALPHA1-3 : bond 0.01022 ( 6) link_ALPHA1-3 : angle 3.44219 ( 18) hydrogen bonds : bond 0.04918 ( 983) hydrogen bonds : angle 4.28585 ( 2925) link_BETA1-6 : bond 0.00231 ( 4) link_BETA1-6 : angle 1.51034 ( 12) covalent geometry : bond 0.00259 (23058) covalent geometry : angle 0.55563 (31102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 143 time to evaluate : 2.528 Fit side-chains REVERT: C 173 ARG cc_start: 0.3213 (mtt180) cc_final: 0.2422 (ptt180) REVERT: C 291 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.8208 (p90) REVERT: C 404 GLU cc_start: 0.2476 (OUTLIER) cc_final: 0.2251 (tp30) REVERT: C 493 HIS cc_start: 0.3822 (m-70) cc_final: 0.3244 (m-70) REVERT: C 544 GLU cc_start: 0.6931 (tt0) cc_final: 0.6054 (tm-30) REVERT: C 816 MET cc_start: 0.8430 (mmm) cc_final: 0.7976 (mmm) REVERT: D 106 MET cc_start: 0.8722 (mmm) cc_final: 0.8383 (mmm) REVERT: D 142 ASP cc_start: 0.8042 (t0) cc_final: 0.7639 (t0) REVERT: A 89 TRP cc_start: 0.6176 (p-90) cc_final: 0.5747 (p-90) REVERT: A 173 ARG cc_start: 0.3402 (mtt180) cc_final: 0.2684 (ptt180) REVERT: A 185 VAL cc_start: 0.7034 (t) cc_final: 0.6739 (p) REVERT: A 493 HIS cc_start: 0.3960 (m-70) cc_final: 0.3361 (m-70) REVERT: B 23 LYS cc_start: 0.8687 (mttt) cc_final: 0.8011 (mmtm) REVERT: B 106 MET cc_start: 0.8752 (mmm) cc_final: 0.8358 (mmm) REVERT: B 201 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8587 (pm20) REVERT: B 203 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7798 (mp10) outliers start: 56 outliers final: 28 residues processed: 189 average time/residue: 0.3293 time to fit residues: 99.7616 Evaluate side-chains 165 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 203 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 96 optimal weight: 0.9990 chunk 210 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 219 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 239 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.145189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.099489 restraints weight = 41229.215| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.33 r_work: 0.3023 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 23096 Z= 0.105 Angle : 0.545 8.287 31216 Z= 0.261 Chirality : 0.043 0.454 3514 Planarity : 0.004 0.058 3808 Dihedral : 14.584 126.436 5084 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.34 % Allowed : 14.71 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.36 (0.16), residues: 2642 helix: 1.48 (0.15), residues: 1246 sheet: -0.70 (0.29), residues: 306 loop : -0.92 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 89 HIS 0.006 0.001 HIS A 557 PHE 0.017 0.001 PHE C 393 TYR 0.014 0.001 TYR A 869 ARG 0.017 0.000 ARG A 707 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 8) link_NAG-ASN : angle 1.45972 ( 24) link_ALPHA1-6 : bond 0.00776 ( 4) link_ALPHA1-6 : angle 1.68182 ( 12) link_BETA1-2 : bond 0.00563 ( 2) link_BETA1-2 : angle 4.63299 ( 6) link_BETA1-4 : bond 0.00618 ( 14) link_BETA1-4 : angle 3.02065 ( 42) link_ALPHA1-3 : bond 0.01007 ( 6) link_ALPHA1-3 : angle 3.46979 ( 18) hydrogen bonds : bond 0.04395 ( 983) hydrogen bonds : angle 4.11285 ( 2925) link_BETA1-6 : bond 0.00208 ( 4) link_BETA1-6 : angle 1.49290 ( 12) covalent geometry : bond 0.00225 (23058) covalent geometry : angle 0.52111 (31102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 142 time to