Starting phenix.real_space_refine on Sun Aug 24 21:41:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y45_33601/08_2025/7y45_33601.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y45_33601/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/7y45_33601/08_2025/7y45_33601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y45_33601/08_2025/7y45_33601.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y45_33601/08_2025/7y45_33601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y45_33601/08_2025/7y45_33601.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22638 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" 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: "D" 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: "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: "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: "C" 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: "D" 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: "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: "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: A, B, G, K, L, M, N Time building chain proxies: 10.47, per 1000 atoms: 0.46 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=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 150 " distance=2.04 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 215 " - pdb=" SG CYS D 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 150 " distance=2.04 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 215 " - pdb=" SG CYS B 278 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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: 1.88 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.2 microseconds 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: 0.75 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: 4.29 Time building geometry restraints manager: 2.58 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: 13616 27.86 - 55.71: 1093 55.71 - 83.57: 161 83.57 - 111.42: 58 111.42 - 139.28: 38 Dihedral angle restraints: 14966 sinusoidal: 7310 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 14963 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: 2.27 - 2.84: 7005 2.84 - 3.42: 22781 3.42 - 3.99: 40017 3.99 - 4.57: 55290 4.57 - 5.14: 83460 Nonbonded interactions: 208553 Sorted by model distance: nonbonded pdb=" N ASN C 127 " pdb=" OD1 ASN C 127 " model vdw 2.266 3.120 nonbonded pdb=" N ASN A 127 " pdb=" OD1 ASN A 127 " model vdw 2.266 3.120 nonbonded pdb=" O2 PCW C1112 " pdb=" O3 PCW C1112 " model vdw 2.291 2.432 nonbonded pdb=" O2 PCW A1112 " pdb=" O3 PCW A1112 " model vdw 2.291 2.432 nonbonded pdb=" O2 PCW A1111 " pdb=" O3 PCW A1111 " model vdw 2.297 2.432 ... (remaining 208548 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: 0.04 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' } ncs_group { reference = chain 'D' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'N' } 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 25.350 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.460 ------------------------------------------------------------------------------- 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 23102 Z= 0.550 Angle : 1.500 17.574 31228 Z= 0.752 Chirality : 0.068 0.375 3514 Planarity : 0.009 0.141 3808 Dihedral : 20.374 139.275 10036 Min Nonbonded Distance : 2.266 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG B 137 TYR 0.035 0.002 TYR B 206 PHE 0.030 0.003 PHE A 923 TRP 0.026 0.002 TRP B 156 HIS 0.008 0.002 HIS A 919 Details of bonding type rmsd covalent geometry : bond 0.01089 (23058) covalent geometry : angle 1.47751 (31102) SS BOND : bond 0.00336 ( 6) SS BOND : angle 2.09470 ( 12) hydrogen bonds : bond 0.17918 ( 983) hydrogen bonds : angle 7.38773 ( 2925) link_ALPHA1-3 : bond 0.00771 ( 6) link_ALPHA1-3 : angle 3.12893 ( 18) 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_BETA1-6 : bond 0.00251 ( 4) link_BETA1-6 : angle 1.25254 ( 12) link_NAG-ASN : bond 0.01600 ( 8) link_NAG-ASN : angle 3.86327 ( 24) *********************** 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 : 0.686 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: 0.4258 (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: 0.4232 (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: 0.4354 (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: 0.6263 (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: 0.7552 (p) REVERT: B 106 MET cc_start: 0.8454 (mmm) cc_final: 0.8185 (mmm) REVERT: B 142 ASP cc_start: 0.7097 (t0) cc_final: 0.6750 (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: 0.8254 (m-10) REVERT: B 272 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7548 (ttm) outliers start: 254 outliers final: 40 residues processed: 516 average time/residue: 0.1806 time to fit residues: 135.2323 Evaluate side-chains 200 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 144 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 197 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 638 ASN C 656 ASN 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 638 ASN A 696 GLN A 720 ASN A 744 GLN A 904 GLN A1019 GLN B 258 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.146947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.102045 restraints weight = 41239.284| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.29 r_work: 