Starting phenix.real_space_refine on Thu May 22 17:52:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y45_33601/05_2025/7y45_33601.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y45_33601/05_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_33601/05_2025/7y45_33601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y45_33601/05_2025/7y45_33601.map" model { file = "/net/cci-nas-00/data/ceres_data/7y45_33601/05_2025/7y45_33601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y45_33601/05_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 23.51, per 1000 atoms: 1.04 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: 6.33 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: 2.63 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: 9.20 Time building geometry restraints manager: 7.07 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: 1.080 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: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 61.350 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.090 ------------------------------------------------------------------------------- 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 : 2.345 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: 0.4233 time to fit residues: 317.8882 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 : 2.406 ------------------------------------------------------------------------------- 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: 0.3135 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 : 2.522 Fit side-chains revert: symmetry clash REVERT: C 153 LYS cc_start: 0.7720 (mmmt) cc_final: 0.7206 (mmmm) REVERT: C 164 MET cc_start: 0.7696 (mmp) cc_final: 0.7397 (ttm) REVERT: C 173 ARG cc_start: 0.3126 (mtt180) cc_final: 0.2292 (ptt180) REVERT: C 218 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6348 (pp) REVERT: C 267 MET cc_start: 0.6039 (ppp) cc_final: 0.5539 (ppp) REVERT: C 324 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9009 (tp) REVERT: C 493 HIS cc_start: 0.4153 (OUTLIER) cc_final: 0.3198 (m-70) REVERT: C 816 MET cc_start: 0.8377 (mmm) cc_final: 0.8039 (mmm) REVERT: C 952 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7631 (mptt) REVERT: D 14 LYS cc_start: 0.7241 (tptt) cc_final: 0.6586 (mmpt) REVERT: D 106 MET cc_start: 0.8660 (mmm) cc_final: 0.8440 (mmm) REVERT: D 142 ASP cc_start: 0.7636 (t0) cc_final: 0.7243 (t0) REVERT: A 41 MET cc_start: 0.5837 (ppp) cc_final: 0.5361 (ptm) REVERT: A 42 ASP cc_start: 0.4856 (OUTLIER) cc_final: 0.4620 (t70) REVERT: A 153 LYS cc_start: 0.7605 (mmmt) cc_final: 0.7083 (mmmm) REVERT: A 164 MET cc_start: 0.7795 (mmp) cc_final: 0.7436 (ttm) REVERT: A 173 ARG cc_start: 0.3392 (mtt180) cc_final: 0.2683 (ptt180) REVERT: A 267 MET cc_start: 0.6128 (ppp) cc_final: 0.5673 (ppp) REVERT: A 396 GLN cc_start: 0.6569 (tp40) cc_final: 0.5878 (mt0) REVERT: A 493 HIS cc_start: 0.4070 (OUTLIER) cc_final: 0.3051 (m-70) REVERT: A 534 MET cc_start: 0.2768 (mtp) cc_final: 0.2505 (mmm) REVERT: B 23 LYS cc_start: 0.8641 (mttt) cc_final: 0.8097 (mmtm) REVERT: B 106 MET cc_start: 0.8726 (mmm) cc_final: 0.8499 (mmm) REVERT: B 201 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8480 (pm20) REVERT: B 203 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7450 (mp10) outliers start: 82 outliers final: 40 residues processed: 255 average time/residue: 0.3669 time to fit residues: 143.0262 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 : 2.247 ------------------------------------------------------------------------------- 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: 3.9990 chunk 233 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 151 optimal weight: 40.0000 chunk 65 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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** D 56 GLN ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.145127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.100401 restraints weight = 40780.142| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.37 r_work: 0.3008 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3309 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= 0.154 Angle : 0.633 9.564 31216 Z= 0.308 Chirality : 0.045 0.415 3514 Planarity : 0.005 0.065 3808 Dihedral : 16.336 131.859 5118 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.87 % Allowed : 13.38 % Favored : 83.75 % 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: -0.49 (0.16), residues: 2642 helix: 0.79 (0.15), residues: 1232 sheet: -1.53 (0.30), residues: 262 loop : -1.23 