Starting phenix.real_space_refine on Fri Jun 20 04:36:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wyy_32898/06_2025/7wyy_32898.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wyy_32898/06_2025/7wyy_32898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wyy_32898/06_2025/7wyy_32898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wyy_32898/06_2025/7wyy_32898.map" model { file = "/net/cci-nas-00/data/ceres_data/7wyy_32898/06_2025/7wyy_32898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wyy_32898/06_2025/7wyy_32898.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 P 26 5.49 5 Mg 6 5.21 5 S 118 5.16 5 C 14674 2.51 5 N 3518 2.21 5 O 4314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22656 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7687 Classifications: {'peptide': 993} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 949} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2399 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 278} Chain: "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: "A" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 447 Unusual residues: {' MG': 3, '7Q2': 1, 'CLR': 1, 'PCW': 9} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 190 Unusual residues: {'CLR': 1, 'PCW': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Restraints were copied for chains: C, K, N, L, G, D, M Time building chain proxies: 23.63, per 1000 atoms: 1.04 Number of scatterers: 22656 At special positions: 0 Unit cell: (216.276, 180.768, 103.296, 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) S 118 16.00 P 26 15.00 Mg 6 11.99 O 4314 8.00 N 3518 7.00 C 14674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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 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 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 B 114 " " NAG H 1 " - " ASN B 159 " " NAG I 1 " - " ASN B 194 " " NAG J 1 " - " ASN B 267 " " NAG K 1 " - " ASN D 114 " " NAG L 1 " - " ASN D 159 " " NAG M 1 " - " ASN D 194 " " NAG N 1 " - " ASN D 267 " Time building additional restraints: 7.27 Conformation dependent library (CDL) restraints added in 2.8 seconds 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 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: 114 helices and 22 sheets defined 50.0% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 87 through 97 removed outlier: 3.558A 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 160 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 261 through 264 removed outlier: 3.543A 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 276 Processing helix chain 'A' and resid 282 through 313 removed outlier: 3.587A pdb=" N ILE A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.684A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN A 331 " --> pdb=" O ILE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.109A pdb=" N ALA A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 removed outlier: 3.921A pdb=" N VAL A 364 " --> pdb=" O LEU A 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 364' Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.502A pdb=" N SER A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 428 removed outlier: 3.691A 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 609 Processing helix chain 'A' and resid 620 through 632 removed outlier: 3.933A pdb=" N ALA A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.657A pdb=" N ALA A 660 " --> pdb=" O PRO A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 671 Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 694 through 707 Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 728 removed outlier: 3.637A 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 756 through 782 removed outlier: 3.773A pdb=" N ARG A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 786 Processing helix chain 'A' and resid 787 through 797 Processing helix chain 'A' and resid 803 through 812 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: 3.671A pdb=" N ILE A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 876 Processing helix chain 'A' and resid 879 through 884 removed outlier: 4.248A pdb=" N ILE A 884 " --> pdb=" O PRO A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 892 Processing helix chain 'A' and resid 907 through 939 removed outlier: 3.515A pdb=" N VAL A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 4.324A 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: 3.557A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 965 " --> pdb=" O GLU A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 978 Processing helix chain 'A' and resid 986 through 990 removed outlier: 3.760A pdb=" N PHE A 989 " --> pdb=" O SER A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.513A pdb=" N PHE A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 