evaluate : 2.426 Fit side-chains REVERT: C 173 ARG cc_start: 0.3257 (mtt180) cc_final: 0.2456 (ptt180) REVERT: C 291 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8167 (p90) REVERT: C 490 LEU cc_start: 0.4054 (OUTLIER) cc_final: 0.3679 (pt) REVERT: C 493 HIS cc_start: 0.3802 (OUTLIER) cc_final: 0.3288 (m-70) REVERT: C 512 GLU cc_start: 0.4841 (OUTLIER) cc_final: 0.4425 (mp0) REVERT: C 544 GLU cc_start: 0.7010 (tt0) cc_final: 0.6158 (tm-30) REVERT: C 763 GLU cc_start: 0.7785 (tt0) cc_final: 0.7430 (tt0) REVERT: C 816 MET cc_start: 0.8385 (mmm) cc_final: 0.7931 (mmm) REVERT: D 106 MET cc_start: 0.8693 (mmm) cc_final: 0.8337 (mmm) REVERT: D 142 ASP cc_start: 0.8042 (t0) cc_final: 0.7616 (t0) REVERT: A 89 TRP cc_start: 0.6174 (p-90) cc_final: 0.5652 (p-90) REVERT: A 173 ARG cc_start: 0.3223 (mtt180) cc_final: 0.2474 (ptt180) REVERT: A 185 VAL cc_start: 0.7000 (t) cc_final: 0.6704 (p) REVERT: A 493 HIS cc_start: 0.3944 (OUTLIER) cc_final: 0.3259 (m-70) REVERT: A 512 GLU cc_start: 0.4355 (OUTLIER) cc_final: 0.4100 (mp0) REVERT: A 578 PHE cc_start: 0.1890 (OUTLIER) cc_final: 0.0744 (p90) REVERT: A 589 MET cc_start: 0.7646 (mmm) cc_final: 0.6585 (mpp) REVERT: B 23 LYS cc_start: 0.8701 (mttt) cc_final: 0.8071 (mmtm) REVERT: B 85 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7972 (tp) REVERT: B 201 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8499 (pm20) REVERT: B 203 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7689 (mp10) outliers start: 53 outliers final: 30 residues processed: 186 average time/residue: 0.3770 time to fit residues: 110.3814 Evaluate side-chains 176 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 203 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 216 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 chunk 53 optimal weight: 40.0000 chunk 43 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 489 GLN D 243 GLN ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 GLN B 243 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.139893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.083478 restraints weight = 41024.942| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.96 r_work: 0.2882 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 23096 Z= 0.235 Angle : 0.692 8.293 31216 Z= 0.337 Chirality : 0.048 0.429 3514 Planarity : 0.005 0.094 3808 Dihedral : 15.070 126.152 5084 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.87 % Allowed : 14.40 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 2642 helix: 1.26 (0.15), residues: 1210 sheet: -0.74 (0.28), residues: 312 loop : -0.93 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 894 HIS 0.007 0.001 HIS C 557 PHE 0.031 0.002 PHE A 923 TYR 0.028 0.002 TYR A 131 ARG 0.014 0.001 ARG C 889 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 8) link_NAG-ASN : angle 1.63776 ( 24) link_ALPHA1-6 : bond 0.00786 ( 4) link_ALPHA1-6 : angle 1.61062 ( 12) link_BETA1-2 : bond 0.00391 ( 2) link_BETA1-2 : angle 4.98557 ( 6) link_BETA1-4 : bond 0.00528 ( 14) link_BETA1-4 : angle 3.32616 ( 42) link_ALPHA1-3 : bond 0.00905 ( 6) link_ALPHA1-3 : angle 3.11091 ( 18) hydrogen bonds : bond 0.07067 ( 983) hydrogen bonds : angle 4.54474 ( 2925) link_BETA1-6 : bond 0.00314 ( 4) link_BETA1-6 : angle 1.73148 ( 12) covalent geometry : bond 0.00583 (23058) covalent geometry : angle 0.67206 (31102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 135 time to evaluate : 2.492 Fit side-chains REVERT: C 173 ARG cc_start: 0.3503 (mtt180) cc_final: 0.2680 (ptt180) REVERT: C 277 LEU cc_start: 0.8102 (tp) cc_final: 0.7767 (tt) REVERT: C 291 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8609 (p90) REVERT: C 490 LEU cc_start: 0.4170 (OUTLIER) cc_final: 0.3858 (pt) REVERT: C 493 HIS cc_start: 0.3677 (m-70) cc_final: 0.3361 (m-70) REVERT: C 512 GLU cc_start: 0.4547 (OUTLIER) cc_final: 0.4300 (mp0) REVERT: C 544 GLU cc_start: 0.6999 (tt0) cc_final: 0.6132 (tm-30) REVERT: C 763 GLU cc_start: 0.7912 (tt0) cc_final: 0.7597 (mt-10) REVERT: C 816 MET cc_start: 0.8471 (mmm) cc_final: 0.7948 (mmm) REVERT: D 23 LYS cc_start: 0.7928 (mmtp) cc_final: 0.7626 (mmtm) REVERT: D 106 MET cc_start: 0.8793 (mmm) cc_final: 0.8348 (mtp) REVERT: D 121 ASN cc_start: 0.7220 (m110) cc_final: 0.6993 (m-40) REVERT: A 173 ARG cc_start: 0.3220 (mtt180) cc_final: 0.2534 (ptt180) REVERT: A 490 LEU cc_start: 0.3964 (OUTLIER) cc_final: 0.3461 (pt) REVERT: A 512 GLU cc_start: 0.4292 (OUTLIER) cc_final: 0.4007 (mp0) REVERT: A 578 PHE cc_start: 0.1762 (OUTLIER) cc_final: 0.0857 (p90) REVERT: A 889 ARG cc_start: 0.8695 (mtt-85) cc_final: 0.8485 (mmm-85) REVERT: B 23 LYS cc_start: 0.8686 (mttt) cc_final: 0.8040 (mmtm) REVERT: B 106 MET cc_start: 0.8822 (mmm) cc_final: 0.8320 (mtp) REVERT: B 203 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7728 (mp10) outliers start: 65 outliers final: 33 residues processed: 187 average time/residue: 0.3509 time to fit residues: 103.7124 Evaluate side-chains 166 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 203 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 202 optimal weight: 0.4980 chunk 230 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 245 optimal weight: 0.0970 chunk 5 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 chunk 18 optimal weight: 40.0000 chunk 132 optimal weight: 30.0000 chunk 57 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 489 GLN A 398 HIS A 489 GLN ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.141967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.084306 restraints weight = 41015.349| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.27 r_work: 0.2996 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23096 Z= 0.132 Angle : 0.568 8.302 31216 Z= 0.276 Chirality : 0.044 0.436 3514 Planarity : 0.004 0.061 3808 Dihedral : 14.407 133.892 5082 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.61 % Allowed : 14.84 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.47 (0.16), residues: 2642 helix: 1.55 (0.15), residues: 1226 sheet: -0.55 (0.28), residues: 308 loop : -0.82 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 89 HIS 0.006 0.001 HIS A 557 PHE 0.014 0.001 PHE A 306 TYR 0.015 0.001 TYR C 869 ARG 0.011 0.000 ARG C 889 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 8) link_NAG-ASN : angle 1.37186 ( 24) link_ALPHA1-6 : bond 0.00812 ( 4) link_ALPHA1-6 : angle 1.50043 ( 12) link_BETA1-2 : bond 0.00477 ( 2) link_BETA1-2 : angle 5.02393 ( 6) link_BETA1-4 : bond 0.00518 ( 14) link_BETA1-4 : angle 2.77731 ( 42) link_ALPHA1-3 : bond 0.00875 ( 6) link_ALPHA1-3 : angle 3.29756 ( 18) hydrogen bonds : bond 0.05152 ( 983) hydrogen bonds : angle 4.23250 ( 2925) link_BETA1-6 : bond 0.00200 ( 4) link_BETA1-6 : angle 1.60080 ( 12) covalent geometry : bond 0.00308 (23058) covalent geometry : angle 0.54627 (31102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 132 time to evaluate : 3.064 Fit side-chains REVERT: C 173 ARG cc_start: 0.3579 (mtt180) cc_final: 0.2721 (ptt180) REVERT: C 291 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8465 (p90) REVERT: C 493 HIS cc_start: 0.3713 (m-70) cc_final: 0.3439 (m-70) REVERT: C 512 GLU cc_start: 0.4489 (OUTLIER) cc_final: 0.4219 (mp0) REVERT: C 544 GLU cc_start: 0.7102 (tt0) cc_final: 0.6256 (tm-30) REVERT: C 578 PHE cc_start: 0.1687 (OUTLIER) cc_final: 0.0477 (p90) REVERT: C 763 GLU cc_start: 0.8126 (tt0) cc_final: 0.7888 (mt-10) REVERT: C 816 MET cc_start: 0.8532 (mmm) cc_final: 0.8031 (mmm) REVERT: D 23 LYS cc_start: 0.7967 (mmtp) cc_final: 0.7677 (mmtt) REVERT: A 173 ARG cc_start: 0.3168 (mtt180) cc_final: 0.2462 (ptt180) REVERT: A 385 ARG cc_start: 0.3869 (OUTLIER) cc_final: 0.3644 (ptt90) REVERT: A 490 LEU cc_start: 0.3967 (OUTLIER) cc_final: 0.3470 (pt) REVERT: A 512 GLU cc_start: 0.4429 (OUTLIER) cc_final: 0.4209 (mp0) REVERT: A 578 PHE cc_start: 0.1860 (OUTLIER) cc_final: 0.0762 (p90) REVERT: B 106 MET cc_start: 0.8827 (mmm) cc_final: 0.8274 (mtp) REVERT: B 203 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7812 (mp10) outliers start: 59 outliers final: 34 residues processed: 184 average time/residue: 0.4692 time to fit residues: 138.4215 Evaluate side-chains 167 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain G residue 37 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 42 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 150 optimal weight: 40.0000 chunk 14 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 198 optimal weight: 5.9990 chunk 202 optimal weight: 0.0060 chunk 174 optimal weight: 6.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.141164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.096470 restraints weight = 40793.984| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.80 r_work: 0.2948 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23096 Z= 0.151 Angle : 0.590 8.283 31216 Z= 0.285 Chirality : 0.044 0.430 3514 Planarity : 0.005 0.083 3808 Dihedral : 13.981 129.169 5082 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.16 % Allowed : 14.89 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.56 (0.16), residues: 2642 helix: 1.60 (0.15), residues: 1226 sheet: -0.28 (0.29), residues: 296 loop : -0.80 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 89 HIS 0.006 0.001 HIS A 557 PHE 0.019 0.002 PHE A 923 TYR 0.017 0.001 TYR C 869 ARG 0.013 0.000 ARG C 889 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 8) link_NAG-ASN : angle 1.48627 ( 24) link_ALPHA1-6 : bond 0.00847 ( 4) link_ALPHA1-6 : angle 1.49383 ( 12) link_BETA1-2 : bond 0.00378 ( 2) link_BETA1-2 : angle 5.03985 ( 6) link_BETA1-4 : bond 0.00498 ( 14) link_BETA1-4 : angle 2.75804 ( 42) link_ALPHA1-3 : bond 0.00915 ( 6) link_ALPHA1-3 : angle 3.20520 ( 18) hydrogen bonds : bond 0.05389 ( 983) hydrogen bonds : angle 4.19997 ( 2925) link_BETA1-6 : bond 0.00182 ( 4) link_BETA1-6 : angle 1.60961 ( 12) covalent geometry : bond 0.00361 (23058) covalent geometry : angle 0.56962 (31102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 127 time to evaluate : 3.768 Fit side-chains REVERT: C 173 ARG cc_start: 0.3758 (mtt180) cc_final: 0.2881 (ptt180) REVERT: C 277 LEU cc_start: 0.8177 (tp) cc_final: 0.7728 (tt) REVERT: C 291 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8532 (p90) REVERT: C 490 LEU cc_start: 0.4050 (OUTLIER) cc_final: 0.3489 (pt) REVERT: C 493 HIS cc_start: 0.3720 (m-70) cc_final: 0.3442 (m-70) REVERT: C 512 GLU cc_start: 0.4451 (OUTLIER) cc_final: 0.4235 (mp0) REVERT: C 544 GLU cc_start: 0.7065 (tt0) cc_final: 0.6250 (tm-30) REVERT: C 578 PHE cc_start: 0.1697 (OUTLIER) cc_final: 0.0566 (p90) REVERT: D 23 LYS cc_start: 0.7975 (mmtp) cc_final: 0.7704 (mmtt) REVERT: D 106 MET cc_start: 0.8779 (mmm) cc_final: 0.8316 (mtp) REVERT: A 230 GLU cc_start: 0.7723 (mp0) cc_final: 0.6874 (tt0) REVERT: A 385 ARG cc_start: 0.4061 (OUTLIER) cc_final: 0.3692 (ptt90) REVERT: A 391 MET cc_start: 0.6976 (mmp) cc_final: 0.6702 (mmp) REVERT: A 490 LEU cc_start: 0.3978 (OUTLIER) cc_final: 0.3511 (pt) REVERT: A 512 GLU cc_start: 0.4554 (OUTLIER) cc_final: 0.4260 (mp0) REVERT: A 578 PHE cc_start: 0.1692 (OUTLIER) cc_final: 0.0732 (p90) REVERT: B 106 MET cc_start: 0.8747 (mmm) cc_final: 0.8189 (mtp) REVERT: B 203 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7797 (mp10) outliers start: 49 outliers final: 33 residues processed: 171 average time/residue: 0.4224 time to fit residues: 117.4336 Evaluate side-chains 164 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain G residue 37 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 6 optimal weight: 3.9990 chunk 180 optimal weight: 30.0000 chunk 249 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 212 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 206 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 203 optimal weight: 0.2980 chunk 215 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.141326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.096141 restraints weight = 40869.000| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.03 r_work: 0.2939 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23096 Z= 0.141 Angle : 0.569 8.448 31216 Z= 0.276 Chirality : 0.044 0.435 3514 Planarity : 0.004 0.061 3808 Dihedral : 13.669 129.227 5082 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.16 % Allowed : 14.80 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.16), residues: 2642 helix: 1.65 (0.15), residues: 1236 sheet: -0.42 (0.28), residues: 320 loop : -0.73 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 89 HIS 0.006 0.001 HIS C 557 PHE 0.016 0.001 PHE A 923 TYR 0.015 0.001 TYR C 869 ARG 0.008 0.000 ARG A 889 Details of bonding type rmsd link_NAG-ASN : bond 0.00431 ( 8) link_NAG-ASN : angle 1.50226 ( 24) link_ALPHA1-6 : bond 0.00818 ( 4) link_ALPHA1-6 : angle 1.41973 ( 12) link_BETA1-2 : bond 0.00416 ( 2) link_BETA1-2 : angle 5.11686 ( 6) link_BETA1-4 : bond 0.00500 ( 14) link_BETA1-4 : angle 2.58244 ( 42) link_ALPHA1-3 : bond 0.00808 ( 6) link_ALPHA1-3 : angle 3.14409 ( 18) hydrogen bonds : bond 0.05103 ( 983) hydrogen bonds : angle 4.13128 ( 2925) link_BETA1-6 : bond 0.00144 ( 4) link_BETA1-6 : angle 1.58349 ( 12) covalent geometry : bond 0.00335 (23058) covalent geometry : angle 0.54963 (31102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 130 time to evaluate : 2.253 Fit side-chains REVERT: C 173 ARG cc_start: 0.3778 (mtt180) cc_final: 0.2897 (ptt180) REVERT: C 277 LEU cc_start: 0.8111 (tp) cc_final: 0.7671 (tt) REVERT: C 291 