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 89 HIS 0.007 0.001 HIS C 557 PHE 0.019 0.002 PHE A 923 TYR 0.015 0.001 TYR B 248 ARG 0.007 0.000 ARG C 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 8) link_NAG-ASN : angle 1.76486 ( 24) link_ALPHA1-6 : bond 0.00745 ( 4) link_ALPHA1-6 : angle 1.66909 ( 12) link_BETA1-2 : bond 0.00623 ( 2) link_BETA1-2 : angle 4.54321 ( 6) link_BETA1-4 : bond 0.00739 ( 14) link_BETA1-4 : angle 3.57161 ( 42) link_ALPHA1-3 : bond 0.01053 ( 6) link_ALPHA1-3 : angle 3.28671 ( 18) hydrogen bonds : bond 0.05795 ( 983) hydrogen bonds : angle 4.60351 ( 2925) link_BETA1-6 : bond 0.00460 ( 4) link_BETA1-6 : angle 1.49319 ( 12) covalent geometry : bond 0.00360 (23058) covalent geometry : angle 0.60834 (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 214 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 149 time to evaluate : 2.684 Fit side-chains REVERT: C 173 ARG cc_start: 0.3059 (mtt180) cc_final: 0.2259 (ptt180) REVERT: C 816 MET cc_start: 0.8487 (mmm) cc_final: 0.8109 (mmm) REVERT: D 14 LYS cc_start: 0.7506 (tptt) cc_final: 0.6684 (mmpt) REVERT: D 106 MET cc_start: 0.8717 (mmm) cc_final: 0.8460 (mmm) REVERT: D 142 ASP cc_start: 0.8004 (t0) cc_final: 0.7631 (t0) REVERT: A 41 MET cc_start: 0.5638 (ppp) cc_final: 0.5398 (ptm) REVERT: A 164 MET cc_start: 0.7738 (mmp) cc_final: 0.7533 (tmm) REVERT: A 173 ARG cc_start: 0.3402 (mtt180) cc_final: 0.2621 (ptt180) REVERT: A 277 LEU cc_start: 0.7646 (mm) cc_final: 0.7407 (tp) REVERT: A 708 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6761 (tt0) REVERT: B 23 LYS cc_start: 0.8645 (mttt) cc_final: 0.8025 (mmtm) REVERT: B 106 MET cc_start: 0.8815 (mmm) cc_final: 0.8547 (mmm) REVERT: B 110 MET cc_start: 0.8794 (mmp) cc_final: 0.8574 (mmt) REVERT: B 201 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8548 (pm20) REVERT: B 203 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7674 (mp10) outliers start: 65 outliers final: 38 residues processed: 208 average time/residue: 0.3808 time to fit residues: 123.4282 Evaluate side-chains 176 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 2.455 ------------------------------------------------------------------------------- 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 806 THR Chi-restraints excluded: chain C residue 894 TRP 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 37 LYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 583 LEU 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 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 94 SER 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: 0.0570 chunk 33 optimal weight: 0.0570 chunk 160 optimal weight: 1.9990 chunk 154 optimal weight: 40.0000 chunk 14 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 64 optimal weight: 0.1980 chunk 246 optimal weight: 8.9990 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 540 ASN A 398 HIS A 489 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.147486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.102590 restraints weight = 41445.990| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.41 r_work: 0.3093 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23096 Z= 0.104 Angle : 0.564 8.862 31216 Z= 0.271 Chirality : 0.043 0.437 3514 Planarity : 0.004 0.059 3808 Dihedral : 15.226 129.418 5094 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.12 % Allowed : 14.71 % 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: 0.04 (0.16), residues: 2642 helix: 1.27 (0.15), residues: 1244 sheet: -1.19 (0.31), residues: 252 loop : -1.06 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 89 HIS 0.011 0.001 HIS C 398 PHE 0.032 0.001 PHE C 393 TYR 0.012 0.001 TYR C 869 ARG 0.007 0.000 ARG C 889 Details of bonding type rmsd link_NAG-ASN : bond 0.00738 ( 8) link_NAG-ASN : angle 1.54697 ( 24) link_ALPHA1-6 : bond 0.01067 ( 4) link_ALPHA1-6 : angle 1.79778 ( 12) link_BETA1-2 : bond 0.00607 ( 2) link_BETA1-2 : angle 4.41689 ( 6) link_BETA1-4 : bond 0.00626 ( 14) link_BETA1-4 : angle 3.15289 ( 42) link_ALPHA1-3 : bond 0.01084 ( 6) link_ALPHA1-3 : angle 3.52999 ( 18) hydrogen bonds : bond 0.04283 ( 983) hydrogen bonds : angle 4.22132 ( 2925) link_BETA1-6 : bond 0.00284 ( 4) link_BETA1-6 : angle 1.44612 ( 12) covalent geometry : bond 0.00205 (23058) covalent geometry : angle 0.53922 (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 203 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 155 time to evaluate : 2.216 Fit side-chains REVERT: C 173 ARG cc_start: 0.3170 (mtt180) cc_final: 0.2378 (ptt180) REVERT: C 391 MET cc_start: 