3.676A 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 16 No H-bonds generated for 'chain 'B' and resid 14 through 16' Processing helix chain 'B' and resid 29 through 62 removed outlier: 4.119A pdb=" N TRP B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 98 removed outlier: 3.523A 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: 3.580A pdb=" N SER B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 4.006A pdb=" N ALA B 204 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.572A pdb=" N ARG B 223 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.738A 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: 4.146A pdb=" N LEU B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 15 through 40 Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 64 through 76 Processing helix chain 'C' and resid 87 through 97 removed outlier: 3.558A 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 160 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 261 through 264 removed outlier: 3.544A 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 276 Processing helix chain 'C' and resid 282 through 313 removed outlier: 3.586A pdb=" N ILE C 286 " --> pdb=" O THR C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 331 removed outlier: 3.684A pdb=" N ILE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN C 331 " --> pdb=" O ILE C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.109A pdb=" N ALA C 338 " --> pdb=" O GLU C 334 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR C 347 " --> pdb=" O CYS C 343 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 364 removed outlier: 3.920A pdb=" N VAL C 364 " --> pdb=" O LEU C 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 361 through 364' Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.503A pdb=" N SER C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 428 removed outlier: 3.691A 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 609 Processing helix chain 'C' and resid 620 through 632 removed outlier: 3.932A pdb=" N ALA C 626 " --> pdb=" O ILE C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 649 Processing helix chain 'C' and resid 656 through 660 removed outlier: 3.657A pdb=" N ALA C 660 " --> pdb=" O PRO C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 671 Processing helix chain 'C' and resid 674 through 685 Processing helix chain 'C' and resid 694 through 707 Processing helix chain 'C' and resid 718 through 720 No H-bonds generated for 'chain 'C' and resid 718 through 720' Processing helix chain 'C' and resid 721 through 728 removed outlier: 3.637A 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 756 through 782 removed outlier: 3.773A pdb=" N ARG C 766 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 782 " --> pdb=" O TYR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 786 Processing helix chain 'C' and resid 787 through 797 Processing helix chain 'C' and resid 803 through 812 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: 3.671A pdb=" N ILE C 850 " --> pdb=" O ASN C 846 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET C 852 " --> pdb=" O ARG C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 876 Processing helix chain 'C' and resid 879 through 884 removed outlier: 4.249A pdb=" N ILE C 884 " --> pdb=" O PRO C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 892 Processing helix chain 'C' and resid 907 through 939 removed outlier: 3.515A pdb=" N VAL C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA C 932 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 4.324A 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: 3.557A pdb=" N ILE C 955 " --> pdb=" O ASN C 951 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 965 " --> pdb=" O GLU C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 978 Processing helix chain 'C' and resid 986 through 990 removed outlier: 3.760A pdb=" N PHE C 989 " --> pdb=" O SER C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1012 removed outlier: 3.514A pdb=" N PHE C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C1008 " --> pdb=" O MET C1004 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C1009 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 4.486A 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 16 No H-bonds generated for 'chain 'D' and resid 14 through 16' Processing helix chain 'D' and resid 29 through 62 removed outlier: 4.119A pdb=" N TRP D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 removed outlier: 3.524A 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: 3.580A pdb=" N SER D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 removed outlier: 4.007A pdb=" N ALA D 204 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 224 removed outlier: 3.570A pdb=" N ARG D 223 " --> pdb=" O GLU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.738A 