0.3075 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23102 Z= 0.177 Angle : 0.737 11.082 31228 Z= 0.360 Chirality : 0.048 0.430 3514 Planarity : 0.006 0.073 3808 Dihedral : 17.511 135.596 5189 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.62 % Allowed : 12.90 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.15), residues: 2642 helix: 0.01 (0.15), residues: 1206 sheet: -2.08 (0.29), residues: 262 loop : -1.75 (0.16), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 445 TYR 0.018 0.002 TYR C 488 PHE 0.023 0.002 PHE C 393 TRP 0.030 0.002 TRP C 89 HIS 0.007 0.002 HIS A 620 Details of bonding type rmsd covalent geometry : bond 0.00399 (23058) covalent geometry : angle 0.71092 (31102) SS BOND : bond 0.00130 ( 6) SS BOND : angle 1.20172 ( 12) hydrogen bonds : bond 0.06376 ( 983) hydrogen bonds : angle 5.12730 ( 2925) link_ALPHA1-3 : bond 0.01003 ( 6) link_ALPHA1-3 : angle 3.74052 ( 18) link_ALPHA1-6 : bond 0.00690 ( 4) link_ALPHA1-6 : angle 2.20135 ( 12) link_BETA1-2 : bond 0.00737 ( 2) link_BETA1-2 : angle 4.80434 ( 6) link_BETA1-4 : bond 0.01116 ( 14) link_BETA1-4 : angle 3.90366 ( 42) link_BETA1-6 : bond 0.00574 ( 4) link_BETA1-6 : angle 1.69472 ( 12) link_NAG-ASN : bond 0.00763 ( 8) link_NAG-ASN : angle 2.20101 ( 24) *********************** 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 251 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 169 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7291 (mmmm) REVERT: C 173 ARG cc_start: 0.3158 (mtt180) cc_final: 0.2310 (ptt180) REVERT: C 218 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6348 (pp) REVERT: C 324 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9054 (tp) REVERT: C 816 MET cc_start: 0.8378 (mmm) cc_final: 0.8038 (mmm) REVERT: C 952 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7715 (mptt) REVERT: D 14 LYS cc_start: 0.7253 (tptt) cc_final: 0.6558 (mmpt) REVERT: D 106 MET cc_start: 0.8751 (mmm) cc_final: 0.8511 (mmm) REVERT: D 142 ASP cc_start: 0.7806 (t0) cc_final: 0.7402 (t0) REVERT: A 41 MET cc_start: 0.5873 (ppp) cc_final: 0.5429 (ptm) REVERT: A 42 ASP cc_start: 0.4954 (OUTLIER) cc_final: 0.4592 (t70) REVERT: A 153 LYS cc_start: 0.7645 (mmmt) cc_final: 0.7173 (mmmm) REVERT: A 164 MET cc_start: 0.7778 (mmp) cc_final: 0.7549 (ttm) REVERT: A 173 ARG cc_start: 0.3398 (mtt180) cc_final: 0.2679 (ptt180) REVERT: A 396 GLN cc_start: 0.6581 (tp40) cc_final: 0.5879 (mt0) REVERT: A 571 PHE cc_start: 0.3979 (OUTLIER) cc_final: 0.3776 (m-80) REVERT: A 816 MET cc_start: 0.8492 (mmm) cc_final: 0.8246 (mmm) REVERT: A 832 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8484 (tpt) REVERT: B 23 LYS cc_start: 0.8619 (mttt) cc_final: 0.8067 (mmtm) REVERT: B 106 MET cc_start: 0.8790 (mmm) cc_final: 0.8522 (mmm) REVERT: B 201 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8488 (pm20) REVERT: B 203 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7408 (mp10) outliers start: 82 outliers final: 41 residues processed: 245 average time/residue: 0.1617 time to fit residues: 59.9287 Evaluate side-chains 186 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 137 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 454 SER Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 655 VAL 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 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 61 THR 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 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 571 PHE 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 834 ARG Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE 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 81 optimal weight: 7.9990 chunk 203 optimal weight: 0.9980 chunk 250 optimal weight: 0.0870 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 145 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 398 HIS C 489 GLN ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 HIS ** C 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 708 GLN D 56 GLN A 489 GLN B 56 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.144480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.099943 restraints weight = 41187.467| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.12 r_work: 0.3002 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 23102 Z= 0.160 Angle : 0.637 10.237 31228 Z= 0.312 Chirality : 0.045 0.415 3514 Planarity : 0.005 0.061 3808 Dihedral : 16.199 121.413 5117 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.61 % Allowed : 14.00 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.16), residues: 2642 helix: 0.88 (0.15), residues: 1230 sheet: -1.53 (0.30), residues: 262 loop : -1.17 (0.17), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 889 TYR 0.028 0.001 TYR A 131 PHE 0.018 0.002 PHE A 923 TRP 0.020 0.002 TRP C 89 HIS 0.006 0.001 HIS C 398 Details of bonding type rmsd covalent geometry : bond 0.00366 (23058) covalent geometry : angle 0.61229 (31102) SS BOND : bond 0.00157 ( 6) SS BOND : angle 1.37368 ( 12) hydrogen bonds : bond 0.05821 ( 983) hydrogen bonds : angle 4.55196 ( 2925) link_ALPHA1-3 : bond 0.01096 ( 6) link_ALPHA1-3 : angle 3.20162 ( 18) link_ALPHA1-6 : bond 0.00853 ( 4) link_ALPHA1-6 : angle 1.59368 ( 12) link_BETA1-2 : bond 0.00651 ( 2) link_BETA1-2 : angle 4.47587 ( 6) link_BETA1-4 : bond 0.00794 ( 14) link_BETA1-4 : angle 3.60313 ( 42) link_BETA1-6 : bond 