0.7277 (mmt) cc_final: 0.6802 (mmp) REVERT: C 493 HIS cc_start: 0.4005 (m-70) cc_final: 0.3413 (m-70) REVERT: C 544 GLU cc_start: 0.6875 (tt0) cc_final: 0.6042 (tm-30) REVERT: C 816 MET cc_start: 0.8483 (mmm) cc_final: 0.8145 (mmm) REVERT: D 14 LYS cc_start: 0.7561 (tptt) cc_final: 0.6685 (mmpt) REVERT: D 106 MET cc_start: 0.8774 (mmm) cc_final: 0.8515 (mmm) REVERT: D 142 ASP cc_start: 0.8119 (t0) cc_final: 0.7729 (t0) REVERT: A 89 TRP cc_start: 0.6230 (p-90) cc_final: 0.5712 (p-90) REVERT: A 173 ARG cc_start: 0.3291 (mtt180) cc_final: 0.2600 (ptt180) REVERT: A 185 VAL cc_start: 0.7035 (t) cc_final: 0.6767 (p) REVERT: A 267 MET cc_start: 0.6231 (ppp) cc_final: 0.5916 (ppp) REVERT: A 396 GLN cc_start: 0.6383 (tm-30) cc_final: 0.5414 (mt0) REVERT: A 493 HIS cc_start: 0.3925 (OUTLIER) cc_final: 0.3344 (m-70) REVERT: A 544 GLU cc_start: 0.6768 (tt0) cc_final: 0.5891 (tm-30) REVERT: B 23 LYS cc_start: 0.8685 (mttt) cc_final: 0.7991 (mmtm) REVERT: B 106 MET cc_start: 0.8794 (mmm) cc_final: 0.8488 (mmm) REVERT: B 201 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8618 (pm20) REVERT: B 203 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7738 (mp10) outliers start: 48 outliers final: 22 residues processed: 193 average time/residue: 0.3420 time to fit residues: 103.2267 Evaluate side-chains 163 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 2.191 ------------------------------------------------------------------------------- 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 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 719 VAL Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain C residue 986 SER Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 96 LEU 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 583 LEU 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 94 SER 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: 2.9990 chunk 210 optimal weight: 6.9990 chunk 200 optimal weight: 8.9990 chunk 201 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 216 optimal weight: 0.8980 chunk 239 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 HIS A 708 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.142878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.087547 restraints weight = 41254.919| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.89 r_work: 0.2964 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4098 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= 0.163 Angle : 0.606 8.444 31216 Z= 0.294 Chirality : 0.045 0.441 3514 Planarity : 0.005 0.059 3808 Dihedral : 14.754 124.312 5085 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.21 % Allowed : 14.84 % 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: 0.25 (0.16), residues: 2642 helix: 1.38 (0.15), residues: 1234 sheet: -0.81 (0.29), residues: 296 loop : -0.91 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 894 HIS 0.006 0.001 HIS C 557 PHE 0.023 0.002 PHE A 923 TYR 0.018 0.002 TYR D 248 ARG 0.010 0.001 ARG C 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 8) link_NAG-ASN : angle 1.55218 ( 24) link_ALPHA1-6 : bond 0.00816 ( 4) link_ALPHA1-6 : angle 1.68447 ( 12) link_BETA1-2 : bond 0.00510 ( 2) link_BETA1-2 : angle 4.67246 ( 6) link_BETA1-4 : bond 0.00592 ( 14) link_BETA1-4 : angle 3.22375 ( 42) link_ALPHA1-3 : bond 0.00983 ( 6) link_ALPHA1-3 : angle 3.34681 ( 18) hydrogen bonds : bond 0.05610 ( 983) hydrogen bonds : angle 4.30021 ( 2925) link_BETA1-6 : bond 0.00274 ( 4) link_BETA1-6 : angle 1.58737 ( 12) covalent geometry : bond 0.00393 (23058) covalent geometry : angle 0.58353 (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 190 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 2.338 Fit side-chains REVERT: C 173 ARG cc_start: 0.3241 (mtt180) cc_final: 0.2453 (ptt180) REVERT: C 277 LEU cc_start: 0.7966 (tp) cc_final: 0.7632 (tt) REVERT: C 291 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8297 (p90) REVERT: C 493 HIS cc_start: 0.3755 (OUTLIER) cc_final: 0.3239 (m-70) REVERT: C 512 GLU cc_start: 0.4722 (OUTLIER) cc_final: 0.4474 (mp0) REVERT: C 544 GLU cc_start: 0.7004 (tt0) cc_final: 0.6148 (tm-30) REVERT: C 816 MET cc_start: 0.8465 (mmm) cc_final: 0.7969 (mmm) REVERT: D 106 MET cc_start: 0.8753 (mmm) cc_final: 0.8445 (mmm) REVERT: D 142 ASP cc_start: 0.8092 (t0) cc_final: 0.7729 (t0) REVERT: A 89 TRP cc_start: 0.6124 (p-90) cc_final: 0.5637 (p-90) REVERT: A 173 ARG cc_start: 0.3209 (mtt180) cc_final: 0.2526 (ptt180) REVERT: A 185 VAL cc_start: 0.6830 (t) cc_final: 0.6495 (p) REVERT: A 391 MET cc_start: 0.7394 (mmp) cc_final: 0.6957 (mmp) REVERT: A 490 LEU cc_start: 0.3994 (OUTLIER) cc_final: 0.3635 (pt) REVERT: B 23 LYS cc_start: 0.8696 (mttt) cc_final: 0.8055 (mmtm) REVERT: B 201 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8542 (pm20) REVERT: B 203 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7667 (mp10) outliers start: 50 outliers final: 28 residues processed: 182 average time/residue: 0.3385 time to fit residues: 98.7552 Evaluate side-chains 165 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 2.225 ------------------------------------------------------------------------------- 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 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 493 HIS 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 D residue 29 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 37 LYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 686 THR 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 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 Chi-restraints excluded: chain G residue 37 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 216 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 40.0000 chunk 61 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 181 optimal weight: 0.9980 chunk 247 optimal weight: 5.9990 chunk 53 optimal weight: 30.0000 chunk 43 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 243 GLN A 489 GLN A 683 HIS A 946 GLN B 243 GLN B 258 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.140549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.085699 restraints weight = 41091.515| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.96 r_work: 0.2908 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 23096 Z= 0.214 Angle : 0.645 8.266 31216 Z= 0.315 Chirality : 0.047 0.436 3514 Planarity : 0.005 0.069 3808 Dihedral : 14.933 128.246 5082 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.74 % Allowed : 14.40 % Favored : 82.86 % 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: 0.16 (0.16), residues: 2642 helix: 1.29 (0.15), residues: 1226 sheet: -0.68 (0.28), residues: 312 loop : -0.98 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 89 HIS 0.006 0.001 HIS C 557 PHE 0.022 0.002 PHE D 297 TYR 0.022 0.002 TYR B 44 ARG 0.018 0.001 ARG A 707 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 8) link_NAG-ASN : angle 1.51976 ( 24) link_ALPHA1-6 : bond 0.00873 ( 4) link_ALPHA1-6 : angle 1.59165 ( 12) link_BETA1-2 : bond 0.00455 ( 2) link_BETA1-2 : angle 4.93309 ( 6) link_BETA1-4 : bond 0.00570 ( 14) link_BETA1-4 : angle 3.17520 ( 42) link_ALPHA1-3 : bond 0.00962 ( 6) link_ALPHA1-3 : angle 3.22570 ( 18) hydrogen bonds : bond 0.06222 ( 983) hydrogen bonds : angle 4.40089 ( 2925) link_BETA1-6 : bond 0.00250 ( 4) link_BETA1-6 : angle 1.65872 ( 12) covalent geometry : bond 0.00527 (23058) covalent geometry : angle 0.62422 (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 196 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 134 time to evaluate : 2.247 Fit side-chains REVERT: C 173 ARG cc_start: 0.3452 (mtt180) cc_final: 0.2624 (ptt180) REVERT: C 291 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8532 (p90) REVERT: C 386 MET cc_start: 0.5537 (ptp) cc_final: 0.5269 (ptp) REVERT: C 391 MET cc_start: 0.7247 (mmt) cc_final: 0.6833 (mmp) REVERT: C 490 LEU cc_start: 0.4114 (OUTLIER) cc_final: 0.3500 (pt) REVERT: C 493 HIS cc_start: 0.3728 (OUTLIER) cc_final: 0.3226 (m-70) REVERT: C 512 GLU cc_start: 0.4623 (OUTLIER) cc_final: 0.4371 (mp0) REVERT: C 544 GLU cc_start: 0.7110 (tt0) cc_final: 0.6270 (tm-30) REVERT: C 578 PHE cc_start: 0.1793 (OUTLIER) cc_final: 0.0703 (p90) REVERT: C 816 MET cc_start: 0.8447 (mmm) cc_final: 0.7913 (mmm) REVERT: D 23 LYS cc_start: 0.7910 (mmtp) cc_final: 0.7611 (mmtt) REVERT: D 106 MET cc_start: 0.8744 (mmm) cc_final: 0.8280 (mtp) REVERT: D 121 ASN cc_start: 0.7165 (m110) cc_final: 0.6941 (m-40) REVERT: A 173 ARG cc_start: 0.3175 (mtt180) cc_final: 0.2484 (ptt180) REVERT: A 385 ARG cc_start: 0.3862 (OUTLIER) cc_final: 0.3520 (ptt90) REVERT: A 391 MET cc_start: 0.7118 (mmp) cc_final: 0.6667 (mmp) REVERT: A 396 GLN cc_start: 0.7122 (tm-30) cc_final: 0.6212 (pt0) REVERT: A 493 HIS cc_start: 0.4082 (m-70) cc_final: 0.3490 (m-70) REVERT: A 512 GLU cc_start: 0.4389 (OUTLIER) cc_final: 0.4085 (mp0) REVERT: A 578 PHE cc_start: 0.2023 (OUTLIER) cc_final: 0.0979 (p90) REVERT: B 23 LYS cc_start: 0.8686 (mttt) cc_final: 0.8081 (mmtm) REVERT: B 106 MET cc_start: 0.8764 (mmm) cc_final: 0.8228 (mtp) REVERT: B 203 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7873 (mp10) outliers start: 