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8510 (p90) REVERT: C 490 LEU cc_start: 0.3998 (OUTLIER) cc_final: 0.3526 (pt) REVERT: C 493 HIS cc_start: 0.3719 (OUTLIER) cc_final: 0.3472 (m-70) REVERT: C 512 GLU cc_start: 0.4444 (OUTLIER) cc_final: 0.4230 (mp0) REVERT: C 544 GLU cc_start: 0.7107 (tt0) cc_final: 0.6806 (pt0) REVERT: C 578 PHE cc_start: 0.1654 (OUTLIER) cc_final: 0.0630 (p90) REVERT: C 589 MET cc_start: 0.7788 (mmm) cc_final: 0.7039 (mtm) REVERT: C 734 MET cc_start: 0.8069 (mmm) cc_final: 0.7814 (mmm) REVERT: C 816 MET cc_start: 0.8430 (mmm) cc_final: 0.7961 (mmm) REVERT: D 106 MET cc_start: 0.8776 (mmm) cc_final: 0.8248 (mtp) REVERT: A 230 GLU cc_start: 0.7721 (mp0) cc_final: 0.6910 (tt0) REVERT: A 385 ARG cc_start: 0.4050 (OUTLIER) cc_final: 0.3846 (ptt90) REVERT: A 396 GLN cc_start: 0.6905 (tm-30) cc_final: 0.6118 (mp10) REVERT: A 490 LEU cc_start: 0.4020 (OUTLIER) cc_final: 0.3546 (pt) REVERT: A 512 GLU cc_start: 0.4508 (OUTLIER) cc_final: 0.4258 (mp0) REVERT: A 578 PHE cc_start: 0.1585 (OUTLIER) cc_final: 0.0672 (p90) REVERT: A 615 MET cc_start: 0.6180 (ttp) cc_final: 0.5796 (ttp) REVERT: B 106 MET cc_start: 0.8738 (mmm) cc_final: 0.8166 (mtp) REVERT: B 203 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7776 (mp10) outliers start: 49 outliers final: 33 residues processed: 170 average time/residue: 0.3220 time to fit residues: 88.5145 Evaluate side-chains 167 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain G residue 37 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 32 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 149 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 210 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 243 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.142597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.098554 restraints weight = 40663.685| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.10 r_work: 0.3025 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23096 Z= 0.102 Angle : 0.536 8.310 31216 Z= 0.259 Chirality : 0.043 0.436 3514 Planarity : 0.004 0.069 3808 Dihedral : 12.984 127.290 5082 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.50 % Allowed : 15.68 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.89 (0.16), residues: 2642 helix: 1.99 (0.15), residues: 1210 sheet: -0.36 (0.29), residues: 318 loop : -0.68 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 89 HIS 0.009 0.001 HIS C 557 PHE 0.013 0.001 PHE A 306 TYR 0.016 0.001 TYR A 488 ARG 0.008 0.000 ARG C 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00623 ( 8) link_NAG-ASN : angle 1.40826 ( 24) link_ALPHA1-6 : bond 0.00730 ( 4) link_ALPHA1-6 : angle 1.40734 ( 12) link_BETA1-2 : bond 0.00478 ( 2) link_BETA1-2 : angle 4.97979 ( 6) link_BETA1-4 : bond 0.00540 ( 14) link_BETA1-4 : angle 2.40897 ( 42) link_ALPHA1-3 : bond 0.00840 ( 6) link_ALPHA1-3 : angle 3.21107 ( 18) hydrogen bonds : bond 0.04205 ( 983) hydrogen bonds : angle 3.97389 ( 2925) link_BETA1-6 : bond 0.00129 ( 4) link_BETA1-6 : angle 1.52769 ( 12) covalent geometry : bond 0.00221 (23058) covalent geometry : angle 0.51668 (31102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 2.490 Fit side-chains REVERT: C 158 MET cc_start: 0.4595 (tpt) cc_final: 0.4369 (mmt) REVERT: C 173 ARG cc_start: 0.3738 (mtt180) cc_final: 0.2816 (ptt180) REVERT: C 277 LEU cc_start: 