0.00374 ( 4) link_BETA1-6 : angle 1.51015 ( 12) link_NAG-ASN : bond 0.00647 ( 8) link_NAG-ASN : angle 1.78240 ( 24) *********************** 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 208 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 149 time to evaluate : 0.671 Fit side-chains REVERT: C 164 MET cc_start: 0.7280 (ttm) cc_final: 0.6462 (tmm) REVERT: C 173 ARG cc_start: 0.3149 (mtt180) cc_final: 0.2353 (ptt180) REVERT: C 267 MET cc_start: 0.6104 (ppp) cc_final: 0.5852 (ppp) REVERT: C 277 LEU cc_start: 0.7774 (mm) cc_final: 0.7565 (tp) REVERT: C 391 MET cc_start: 0.6467 (mpp) cc_final: 0.6235 (mmt) REVERT: C 493 HIS cc_start: 0.4111 (OUTLIER) cc_final: 0.3405 (m-70) REVERT: C 589 MET cc_start: 0.7985 (mmm) cc_final: 0.7658 (mmp) REVERT: C 816 MET cc_start: 0.8494 (mmm) cc_final: 0.8091 (mmm) REVERT: D 14 LYS cc_start: 0.7526 (tptt) cc_final: 0.6642 (mmpt) REVERT: D 106 MET cc_start: 0.8703 (mmm) cc_final: 0.8402 (mmm) REVERT: D 142 ASP cc_start: 0.8037 (t0) cc_final: 0.7644 (t0) REVERT: A 41 MET cc_start: 0.5468 (ppp) cc_final: 0.5204 (ptm) REVERT: A 173 ARG cc_start: 0.3249 (mtt180) cc_final: 0.2484 (ptt180) REVERT: A 267 MET cc_start: 0.6097 (ppp) cc_final: 0.5773 (ppp) REVERT: A 396 GLN cc_start: 0.6526 (tp40) cc_final: 0.5864 (mt0) REVERT: A 493 HIS cc_start: 0.4084 (OUTLIER) cc_final: 0.3380 (m-70) REVERT: A 816 MET cc_start: 0.8505 (mmm) cc_final: 0.8188 (mmm) REVERT: B 23 LYS cc_start: 0.8676 (mttt) cc_final: 0.8054 (mmtm) REVERT: B 106 MET cc_start: 0.8832 (mmm) cc_final: 0.8548 (mmm) REVERT: B 110 MET cc_start: 0.8741 (mmp) cc_final: 0.8518 (mmt) REVERT: B 201 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8575 (pm20) REVERT: B 203 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7733 (mp10) outliers start: 59 outliers final: 35 residues processed: 203 average time/residue: 0.1446 time to fit residues: 45.4734 Evaluate side-chains 170 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 493 HIS 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 719 VAL 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 140 LEU 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 121 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain A residue 921 SER 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 104 LYS Chi-restraints excluded: chain B residue 140 LEU 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 241 optimal weight: 0.8980 chunk 37 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 68 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 123 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 540 ASN D 56 GLN D 243 GLN A 557 HIS B 243 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.142204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.097325 restraints weight = 41025.520| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.31 r_work: 0.2954 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23102 Z= 0.183 Angle : 0.634 9.981 31228 Z= 0.308 Chirality : 0.046 0.421 3514 Planarity : 0.005 0.061 3808 Dihedral : 15.588 119.444 5086 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.27 % Allowed : 14.05 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.16), residues: 2642 helix: 1.09 (0.15), residues: 1232 sheet: -0.98 (0.28), residues: 306 loop : -1.02 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 889 TYR 0.018 0.002 TYR B 44 PHE 0.021 0.002 PHE A 923 TRP 0.015 0.002 TRP C 89 HIS 0.006 0.001 HIS C 557 Details of bonding type rmsd covalent geometry : bond 0.00440 (23058) covalent geometry : angle 0.60947 (31102) SS BOND : bond 0.00409 ( 6) SS BOND : angle 1.45285 ( 12) hydrogen bonds : bond 0.05965 ( 983) hydrogen bonds : angle 4.43117 ( 2925) link_ALPHA1-3 : bond 0.00943 ( 6) link_ALPHA1-3 : angle 3.25704 ( 18) link_ALPHA1-6 : bond 0.00848 ( 4) link_ALPHA1-6 : angle 1.73212 ( 12) link_BETA1-2 : bond 0.00549 ( 2) link_BETA1-2 : angle 4.59533 ( 6) link_BETA1-4 : bond 0.00662 ( 14) link_BETA1-4 : angle 3.52071 ( 42) link_BETA1-6 : bond 0.00250 ( 4) link_BETA1-6 : angle 1.62406 ( 12) link_NAG-ASN : bond 0.00606 ( 8) link_NAG-ASN : angle 1.62484 ( 24) *********************** 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 210 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 136 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: C 164 MET cc_start: 0.6775 (ttm) cc_final: 0.6177 (tmm) REVERT: C 173 ARG cc_start: 0.3155 (mtt180) cc_final: 0.2370 (ptt180) REVERT: C 267 MET cc_start: 0.6163 (ppp) cc_final: 0.5922 (ppp) REVERT: C 277 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7629 (tp) REVERT: C 291 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8432 (p90) REVERT: C 493 HIS cc_start: 0.4079 (OUTLIER) cc_final: 0.3441 (m-70) REVERT: C 512 GLU cc_start: 0.5167 (OUTLIER) cc_final: 0.4518 (mp0) REVERT: C 534 MET cc_start: 0.4245 (OUTLIER) cc_final: 0.3889 (mtp) REVERT: C 816 MET cc_start: 0.8441 (mmm) cc_final: 0.7982 (mmm) REVERT: D 142 ASP cc_start: 0.8086 (t0) cc_final: 0.7676 (t0) REVERT: A 173 ARG cc_start: 0.3249 (mtt180) cc_final: 0.2550 (ptt180) REVERT: A 493 HIS cc_start: 0.4026 (OUTLIER) cc_final: 0.3335 (m-70) REVERT: A 512 GLU cc_start: 0.4370 (OUTLIER) cc_final: 0.4134 (mp0) REVERT: A 816 MET cc_start: 0.8466 (mmm) cc_final: 0.8060 (mmm) REVERT: B 23 LYS cc_start: 0.8692 (mttt) cc_final: 0.8070 (mmtm) REVERT: B 106 MET cc_start: 0.8801 (mmm) cc_final: 0.7811 (mmm) REVERT: B 110 MET cc_start: 0.8863 (mmp) cc_final: 0.8591 (mmt) REVERT: B 203 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7796 (mp10) outliers start: 74 outliers final: 40 residues processed: 198 average time/residue: 0.1412 time to fit residues: 44.3667 Evaluate side-chains 177 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 129 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 277 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 515 LEU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 548 LEU 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 935 ILE Chi-restraints excluded: chain C residue 986 SER Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 655 VAL 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 834 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 272 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 126 optimal weight: 5.9990 chunk 250 optimal weight: 0.0030 chunk 229 optimal weight: 0.7980 chunk 240 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 203 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 216 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 63 optimal weight: 30.0000 chunk 3 optimal weight: 30.0000 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 708 GLN A 557 HIS A 708 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.144081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.098886 restraints weight = 40818.717| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 3.35 r_work: 0.3002 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23102 Z= 0.109 Angle : 0.553 8.669 31228 Z= 0.267 Chirality : 0.043 0.447 3514 Planarity : 0.004 0.059 3808 Dihedral : 14.819 121.110 5085 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.16 % Allowed : 15.28 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.16), residues: 2642 helix: 1.44 (0.15), residues: 1234 sheet: -0.70 (0.29), residues: 310 loop : -0.87 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 889 TYR 0.014 0.001 TYR C 869 PHE 0.024 0.001 PHE A 393 TRP 0.015 0.001 TRP C 89 HIS 0.017 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00228 (23058) covalent geometry : angle 0.52810 (31102) SS BOND : bond 0.00128 ( 6) SS BOND : angle 0.90894 ( 12) hydrogen bonds : bond 0.04743 ( 983) hydrogen bonds : angle 4.17685 ( 2925) link_ALPHA1-3 : bond 0.01038 ( 6) link_ALPHA1-3 : angle 3.44228 ( 18) link_ALPHA1-6 : bond 0.00775 ( 4) link_ALPHA1-6 : angle 1.68438 ( 12) link_BETA1-2 : bond 0.00570 ( 2) link_BETA1-2 : angle 4.74193 ( 6) link_BETA1-4 : bond 0.00629 ( 14) link_BETA1-4 : angle 3.09404 ( 42) link_BETA1-6 : bond 0.00194 ( 4) link_BETA1-6 : angle 1.52885 ( 12) link_NAG-ASN : bond 0.00652 ( 8) link_NAG-ASN : angle 1.60561 ( 24) *********************** 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 187 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 138 time to evaluate : 0.802 Fit side-chains REVERT: C 164 MET cc_start: 0.7052 (ttm) cc_final: 0.6485 (tmm) REVERT: C 173 ARG cc_start: 0.3196 (mtt180) cc_final: 0.2404 (ptt180) REVERT: C 291 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8345 (p90) REVERT: C 391 MET cc_start: 0.7266 (mmt) cc_final: 0.6766 (mmp) REVERT: C 490 LEU cc_start: 0.4108 (OUTLIER) cc_final: 0.3433 (pt) REVERT: C 493 HIS cc_start: 0.4030 (OUTLIER) cc_final: 0.3262 (m-70) REVERT: C 534 MET cc_start: 0.4092 (OUTLIER) cc_final: 0.3718 (mtp) REVERT: C 544 GLU cc_start: 0.6952 (tt0) cc_final: 0.6062 (tm-30) REVERT: C 578 PHE cc_start: 0.1681 (OUTLIER) cc_final: 0.0747 (p90) REVERT: C 816 MET cc_start: 0.8514 (mmm) cc_final: 0.8120 (mmm) REVERT: D 23 LYS cc_start: 0.7845 (mmtp) cc_final: 0.7614 (mmtm) REVERT: D 106 MET cc_start: 0.8809 (mmm) cc_final: 0.8339 (mmm) REVERT: D 121 ASN cc_start: 0.7316 (m110) cc_final: 0.7004 (m-40) REVERT: D 142 ASP cc_start: 0.8222 (t0) cc_final: 0.7857 (t0) REVERT: A 173 ARG cc_start: 0.3244 (mtt180) cc_final: 0.2532 (ptt180) REVERT: A 391 MET cc_start: 0.7112 (mmp) cc_final: 0.6819 (mmp) REVERT: A 493 HIS cc_start: 0.4023 (OUTLIER) cc_final: 0.3399 (m-70) REVERT: A 578 PHE cc_start: 0.2109 (OUTLIER) cc_final: 0.0970 (p90) REVERT: A 816 MET cc_start: 0.8552 (mmm) cc_final: 0.8189 (mmm) REVERT: B 23 LYS cc_start: 0.8711 (mttt) cc_final: 0.8010 (mmtm) REVERT: B 203 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7845 (mp10) outliers start: 49 outliers final: 24 residues processed: 179 average time/residue: 0.1389 time to fit residues: 39.2058 Evaluate side-chains 162 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 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 515 LEU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 578 PHE 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 B residue 79 SER Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 272 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 225 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 216 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 200 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 187 optimal weight: 50.0000 chunk 232 optimal weight: 0.