62 outliers final: 31 residues processed: 185 average time/residue: 0.3499 time to fit residues: 101.6846 Evaluate side-chains 167 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 2.458 ------------------------------------------------------------------------------- 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 578 PHE 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 1000 LEU 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 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 385 ARG Chi-restraints excluded: chain A residue 485 THR 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 655 VAL 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 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: 0.6980 chunk 230 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 245 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 263 optimal weight: 8.9990 chunk 18 optimal weight: 40.0000 chunk 132 optimal weight: 30.0000 chunk 57 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 GLN ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.142182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.085342 restraints weight = 41111.003| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.57 r_work: 0.2994 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4658 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= 0.126 Angle : 0.563 8.198 31216 Z= 0.273 Chirality : 0.044 0.438 3514 Planarity : 0.005 0.061 3808 Dihedral : 14.325 137.671 5082 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.94 % Allowed : 15.19 % Favored : 82.86 % 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: 0.48 (0.16), residues: 2642 helix: 1.54 (0.15), residues: 1238 sheet: -0.48 (0.28), residues: 310 loop : -0.83 (0.17), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 89 HIS 0.006 0.001 HIS A 557 PHE 0.014 0.001 PHE C 306 TYR 0.015 0.001 TYR C 869 ARG 0.012 0.000 ARG C 889 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 8) link_NAG-ASN : angle 1.46681 ( 24) link_ALPHA1-6 : bond 0.00841 ( 4) link_ALPHA1-6 : angle 1.51773 ( 12) link_BETA1-2 : bond 0.00483 ( 2) link_BETA1-2 : angle 4.95952 ( 6) link_BETA1-4 : bond 0.00555 ( 14) link_BETA1-4 : angle 2.78047 ( 42) link_ALPHA1-3 : bond 0.00937 ( 6) link_ALPHA1-3 : angle 3.32856 ( 18) hydrogen bonds : bond 0.05003 ( 983) hydrogen bonds : angle 4.18479 ( 2925) link_BETA1-6 : bond 0.00155 ( 4) link_BETA1-6 : angle 1.59904 ( 12) covalent geometry : bond 0.00289 (23058) covalent geometry : angle 0.54161 (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 174 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 2.346 Fit side-chains REVERT: C 173 ARG cc_start: 0.3552 (mtt180) cc_final: 0.2702 (ptt180) REVERT: C 277 LEU cc_start: 0.7902 (tp) cc_final: 0.7446 (tt) REVERT: C 291 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8404 (p90) REVERT: C 391 MET cc_start: 0.7210 (mmt) cc_final: 0.6762 (mmp) REVERT: C 490 LEU cc_start: 0.4055 (OUTLIER) cc_final: 0.3721 (pt) REVERT: C 493 HIS cc_start: 0.3700 (OUTLIER) cc_final: 0.3223 (m-70) REVERT: C 512 GLU cc_start: 0.4531 (OUTLIER) cc_final: 0.4250 (mp0) REVERT: C 544 GLU cc_start: 0.7059 (tt0) cc_final: 0.6815 (pt0) REVERT: C 816 MET cc_start: 0.8540 (mmm) cc_final: 0.8028 (mmm) REVERT: D 23 LYS cc_start: 0.7930 (mmtp) cc_final: 0.7629 (mmtt) REVERT: D 121 ASN cc_start: 0.7340 (m110) cc_final: 0.7135 (m-40) REVERT: A 173 ARG cc_start: 0.3235 (mtt180) cc_final: 0.2523 (ptt180) REVERT: A 391 MET cc_start: 0.7067 (mmp) cc_final: 0.6813 (mmp) REVERT: A 396 GLN cc_start: 0.7130 (tm-30) cc_final: 0.6307 (pt0) REVERT: A 493 HIS cc_start: 0.3933 (OUTLIER) cc_final: 0.3420 (m-70) REVERT: A 512 GLU cc_start: 0.4439 (OUTLIER) cc_final: 0.4210 (mp0) REVERT: A 578 PHE cc_start: 0.1869 (OUTLIER) cc_final: 0.0884 (p90) REVERT: B 106 MET cc_start: 0.8816 (mmm) cc_final: 0.8310 (mtp) REVERT: B 203 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7849 (mp10) outliers start: 44 outliers final: 23 residues processed: 166 average time/residue: 0.3472 time to fit residues: 90.4174 Evaluate side-chains 155 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 2.179 ------------------------------------------------------------------------------- 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 186 VAL 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 548 LEU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 201 GLU 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 485 THR Chi-restraints excluded: chain A residue 493 HIS 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 655 VAL 