0.8260 (tp) cc_final: 0.7806 (tt) REVERT: C 291 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8390 (p90) REVERT: C 490 LEU cc_start: 0.4024 (OUTLIER) cc_final: 0.3547 (pt) REVERT: C 493 HIS cc_start: 0.3711 (OUTLIER) cc_final: 0.3481 (m-70) REVERT: C 544 GLU cc_start: 0.7154 (tt0) cc_final: 0.6848 (pt0) REVERT: C 578 PHE cc_start: 0.1552 (OUTLIER) cc_final: 0.0646 (p90) REVERT: C 816 MET cc_start: 0.8553 (mmm) cc_final: 0.8118 (mmm) REVERT: D 85 ILE cc_start: 0.8603 (mm) cc_final: 0.8365 (tp) REVERT: D 106 MET cc_start: 0.8808 (mmm) cc_final: 0.8264 (mtp) REVERT: A 230 GLU cc_start: 0.7689 (mp0) cc_final: 0.6925 (tt0) REVERT: A 385 ARG cc_start: 0.4068 (OUTLIER) cc_final: 0.3824 (ptt90) REVERT: A 490 LEU cc_start: 0.4034 (OUTLIER) cc_final: 0.3564 (pt) REVERT: A 512 GLU cc_start: 0.4522 (OUTLIER) cc_final: 0.4271 (mp0) REVERT: A 578 PHE cc_start: 0.1724 (OUTLIER) cc_final: 0.0768 (p90) REVERT: A 615 MET cc_start: 0.6415 (ttp) cc_final: 0.6029 (ttp) REVERT: A 734 MET cc_start: 0.8106 (mmm) cc_final: 0.7876 (mmm) REVERT: B 85 ILE cc_start: 0.8624 (mm) cc_final: 0.8379 (tp) REVERT: B 106 MET cc_start: 0.8770 (mmm) cc_final: 0.8211 (mtp) REVERT: B 203 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7895 (mp10) outliers start: 34 outliers final: 20 residues processed: 169 average time/residue: 0.3277 time to fit residues: 90.3969 Evaluate side-chains 159 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 203 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 71 optimal weight: 5.9990 chunk 200 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 192 optimal weight: 0.0050 chunk 70 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 overall best weight: 1.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 946 GLN ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 HIS ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.141662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.097086 restraints weight = 40797.047| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.86 r_work: 0.2969 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23096 Z= 0.129 Angle : 0.560 8.262 31216 Z= 0.271 Chirality : 0.043 0.440 3514 Planarity : 0.004 0.069 3808 Dihedral : 12.891 126.802 5080 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.46 % Allowed : 15.86 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.90 (0.16), residues: 2642 helix: 1.94 (0.15), residues: 1210 sheet: -0.32 (0.28), residues: 320 loop : -0.62 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 89 HIS 0.008 0.001 HIS C 557 PHE 0.016 0.001 PHE A 923 TYR 0.017 0.001 TYR A 488 ARG 0.006 0.000 ARG A 889 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 8) link_NAG-ASN : angle 1.53766 ( 24) link_ALPHA1-6 : bond 0.00731 ( 4) link_ALPHA1-6 : angle 1.41099 ( 12) link_BETA1-2 : bond 0.00405 ( 2) link_BETA1-2 : angle 4.99819 ( 6) link_BETA1-4 : bond 0.00501 ( 14) link_BETA1-4 : angle 2.47489 ( 42) link_ALPHA1-3 : bond 0.00809 ( 6) link_ALPHA1-3 : angle 3.13889 ( 18) hydrogen bonds : bond 0.04835 ( 983) hydrogen bonds : angle 4.03795 ( 2925) link_BETA1-6 : bond 0.00144 ( 4) link_BETA1-6 : angle 1.55278 ( 12) covalent geometry : bond 0.00302 (23058) covalent geometry : angle 0.54069 (31102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13686.50 seconds wall clock time: 240 minutes 24.43 seconds (14424.43 seconds total)