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 GLN C 708 GLN ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 HIS ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.141970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.087254 restraints weight = 40979.801| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.88 r_work: 0.2945 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23102 Z= 0.162 Angle : 0.592 8.544 31228 Z= 0.287 Chirality : 0.045 0.442 3514 Planarity : 0.005 0.067 3808 Dihedral : 14.609 123.888 5084 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.43 % Allowed : 14.84 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.16), residues: 2642 helix: 1.40 (0.15), residues: 1248 sheet: -0.56 (0.29), residues: 310 loop : -0.88 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 707 TYR 0.017 0.001 TYR C 869 PHE 0.020 0.002 PHE A 923 TRP 0.015 0.001 TRP C 89 HIS 0.009 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00390 (23058) covalent geometry : angle 0.56892 (31102) SS BOND : bond 0.00397 ( 6) SS BOND : angle 1.13336 ( 12) hydrogen bonds : bond 0.05499 ( 983) hydrogen bonds : angle 4.23286 ( 2925) link_ALPHA1-3 : bond 0.00952 ( 6) link_ALPHA1-3 : angle 3.29651 ( 18) link_ALPHA1-6 : bond 0.00863 ( 4) link_ALPHA1-6 : angle 1.62564 ( 12) link_BETA1-2 : bond 0.00460 ( 2) link_BETA1-2 : angle 4.88277 ( 6) link_BETA1-4 : bond 0.00581 ( 14) link_BETA1-4 : angle 3.12683 ( 42) link_BETA1-6 : bond 0.00168 ( 4) link_BETA1-6 : angle 1.57878 ( 12) link_NAG-ASN : bond 0.00620 ( 8) link_NAG-ASN : angle 1.54949 ( 24) *********************** 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 188 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 133 time to evaluate : 0.737 Fit side-chains REVERT: C 164 MET cc_start: 0.6898 (ttm) cc_final: 0.6493 (tmm) REVERT: C 173 ARG cc_start: 0.3198 (mtt180) cc_final: 0.2402 (ptt180) REVERT: C 267 MET cc_start: 0.6060 (ppp) cc_final: 0.5831 (ppp) REVERT: C 277 LEU cc_start: 0.7973 (tp) cc_final: 0.7572 (tt) REVERT: C 291 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8484 (p90) REVERT: C 386 MET cc_start: 0.5106 (ptp) cc_final: 0.4773 (ptp) REVERT: C 391 MET cc_start: 0.7138 (mmt) cc_final: 0.6633 (mmp) REVERT: C 490 LEU cc_start: 0.4063 (OUTLIER) cc_final: 0.3754 (pt) REVERT: C 493 HIS cc_start: 0.3924 (OUTLIER) cc_final: 0.3358 (m-70) REVERT: C 512 GLU cc_start: 0.4624 (OUTLIER) cc_final: 0.4380 (mp0) REVERT: C 534 MET cc_start: 0.3926 (OUTLIER) cc_final: 0.3693 (mmm) REVERT: C 544 GLU cc_start: 0.7031 (tt0) cc_final: 0.6145 (tm-30) REVERT: C 816 MET cc_start: 0.8489 (mmm) cc_final: 0.8064 (mmm) REVERT: D 23 LYS cc_start: 0.7889 (mmtp) cc_final: 0.7598 (mmtt) REVERT: D 106 MET cc_start: 0.8846 (mmm) cc_final: 0.8406 (mtp) REVERT: D 121 ASN cc_start: 0.7382 (m110) cc_final: 0.7150 (m-40) REVERT: A 173 ARG cc_start: 0.3139 (mtt180) cc_final: 0.2431 (ptt180) REVERT: A 490 LEU cc_start: 0.3980 (OUTLIER) cc_final: 0.3367 (pt) REVERT: A 493 HIS cc_start: 0.3945 (OUTLIER) cc_final: 0.3413 (m-70) REVERT: A 512 GLU cc_start: 0.4345 (OUTLIER) cc_final: 0.3985 (mp0) REVERT: A 578 PHE cc_start: 0.2081 (OUTLIER) cc_final: 0.1028 (p90) REVERT: A 816 MET cc_start: 0.8557 (mmm) cc_final: 0.8108 (mmm) REVERT: A 886 LYS cc_start: 0.8849 (mtpp) cc_final: 0.8587 (ttmm) REVERT: B 23 LYS cc_start: 0.8698 (mttt) cc_final: 0.8040 (mmtm) REVERT: B 106 MET cc_start: 0.8861 (mmm) cc_final: 0.8440 (mmm) REVERT: B 203 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7786 (mp10) outliers start: 55 outliers final: 33 residues processed: 178 average time/residue: 0.1337 time to fit residues: 38.0281 Evaluate side-chains 171 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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 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 534 MET Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 272 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 46 optimal weight: 40.0000 chunk 181 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 chunk 126 optimal weight: 2.9990 chunk 137 optimal weight: 30.0000 chunk 196 optimal weight: 0.0010 chunk 185 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 HIS ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** 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 = 0.4093 r_free = 0.4093 target = 0.141943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.086763 restraints weight = 40946.219| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.94 r_work: 0.2948 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23102 Z= 0.146 Angle : 0.571 8.281 31228 Z= 0.277 Chirality : 0.044 0.441 3514 Planarity : 0.004 0.061 3808 Dihedral : 14.188 127.383 5082 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.87 % Allowed : 14.89 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.16), residues: 2642 helix: 1.51 (0.15), residues: 1250 sheet: -0.43 (0.29), residues: 310 loop : -0.82 (0.17), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 889 TYR 0.015 0.001 TYR C 869 PHE 0.016 0.001 PHE C1007 TRP 0.020 0.001 TRP C 89 HIS 0.010 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00347 (23058) covalent geometry : angle 0.54812 (31102) SS BOND : bond 0.00338 ( 6) SS BOND : angle 1.01640 ( 12) hydrogen bonds : bond 0.05210 ( 983) hydrogen bonds : angle 4.15949 ( 2925) link_ALPHA1-3 : bond 0.00929 ( 6) link_ALPHA1-3 : angle 3.29938 ( 18) link_ALPHA1-6 : bond 0.00904 ( 4) link_ALPHA1-6 : angle 1.54993 ( 12) link_BETA1-2 : bond 0.00490 ( 2) link_BETA1-2 : angle 5.01745 ( 6) link_BETA1-4 : bond 0.00540 ( 14) link_BETA1-4 : angle 2.88885 ( 42) link_BETA1-6 : bond 0.00171 ( 4) link_BETA1-6 : angle 1.57575 ( 12) link_NAG-ASN : bond 0.00503 ( 8) link_NAG-ASN : angle 1.49465 ( 24) *********************** 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 193 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 128 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: C 164 MET cc_start: 0.6846 (ttm) cc_final: 0.6592 (tmm) REVERT: C 173 ARG cc_start: 0.3492 (mtt180) cc_final: 0.2660 (ptt180) REVERT: C 267 MET cc_start: 0.6187 (ppp) cc_final: 0.5950 (ppp) REVERT: C 291 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8471 (p90) REVERT: C 391 MET cc_start: 0.7131 (mmt) cc_final: 0.6903 (mmt) REVERT: C 490 LEU cc_start: 0.4048 (OUTLIER) cc_final: 0.3477 (pt) REVERT: C 493 HIS cc_start: 0.3944 (OUTLIER) cc_final: 0.3410 (m-70) REVERT: C 512 GLU cc_start: 0.4458 (OUTLIER) cc_final: 0.4202 (mp0) REVERT: C 534 MET cc_start: 0.3700 (OUTLIER) cc_final: 0.3460 (mmm) REVERT: C 544 GLU cc_start: 0.7086 (tt0) cc_final: 0.6241 (tm-30) REVERT: C 578 PHE cc_start: 0.1721 (OUTLIER) cc_final: 0.0538 (p90) REVERT: D 23 LYS cc_start: 0.8020 (mmtp) cc_final: 0.7745 (mmtt) REVERT: D 106 MET cc_start: 0.8840 (mmm) cc_final: 0.8411 (mtp) REVERT: A 490 LEU cc_start: 0.4112 (OUTLIER) cc_final: 0.3606 (pt) REVERT: A 493 HIS cc_start: 0.3888 (OUTLIER) cc_final: 0.3376 (m-70) REVERT: A 512 GLU cc_start: 0.4391 (OUTLIER) cc_final: 0.4182 (mp0) REVERT: A 578 PHE cc_start: 0.1878 (OUTLIER) cc_final: 0.1006 (p90) REVERT: B 106 MET cc_start: 0.8866 (mmm) cc_final: 0.8355 (mtp) REVERT: B 203 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7791 (mp10) outliers start: 65 outliers final: 37 residues processed: 185 average time/residue: 0.1236 time to fit residues: 36.0830 Evaluate side-chains 172 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 124 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 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 515 LEU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 440 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 608 SER 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 79 SER Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 213 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 97 optimal weight: 0.7980 chunk 216 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 250 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** 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 = 0.4109 r_free = 0.4109 target = 0.143338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.098412 restraints weight = 40651.378| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.83 r_work: 0.3002 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23102 Z= 0.105 Angle : 0.540 8.528 31228 Z= 0.260 Chirality : 0.043 0.440 3514 Planarity : 0.004 0.060 3808 Dihedral : 13.510 126.117 5082 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.12 % Allowed : 15.24 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.16), residues: 2642 helix: 1.81 (0.15), residues: 1234 sheet: -0.28 (0.29), residues: 308 loop : -0.71 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 517 TYR 0.015 0.001 TYR C 869 PHE 0.018 0.001 PHE A 393 TRP 0.029 0.001 TRP C 89 HIS 0.009 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00231 (23058) covalent geometry : angle 0.51801 (31102) SS BOND : bond 0.00184 ( 6) SS BOND : angle 0.84419 ( 12) hydrogen bonds : bond 0.04373 ( 983) hydrogen bonds : angle 3.97926 ( 2925) link_ALPHA1-3 : bond 0.00918 ( 6) link_ALPHA1-3 : angle 3.34532 ( 18) link_ALPHA1-6 : bond 0.00776 ( 4) link_ALPHA1-6 : angle 1.49445 ( 12) link_BETA1-2 : bond 0.00467 ( 2) link_BETA1-2 : angle 4.98078 ( 6) link_BETA1-4 : bond 0.00546 ( 14) link_BETA1-4 : angle 2.66317 ( 42) link_BETA1-6 : bond 0.00132 ( 4) link_BETA1-6 : angle 1.51471 ( 12) link_NAG-ASN : bond 0.00559 ( 8) link_NAG-ASN : angle 1.34601 ( 24) *********************** 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 183 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: C 164 MET cc_start: 0.6871 (ttm) cc_final: 0.6620 (tmm) REVERT: C 173 ARG cc_start: 0.3608 (mtt180) cc_final: 0.2754 (ptt180) REVERT: C 267 MET cc_start: 0.6197 (ppp) cc_final: 0.5997 (ppp) REVERT: C 277 LEU cc_start: 0.8295 (tp) cc_final: 0.7974 (tt) REVERT: C 291 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8306 (p90) REVERT: C 386 MET cc_start: 0.5489 (ptp) cc_final: 0.5121 (ptp) REVERT: C 490 LEU cc_start: 0.4071 (OUTLIER) cc_final: 0.3510 (pt) REVERT: C 493 HIS cc_start: 0.3897 (OUTLIER) cc_final: 0.3424 (m-70) REVERT: C 512 GLU cc_start: 0.4484 (OUTLIER) cc_final: 0.4227 (mp0) REVERT: C 544 GLU cc_start: 0.7078 (tt0) cc_final: 0.6822 (pt0) REVERT: C 578 PHE cc_start: 0.1687 (OUTLIER) cc_final: 0.0556 (p90) REVERT: C 589 MET cc_start: 0.7779 (mmm) cc_final: 0.7132 (mtm) REVERT: D 23 LYS cc_start: 0.7990 (mmtp) cc_final: 0.7739 (mmtt) REVERT: D 85 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8082 (tp) REVERT: D 106 MET cc_start: 0.8708 (mmm) cc_final: 0.8229 (mtp) REVERT: D 234 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8930 (tp) REVERT: A 230 GLU cc_start: 0.7809 (mp0) cc_final: 0.6954 (tt0) REVERT: A 490 LEU cc_start: 0.3839 (OUTLIER) cc_final: 0.3261 (pt) REVERT: A 493 HIS cc_start: 0.3995 (OUTLIER) cc_final: 0.3474 (m-70) REVERT: A 512 GLU cc_start: 0.4414 (OUTLIER) cc_final: 0.4204 (mp0) REVERT: A 578 PHE cc_start: 0.1745 (OUTLIER) cc_final: 0.0762 (p90) REVERT: A 615 MET cc_start: 0.5949 (ttp) cc_final: 0.5640 (ttp) REVERT: A 816 MET cc_start: 0.8435 (mmm) cc_final: 0.7968 (mmm) REVERT: B 106 MET cc_start: 0.8724 (mmm) cc_final: 0.7781 (mmm) REVERT: B 203 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7749 (mp10) outliers start: 48 outliers final: 22 residues processed: 171 average time/residue: 0.1363 time to fit residues: 36.7151 Evaluate side-chains 158 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LEU 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 490 LEU Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 272 MET 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 543 LEU 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 B residue 104 LYS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 201 GLU 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 199 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 201 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 207 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 230 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.141646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.096360 restraints weight = 40816.326| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.24 r_work: 0.2953 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23102 Z= 0.152 Angle : 0.576 8.238 31228 Z= 0.280 Chirality : 0.044 0.432 3514 Planarity : 0.004 0.072 3808 Dihedral : 13.495 127.016 5079 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.12 % Allowed : 15.24 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.16), residues: 2642 helix: 1.71 (0.15), residues: 1236 sheet: -0.08 (0.30), residues: 294 loop : -0.74 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 889 TYR 0.016 0.001 TYR A 869 PHE 0.019 0.002 PHE A 923 TRP 0.026 0.001 TRP C 89 HIS 0.009 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00364 (23058) covalent geometry : angle 0.55505 (31102) SS BOND : bond 0.00213 ( 6) SS BOND : angle 1.07603 ( 12) hydrogen bonds : bond 0.05154 ( 983) hydrogen bonds : angle 4.09383 ( 2925) link_ALPHA1-3 : bond 0.00828 ( 6) link_ALPHA1-3 : angle 3.20357 ( 18) link_ALPHA1-6 : bond 0.00782 ( 4) link_ALPHA1-6 : angle 1.47743 ( 12) link_BETA1-2 : bond 0.00395 ( 2) link_BETA1-2 : angle 4.99798 ( 6) link_BETA1-4 : bond 0.00512 ( 14) link_BETA1-4 : angle 2.71516 ( 42) link_BETA1-6 : bond 0.00163 ( 4) link_BETA1-6 : angle 1.57174 ( 12) link_NAG-ASN : bond 0.00464 ( 8) link_NAG-ASN : angle 1.45314 ( 24) *********************** 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 172 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 124 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: C 164 MET cc_start: 0.6872 (ttm) cc_final: 0.6618 (tmm) REVERT: C 173 ARG cc_start: 0.3579 (mtt180) cc_final: 0.2689 (ptt180) REVERT: C 277 LEU cc_start: 0.8314 (tp) cc_final: 0.7993 (tt) REVERT: C 291 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8463 (p90) REVERT: C 386 MET cc_start: 0.5331 (ptp) cc_final: 0.4933 (ptp) REVERT: C 490 LEU cc_start: 0.4029 (OUTLIER) cc_final: 0.3489 (pt) REVERT: C 493 HIS cc_start: 0.3686 (OUTLIER) cc_final: 0.3259 (m-70) REVERT: C 512 GLU cc_start: 0.4379 (OUTLIER) cc_final: 0.4171 (mp0) REVERT: C 544 GLU cc_start: 0.7072 (tt0) cc_final: 0.6818 (pt0) REVERT: C 578 PHE cc_start: 0.1614 (OUTLIER) cc_final: 0.0721 (p90) REVERT: C 589 MET cc_start: 0.7816 (mmm) cc_final: 0.7147 (mtm) REVERT: C 816 MET cc_start: 0.8422 (mmm) cc_final: 0.7954 (mmm) REVERT: D 23 LYS cc_start: 0.8009 (mmtp) cc_final: 0.7754 (mmtt) REVERT: D 106 MET cc_start: 0.8733 (mmm) cc_final: 0.8302 (mtp) REVERT: D 234 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8972 (tp) REVERT: A 230 GLU cc_start: 0.7885 (mp0) cc_final: 0.6980 (tt0) REVERT: A 391 MET cc_start: 0.7149 (mmp) cc_final: 0.6760 (mmp) REVERT: A 396 GLN cc_start: 0.6985 (tm-30) cc_final: 0.5973 (mp10) REVERT: A 490 LEU cc_start: 0.3955 (OUTLIER) cc_final: 0.3454 (pt) REVERT: A 493 HIS cc_start: 0.4023 (OUTLIER) cc_final: 0.3399 (m-70) REVERT: A 512 GLU cc_start: 0.4306 (OUTLIER) cc_final: 0.4027 (mp0) REVERT: A 578 PHE cc_start: 0.1734 (OUTLIER) cc_final: 0.0818 (p90) REVERT: A 816 MET cc_start: 0.8439 (mmm) cc_final: 0.7972 (mmm) REVERT: B 106 MET cc_start: 0.8701 (mmm) cc_final: 0.8110 (mtp) REVERT: B 203 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7732 (mp10) outliers start: 48 outliers final: 32 residues processed: 162 average time/residue: 0.1335 time to fit residues: 35.4127 Evaluate side-chains 163 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 120 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 512 GLU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 540 ASN 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 85 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 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 608 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 272 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 2 optimal weight: 30.0000 chunk 225 optimal weight: 3.9990 chunk 47 optimal weight: 30.0000 chunk 127 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 194 optimal weight: 0.0370 chunk 121 optimal weight: 5.9990 chunk 227 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 21 optimal weight: 20.0000 overall best weight: 1.