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 160 CYS Chi-restraints excluded: chain B residue 203 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 42 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 150 optimal weight: 40.0000 chunk 14 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4093 r_free = 0.4093 target = 0.141759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.088095 restraints weight = 41114.947| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.92 r_work: 0.2949 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23096 Z= 0.139 Angle : 0.572 8.214 31216 Z= 0.276 Chirality : 0.044 0.431 3514 Planarity : 0.004 0.060 3808 Dihedral : 13.942 130.644 5082 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.16 % Allowed : 15.02 % 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: 0.62 (0.16), residues: 2642 helix: 1.62 (0.15), residues: 1238 sheet: -0.20 (0.30), residues: 294 loop : -0.78 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 89 HIS 0.006 0.001 HIS C 557 PHE 0.017 0.001 PHE A 923 TYR 0.016 0.001 TYR C 869 ARG 0.009 0.000 ARG C 889 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 8) link_NAG-ASN : angle 1.48471 ( 24) link_ALPHA1-6 : bond 0.00830 ( 4) link_ALPHA1-6 : angle 1.49867 ( 12) link_BETA1-2 : bond 0.00429 ( 2) link_BETA1-2 : angle 4.97708 ( 6) link_BETA1-4 : bond 0.00539 ( 14) link_BETA1-4 : angle 2.73895 ( 42) link_ALPHA1-3 : bond 0.00900 ( 6) link_ALPHA1-3 : angle 3.24137 ( 18) hydrogen bonds : bond 0.05119 ( 983) hydrogen bonds : angle 4.13687 ( 2925) link_BETA1-6 : bond 0.00166 ( 4) link_BETA1-6 : angle 1.58518 ( 12) covalent geometry : bond 0.00327 (23058) covalent geometry : angle 0.55137 (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 : 2.435 Fit side-chains REVERT: C 173 ARG cc_start: 0.3856 (mtt180) cc_final: 0.2997 (ptt180) REVERT: C 277 LEU cc_start: 0.7995 (tp) cc_final: 0.7509 (tt) REVERT: C 291 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8443 (p90) REVERT: C 386 MET cc_start: 0.5420 (ptp) cc_final: 0.5016 (ptp) REVERT: C 391 MET cc_start: 0.7180 (mmt) cc_final: 0.6660 (mmp) REVERT: C 490 LEU cc_start: 0.4076 (OUTLIER) cc_final: 0.3487 (pt) REVERT: C 493 HIS cc_start: 0.3591 (OUTLIER) cc_final: 0.3172 (m-70) REVERT: C 578 PHE cc_start: 0.1891 (OUTLIER) cc_final: 0.0609 (p90) REVERT: D 23 LYS cc_start: 0.7965 (mmtp) cc_final: 0.7681 (mmtt) REVERT: D 106 MET cc_start: 0.8745 (mmm) cc_final: 0.8242 (mtp) REVERT: A 173 ARG cc_start: 0.3340 (mtt180) cc_final: 0.2653 (ptt180) REVERT: A 230 GLU cc_start: 0.7875 (mp0) cc_final: 0.6993 (tt0) REVERT: A 391 MET cc_start: 0.7255 (mmp) cc_final: 0.6960 (mmp) REVERT: A 396 GLN cc_start: 0.6884 (tm-30) cc_final: 0.6350 (pt0) REVERT: A 490 LEU cc_start: 0.3818 (OUTLIER) cc_final: 0.3250 (pt) REVERT: A 493 HIS cc_start: 0.3826 (OUTLIER) cc_final: 0.3414 (m-70) REVERT: A 512 GLU cc_start: 0.4393 (OUTLIER) cc_final: 0.4092 (mp0) REVERT: A 578 PHE cc_start: 0.1904 (OUTLIER) cc_final: 0.0825 (p90) REVERT: B 106 MET cc_start: 0.8772 (mmm) cc_final: 0.8228 (mtp) REVERT: B 203 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7792 (mp10) outliers start: 49 outliers final: 29 residues processed: 166 average time/residue: 0.3327 time to fit residues: 88.6991 Evaluate side-chains 162 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 2.195 ------------------------------------------------------------------------------- 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 186 VAL 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 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 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 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 485 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 493 HIS 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 655 VAL 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 160 CYS Chi-restraints excluded: chain B residue 203 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 6 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 249 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 212 optimal weight: 0.4980 chunk 42 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4105 r_free = 0.4105 target = 0.142496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.098739 restraints weight = 41205.842| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.22 r_work: 0.2988 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23096 Z= 0.113 Angle : 0.542 8.260 31216 Z= 0.262 Chirality : 0.043 0.433 3514 Planarity : 0.004 0.060 3808 Dihedral : 13.376 126.522 5082 