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: 4.147A pdb=" N LEU D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 13 Processing helix chain 'E' and resid 15 through 40 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 181 removed outlier: 11.695A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP A 202 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 227 removed outlier: 4.615A pdb=" N CYS A 211 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN A 248 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358 removed outlier: 6.719A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLY A 716 " --> pdb=" O MET A 734 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL A 616 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N SER A 375 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N CYS A 663 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ALA A 691 " --> pdb=" O CYS A 663 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL A 665 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 392 Processing sheet with id=AA5, first strand: chain 'A' and resid 432 through 433 removed outlier: 3.836A pdb=" N VAL A 432 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 480 removed outlier: 6.470A pdb=" N LYS A 476 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU A 494 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 490 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR A 503 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N HIS A 557 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N PHE A 585 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 8.441A 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: 7.601A pdb=" N PHE A 585 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE A 521 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N GLY A 587 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 11.554A pdb=" N LEU A 523 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 17.078A pdb=" N MET A 589 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 898 through 899 Processing sheet with id=AA8, first strand: chain 'B' and resid 18 through 19 removed outlier: 3.792A pdb=" N GLU B 24 " --> pdb=" O ASP B 19 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 78 through 80 removed outlier: 3.669A pdb=" N THR B 266 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU B 268 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE B 226 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 88 through 91 Processing sheet with id=AB2, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AB3, first strand: chain 'C' and resid 176 through 181 removed outlier: 11.695A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR C 253 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ALA C 208 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ARG C 255 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP C 202 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 225 through 227 removed outlier: 4.614A pdb=" N CYS C 211 " --> pdb=" O ARG C 227 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN C 248 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 356 through 358 removed outlier: 6.719A pdb=" N VAL C 712 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL C 732 " --> pdb=" O VAL C 712 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL C 714 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N MET C 734 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLY C 716 " --> pdb=" O MET C 734 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE C 373 " --> pdb=" O ILE C 614 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL C 616 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER C 375 " --> pdb=" O VAL C 616 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL C 613 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N PHE C 690 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N MET C 615 " --> pdb=" O PHE C 690 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N CYS C 663 " --> pdb=" O VAL C 689 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ALA C 691 " --> pdb=" O CYS C 663 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL C 665 " --> pdb=" O ALA C 691 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 390 through 392 Processing sheet with id=AB7, first strand: chain 'C' and resid 432 through 433 removed outlier: 3.838A pdb=" N VAL C 432 " --> pdb=" O ALA C 448 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 476 through 480 removed outlier: 6.470A pdb=" N LYS C 476 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU C 494 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 490 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR C 503 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HIS C 557 