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 GLN ** 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 = 0.4092 r_free = 0.4092 target = 0.141996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.097084 restraints weight = 40923.494| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.15 r_work: 0.2956 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23102 Z= 0.130 Angle : 0.558 8.566 31228 Z= 0.271 Chirality : 0.044 0.436 3514 Planarity : 0.004 0.061 3808 Dihedral : 13.172 127.623 5079 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.12 % Allowed : 15.24 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.16), residues: 2642 helix: 1.78 (0.15), residues: 1238 sheet: -0.34 (0.29), residues: 318 loop : -0.65 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 275 TYR 0.015 0.001 TYR C 869 PHE 0.020 0.001 PHE C 555 TRP 0.030 0.001 TRP C 89 HIS 0.008 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00303 (23058) covalent geometry : angle 0.53754 (31102) SS BOND : bond 0.00172 ( 6) SS BOND : angle 0.99112 ( 12) hydrogen bonds : bond 0.04848 ( 983) hydrogen bonds : angle 4.05577 ( 2925) link_ALPHA1-3 : bond 0.00826 ( 6) link_ALPHA1-3 : angle 3.17786 ( 18) link_ALPHA1-6 : bond 0.00741 ( 4) link_ALPHA1-6 : angle 1.40293 ( 12) link_BETA1-2 : bond 0.00406 ( 2) link_BETA1-2 : angle 5.07617 ( 6) link_BETA1-4 : bond 0.00504 ( 14) link_BETA1-4 : angle 2.55837 ( 42) link_BETA1-6 : bond 0.00130 ( 4) link_BETA1-6 : angle 1.52578 ( 12) link_NAG-ASN : bond 0.00486 ( 8) link_NAG-ASN : angle 1.41677 ( 24) ********************** 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 177 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 129 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: C 164 MET cc_start: 0.6933 (ttm) cc_final: 0.6714 (tmm) REVERT: C 173 ARG cc_start: 0.3686 (mtt180) cc_final: 0.2782 (ptt180) REVERT: C 267 MET cc_start: 0.6221 (ppp) cc_final: 0.6001 (ppp) REVERT: C 277 LEU cc_start: 0.8343 (tp) cc_final: 0.8026 (tt) REVERT: C 291 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8440 (p90) REVERT: C 386 MET cc_start: 0.5480 (ptp) cc_final: 0.5125 (ptp) REVERT: C 490 LEU cc_start: 0.4045 (OUTLIER) cc_final: 0.3561 (pt) REVERT: C 493 HIS cc_start: 0.3642 (OUTLIER) cc_final: 0.3237 (m-70) REVERT: C 544 GLU cc_start: 0.7086 (tt0) cc_final: 0.6815 (pt0) REVERT: C 578 PHE cc_start: 0.1502 (OUTLIER) cc_final: 0.0655 (p90) REVERT: C 589 MET cc_start: 0.7920 (mmm) cc_final: 0.6694 (mtm) REVERT: C 816 MET cc_start: 0.8419 (mmm) cc_final: 0.7960 (mmm) REVERT: D 23 LYS cc_start: 0.8030 (mmtp) cc_final: 0.7794 (mmtt) REVERT: D 106 MET cc_start: 0.8701 (mmm) cc_final: 0.8260 (mtp) REVERT: D 234 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8938 (tp) REVERT: A 230 GLU cc_start: 0.7833 (mp0) cc_final: 0.6992 (tt0) REVERT: A 490 LEU cc_start: 0.3960 (OUTLIER) cc_final: 0.3466 (pt) REVERT: A 512 GLU cc_start: 0.4290 (OUTLIER) cc_final: 0.4010 (mp0) REVERT: A 578 PHE cc_start: 0.1776 (OUTLIER) cc_final: 0.0830 (p90) REVERT: A 615 MET cc_start: 0.5938 (ttp) cc_final: 0.5645 (ttp) REVERT: A 816 MET cc_start: 0.8434 (mmm) cc_final: 0.7937 (mmm) REVERT: B 106 MET cc_start: 0.8729 (mmm) cc_final: 0.8145 (mtp) REVERT: B 203 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7803 (mp10) outliers start: 48 outliers final: 32 residues processed: 169 average time/residue: 0.1252 time to fit residues: 34.1663 Evaluate side-chains 166 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 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 540 ASN 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 85 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 272 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 96 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 242 optimal weight: 0.0870 chunk 109 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 255 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 GLN ** 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 = 0.4084 r_free = 0.4084 target = 0.141378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.096538 restraints weight = 40812.890| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.02 r_work: 0.2958 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23102 Z= 0.140 Angle : 0.571 9.726 31228 Z= 0.278 Chirality : 0.044 0.439 3514 Planarity : 0.004 0.068 3808 Dihedral : 13.068 127.460 5079 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.90 % Allowed : 15.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.16), residues: 2642 helix: 1.82 (0.15), residues: 1224 sheet: -0.21 (0.29), residues: 314 loop : -0.66 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 889 TYR 0.016 0.001 TYR C 869 PHE 0.017 0.001 PHE A 923 TRP 0.033 0.002 TRP C 89 HIS 0.008 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00333 (23058) covalent geometry : angle 0.55193 (31102) SS BOND : bond 0.00219 ( 6) SS BOND : angle 1.03464 ( 12) hydrogen bonds : bond 0.05100 ( 983) hydrogen bonds : angle 4.08063 ( 2925) link_ALPHA1-3 : bond 0.00773 ( 6) link_ALPHA1-3 : angle 3.11173 ( 18) link_ALPHA1-6 : bond 0.00739 ( 4) link_ALPHA1-6 : angle 1.39535 ( 12) link_BETA1-2 : bond 0.00383 ( 2) link_BETA1-2 : angle 5.09697 ( 6) link_BETA1-4 : bond 0.00495 ( 14) link_BETA1-4 : angle 2.54101 ( 42) link_BETA1-6 : bond 0.00150 ( 4) link_BETA1-6 : angle 1.56503 ( 12) link_NAG-ASN : bond 0.00443 ( 8) link_NAG-ASN : angle 1.43827 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5499.60 seconds wall clock time: 94 minutes 39.82 seconds (5679.82 seconds total)