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.68 % Allowed : 15.11 % 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: 0.84 (0.16), residues: 2642 helix: 1.92 (0.15), residues: 1210 sheet: -0.29 (0.29), residues: 314 loop : -0.70 (0.18), residues: 1118 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 0.014 0.001 PHE A 306 TYR 0.015 0.001 TYR C 869 ARG 0.005 0.000 ARG C 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 8) link_NAG-ASN : angle 1.45560 ( 24) link_ALPHA1-6 : bond 0.00786 ( 4) link_ALPHA1-6 : angle 1.44693 ( 12) link_BETA1-2 : bond 0.00450 ( 2) link_BETA1-2 : angle 4.97288 ( 6) link_BETA1-4 : bond 0.00521 ( 14) link_BETA1-4 : angle 2.53710 ( 42) link_ALPHA1-3 : bond 0.00863 ( 6) link_ALPHA1-3 : angle 3.24414 ( 18) hydrogen bonds : bond 0.04555 ( 983) hydrogen bonds : angle 4.00218 ( 2925) link_BETA1-6 : bond 0.00134 ( 4) link_BETA1-6 : angle 1.53111 ( 12) covalent geometry : bond 0.00257 (23058) covalent geometry : angle 0.52142 (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 175 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 2.220 Fit side-chains REVERT: C 173 ARG cc_start: 0.3741 (mtt180) cc_final: 0.2870 (ptt180) REVERT: C 277 LEU cc_start: 0.8202 (tp) cc_final: 0.7710 (tt) REVERT: C 291 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8411 (p90) REVERT: C 386 MET cc_start: 0.5388 (ptp) cc_final: 0.4983 (ptp) REVERT: C 391 MET cc_start: 0.7156 (mmt) cc_final: 0.6637 (mmp) REVERT: C 490 LEU cc_start: 0.4159 (OUTLIER) cc_final: 0.3592 (pt) REVERT: C 578 PHE cc_start: 0.1712 (OUTLIER) cc_final: 0.0593 (p90) REVERT: C 816 MET cc_start: 0.8457 (mmm) cc_final: 0.7988 (mmm) REVERT: D 23 LYS cc_start: 0.8008 (mmtp) cc_final: 0.7765 (mmtt) REVERT: D 85 ILE cc_start: 0.8446 (mm) cc_final: 0.8178 (tp) REVERT: D 106 MET cc_start: 0.8697 (mmm) cc_final: 0.7805 (mmm) REVERT: A 230 GLU cc_start: 0.7795 (mp0) cc_final: 0.6953 (tt0) REVERT: A 391 MET cc_start: 0.7350 (mmp) cc_final: 0.7056 (mmp) REVERT: A 396 GLN cc_start: 0.6756 (tm-30) cc_final: 0.6382 (pt0) REVERT: A 490 LEU cc_start: 0.3887 (OUTLIER) cc_final: 0.3299 (pt) REVERT: A 493 HIS cc_start: 0.3880 (OUTLIER) cc_final: 0.3477 (m-70) REVERT: A 512 GLU cc_start: 0.4340 (OUTLIER) cc_final: 0.4057 (mp0) REVERT: A 578 PHE cc_start: 0.1881 (OUTLIER) cc_final: 0.0843 (p90) REVERT: B 85 ILE cc_start: 0.8384 (mm) cc_final: 0.8167 (tp) REVERT: B 106 MET cc_start: 0.8704 (mmm) cc_final: 0.8152 (mtp) REVERT: B 203 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7773 (mp10) outliers start: 38 outliers final: 25 residues processed: 168 average time/residue: 0.3122 time to fit residues: 84.6056 Evaluate side-chains 161 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 2.362 ------------------------------------------------------------------------------- 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 186 VAL 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 485 THR Chi-restraints excluded: chain C residue 490 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 201 GLU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 493 HIS 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 29 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 32 optimal weight: 0.8980 chunk 78 optimal weight: 0.0770 chunk 149 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 chunk 210 optimal weight: 0.8980 chunk 200 optimal weight: 10.0000 chunk 218 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 243 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 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 = 0.4119 r_free = 0.4119 target = 0.143568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.099563 restraints weight = 41254.471| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.01 r_work: 0.3043 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 23096 Z= 0.099 Angle : 0.531 8.218 31216 Z= 0.256 Chirality : 0.042 0.436 3514 Planarity : 0.004 0.068 3808 Dihedral : 12.848 124.748 5081 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.46 % Allowed : 15.42 % Favored : 83.13 % 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: 1.00 (0.17), residues: 2642 helix: 2.09 (0.15), residues: 1208 sheet: -0.21 (0.29), residues: 318 loop : -0.66 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 89 HIS 0.006 0.001 HIS A 557 PHE 0.013 0.001 PHE A 306 TYR 0.015 0.001 TYR C 869 ARG 0.008 0.000 ARG C 889 Details of bonding type rmsd link_NAG-ASN : bond 0.00669 ( 8) link_NAG-ASN : angle 1.50717 ( 24) link_ALPHA1-6 : bond 0.00755 ( 4) link_ALPHA1-6 : angle 1.45393 ( 12) link_BETA1-2 : bond 0.00447 ( 2) link_BETA1-2 : angle 4.90985 ( 6) link_BETA1-4 : bond 0.00554 ( 14) link_BETA1-4 : angle 2.46134 ( 42) link_ALPHA1-3 : bond 0.00820 ( 6) link_ALPHA1-3 : angle 3.26488 ( 18) hydrogen bonds : bond 0.04062 ( 983) hydrogen bonds : angle 3.87320 ( 2925) link_BETA1-6 : bond 0.00200 ( 4) link_BETA1-6 : angle 1.51989 ( 12) covalent geometry : bond 0.00208 (23058) covalent geometry : angle 0.51018 (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 170 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 2.368 Fit side-chains revert: symmetry clash REVERT: C 173 ARG cc_start: 0.3790 (mtt180) cc_final: 0.2874 (ptt180) REVERT: C 291 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8271 (p90) REVERT: C 386 MET cc_start: 0.5836 (ptp) cc_final: 0.5448 (ptp) REVERT: C 391 MET cc_start: 0.7189 (mmt) cc_final: 0.6674 (mmp) REVERT: C 490 LEU cc_start: 0.4487 (OUTLIER) cc_final: 0.3883 (pt) REVERT: C 512 GLU cc_start: 0.4388 (OUTLIER) cc_final: 0.4179 (mp0) REVERT: C 578 PHE cc_start: 0.1645 (OUTLIER) cc_final: 0.0602 (p90) REVERT: C 816 MET cc_start: 0.8556 (mmm) cc_final: 0.8139 (mmm) REVERT: D 23 LYS cc_start: 0.8047 (mmtp) cc_final: 0.7793 (mmtt) REVERT: D 106 MET cc_start: 0.8781 (mmm) cc_final: 0.7893 (mmm) REVERT: A 391 MET cc_start: 0.7304 (mmp) cc_final: 0.7016 (mmp) REVERT: A 396 GLN cc_start: 0.6757 (tm-30) cc_final: 0.6339 (pt0) REVERT: A 490 LEU cc_start: 0.3862 (OUTLIER) cc_final: 0.3289 (pt) REVERT: A 493 HIS cc_start: 0.3911 (OUTLIER) cc_final: 0.3499 (m-70) REVERT: A 512 GLU cc_start: 0.4360 (OUTLIER) cc_final: 0.4076 (mp0) REVERT: A 578 PHE cc_start: 0.1883 (OUTLIER) cc_final: 0.0838 (p90) REVERT: A 615 MET cc_start: 0.6474 (ttp) cc_final: 0.6184 (ttp) REVERT: A 734 MET cc_start: 0.8132 (mmm) cc_final: 0.7868 (mmm) REVERT: A 894 TRP cc_start: 0.6513 (OUTLIER) cc_final: 0.6273 (m100) REVERT: B 29 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7942 (m) REVERT: B 85 ILE cc_start: 0.8543 (mm) cc_final: 0.8053 (tp) REVERT: B 106 MET cc_start: 0.8776 (mmm) cc_final: 0.8192 (mtp) REVERT: B 203 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7870 (mp10) outliers start: 33 outliers final: 22 residues processed: 162 average time/residue: 0.3227 time to fit residues: 85.4042 Evaluate side-chains 163 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 2.507 ------------------------------------------------------------------------------- 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 186 VAL 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 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 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 121 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 493 HIS 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 719 VAL Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain B residue 29 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 71 optimal weight: 0.2980 chunk 200 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 192 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 GLN ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.143847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.099660 restraints weight = 41250.083| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.23 r_work: 0.3034 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23096 Z= 0.096 Angle : 0.522 8.175 31216 Z= 0.251 Chirality : 0.042 0.438 3514 Planarity : 0.004 0.058 3808 Dihedral : 12.397 122.678 5080 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.33 % Allowed : 15.68 % Favored : 82.99 % 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: 1.15 (0.17), residues: 2642 helix: 2.22 (0.15), residues: 1196 sheet: 0.02 (0.29), residues: 314 loop : -0.61 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 89 HIS 0.006 0.001 HIS A 557 PHE 0.013 0.001 PHE A 306 TYR 0.015 0.001 TYR A 869 ARG 0.003 0.000 ARG C 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 8) link_NAG-ASN : angle 1.38716 ( 24) link_ALPHA1-6 : bond 0.00726 ( 4) link_ALPHA1-6 : angle 1.45525 ( 12) link_BETA1-2 : bond 0.00438 ( 2) link_BETA1-2 : angle 4.87541 ( 6) link_BETA1-4 : bond 0.00536 ( 14) link_BETA1-4 : angle 2.39330 ( 42) link_ALPHA1-3 : bond 0.00837 ( 6) link_ALPHA1-3 : angle 3.23691 ( 18) hydrogen bonds : bond 0.03899 ( 983) hydrogen bonds : angle 3.80732 ( 2925) link_BETA1-6 : bond 0.00178 ( 4) link_BETA1-6 : angle 1.47722 ( 12) covalent geometry : bond 0.00205 (23058) covalent geometry : angle 0.50214 (31102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13075.92 seconds wall clock time: 226 minutes 49.78 seconds (13609.78 seconds total)