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE C 585 " --> pdb=" O HIS C 557 " (cutoff:3.500A) removed outlier: 8.441A 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: 7.602A pdb=" N PHE C 585 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE C 521 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N GLY C 587 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 11.554A pdb=" N LEU C 523 " --> pdb=" O GLY C 587 " (cutoff:3.500A) removed outlier: 17.077A pdb=" N MET C 589 " --> pdb=" O LEU C 523 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 898 through 899 Processing sheet with id=AC1, first strand: chain 'D' and resid 18 through 19 removed outlier: 3.791A pdb=" N GLU D 24 " --> pdb=" O ASP D 19 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 78 through 80 removed outlier: 3.669A pdb=" N THR D 266 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU D 268 " --> pdb=" O ILE D 226 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE D 226 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 88 through 91 Processing sheet with id=AC4, first strand: chain 'D' and resid 124 through 125 994 hydrogen bonds defined for protein. 2886 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.91 Time building geometry restraints manager: 8.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6847 1.35 - 1.47: 5211 1.47 - 1.59: 10792 1.59 - 1.71: 60 1.71 - 1.83: 172 Bond restraints: 23082 Sorted by residual: bond pdb=" OD1 PHD A 376 " pdb=" P PHD A 376 " ideal model delta sigma weight residual 1.816 1.508 0.308 2.00e-02 2.50e+03 2.37e+02 bond pdb=" OD1 PHD C 376 " pdb=" P PHD C 376 " ideal model delta sigma weight residual 1.816 1.509 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" C39 PCW G1304 " pdb=" C40 PCW G1304 " ideal model delta sigma weight residual 1.333 1.546 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C39 PCW E1304 " pdb=" C40 PCW E1304 " ideal model delta sigma weight residual 1.333 1.545 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C19 PCW C1109 " pdb=" C20 PCW C1109 " ideal model delta sigma weight residual 1.333 1.541 -0.208 2.00e-02 2.50e+03 1.08e+02 ... (remaining 23077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 28473 2.40 - 4.80: 2096 4.80 - 7.21: 422 7.21 - 9.61: 125 9.61 - 12.01: 32 Bond angle restraints: 31148 Sorted by residual: angle pdb=" N LEU D 157 " pdb=" CA LEU D 157 " pdb=" C LEU D 157 " ideal model delta sigma weight residual 108.67 98.44 10.23 1.55e+00 4.16e-01 4.36e+01 angle pdb=" N LEU B 157 " pdb=" CA LEU B 157 " pdb=" C LEU B 157 " ideal model delta sigma weight residual 108.67 98.45 10.22 1.55e+00 4.16e-01 4.34e+01 angle pdb=" N SER D 32 " pdb=" CA SER D 32 " pdb=" C SER D 32 " ideal model delta sigma weight residual 111.14 116.99 -5.85 1.08e+00 8.57e-01 2.94e+01 angle pdb=" N THR C 57 " pdb=" CA THR C 57 " pdb=" C THR C 57 " ideal model delta sigma weight residual 108.46 116.64 -8.18 1.51e+00 4.39e-01 2.93e+01 angle pdb=" N SER B 32 " pdb=" CA SER B 32 " pdb=" C SER B 32 " ideal model delta sigma weight residual 111.14 116.99 -5.85 1.08e+00 8.57e-01 2.93e+01 ... (remaining 31143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 14167 35.90 - 71.80: 771 71.80 - 107.70: 84 107.70 - 143.61: 40 143.61 - 179.51: 2 Dihedral angle restraints: 15064 sinusoidal: 7408 harmonic: 7656 Sorted by residual: dihedral pdb=" C33 PCW E1303 " pdb=" C31 PCW E1303 " pdb=" C32 PCW E1303 " pdb=" O2 PCW E1303 " ideal model delta sinusoidal sigma weight residual -168.17 11.34 -179.51 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW G1303 " pdb=" C31 PCW G1303 " pdb=" C32 PCW G1303 " pdb=" O2 PCW G1303 " ideal model delta sinusoidal sigma weight residual -168.17 11.21 -179.38 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW A1112 " pdb=" C31 PCW A1112 " pdb=" C32 PCW A1112 " pdb=" O2 PCW A1112 " ideal model delta sinusoidal sigma weight residual -168.17 -29.89 -138.28 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 15061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2871 0.079 - 0.158: 549 0.158 - 0.237: 61 0.237 - 0.316: 23 0.316 - 0.395: 20 Chirality restraints: 3524 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 7.54e+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 -2.23 -0.17 2.00e-02 2.50e+03 7.45e+01 chirality pdb=" C1 FUC F 6 " pdb=" O6 NAG F 1 " pdb=" C2 FUC F 6 " pdb=" O5 FUC F 6 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.70e+00 ... (remaining 3521 not shown) Planarity restraints: 3818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 122 " 0.093 5.00e-02 4.00e+02 1.46e-01 3.39e+01 pdb=" N PRO D 123 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 122 " -0.093 5.00e-02 4.00e+02 1.45e-01 3.38e+01 pdb=" N PRO B 123 " 0.252 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 124 " 0.065 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO A 125 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " 0.052 5.00e-02 4.00e+02 ... (remaining 3815 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 108 2.47 - 3.08: 15030 3.08 - 3.68: 30696 3.68 - 4.29: 47987 4.29 - 4.90: 78168 Nonbonded interactions: 171989 Sorted by model distance: nonbonded pdb=" OP3 PHD C 376 " pdb="MG MG C1101 " model vdw 1.860 2.170 nonbonded pdb=" OP3 PHD A 376 " pdb="MG MG A1101 " model vdw 1.860 2.170 nonbonded pdb=" OD2 ASP A 811 " pdb="MG MG A1103 " model vdw 1.969 2.170 nonbonded pdb=" OD2 ASP C 811 " pdb="MG MG C1103 " model vdw 1.970 2.170 nonbonded pdb="MG MG C1101 " pdb=" O HOH C1202 " model vdw 1.991 2.170 ... (remaining 171984 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'I' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 63.190 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 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 : 0.012 0.308 23126 Z= 0.582 Angle : 1.494 17.198 31274 Z= 0.759 Chirality : 0.069 0.395 3524 Planarity : 0.009 0.146 3810 Dihedral : 20.042 179.507 10134 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.69 % Favored : 90.71 % Rotamer: Outliers : 10.61 % Allowed : 8.97 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.14), residues: 2636 helix: -1.87 (0.13), residues: 1186 sheet: -2.42 (0.29), residues: 250 loop : -2.77 (0.15), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP D 33 HIS 0.010 0.002 HIS C 493 PHE 0.031 0.003 PHE B 297 TYR 0.038 0.002 TYR B 206 ARG 0.014 0.001 ARG C 596 Details of bonding type rmsd link_NAG-ASN : bond 0.01897 ( 8) link_NAG-ASN : angle 4.18387 ( 24) link_ALPHA1-6 : bond 0.00762 ( 4) link_ALPHA1-6 : angle 1.25286 ( 12) link_BETA1-2 : bond 0.00896 ( 2) link_BETA1-2 : angle 5.50601 ( 6) link_BETA1-4 : bond 0.01023 ( 14) link_BETA1-4 : angle 6.27841 ( 42) link_ALPHA1-3 : bond 0.00839 ( 6) link_ALPHA1-3 : angle 3.15551 ( 18) hydrogen bonds : bond 0.17498 ( 994) hydrogen bonds : angle 7.49451 ( 2886) link_BETA1-6 : bond 0.00313 ( 4) link_BETA1-6 : angle 1.39389 ( 12) SS BOND : bond 0.00426 ( 6) SS BOND : angle 2.20050 ( 12) covalent geometry : bond 0.01158 (23082) covalent geometry : angle 1.46977 (31148) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 554 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.5782 (OUTLIER) cc_final: 0.5022 (m-40) REVERT: A 71 ILE cc_start: 0.7036 (mt) cc_final: 0.6592 (mm) REVERT: A 127 ASN cc_start: 0.6881 (OUTLIER) cc_final: 0.6048 (p0) REVERT: A 158 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7828 (tpp) REVERT: A 351 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7569 (mtm) REVERT: A 488 TYR cc_start: 0.7031 (OUTLIER) cc_final: 0.6287 (p90) REVERT: A 504 LEU cc_start: 0.6747 (tp) cc_final: 0.6304 (pp) REVERT: A 721 ASP cc_start: 0.8784 (m-30) cc_final: 0.8156 (m-30) REVERT: A 810 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8540 (mt) REVERT: A 852 MET cc_start: 0.7519 (mmm) cc_final: 0.7283 (mmp) REVERT: B 242 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8666 (mt) REVERT: G 13 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7875 (p) REVERT: C 65 ASN cc_start: 0.5457 (OUTLIER) cc_final: 0.4671 (m-40) REVERT: C 71 ILE cc_start: 0.7226 (mt) cc_final: 0.6725 (mm) REVERT: C 158 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7837 (tpp) REVERT: C 351 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7595 (mtp) REVERT: C 488 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.6313 (p90) REVERT: C 504 LEU cc_start: 0.6590 (tp) cc_final: 0.6264 (pp) REVERT: C 708 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7344 (mt0) REVERT: C 721 ASP cc_start: 0.8742 (m-30) cc_final: 0.8115 (m-30) REVERT: C 815 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.6902 (t0) REVERT: C 852 MET cc_start: 0.7304 (mmm) cc_final: 0.7074 (mmp) REVERT: D 106 MET cc_start: 0.8179 (mmm) cc_final: 0.7908 (mtt) REVERT: D 287 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.7782 (m-80) outliers start: 240 outliers final: 44 residues processed: 722 average time/residue: 0.4191 time to fit residues: 445.2691 Evaluate side-chains 292 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 233 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 708 GLN Chi-restraints excluded: chain C residue 815 ASP Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 287 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 206 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 239 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 209 HIS A 434 GLN A 474 ASN A 486 ASN A 620 HIS A 683 HIS A 744 GLN A 826 GLN A 904 GLN A1019 GLN B 56 GLN B 203 GLN B 258 GLN C 52 HIS C 474 ASN ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 566 ASN C 620 HIS C 683 HIS C 744 GLN C 826 GLN C 904 GLN C1019 GLN D 56 GLN D 146 GLN D 258 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.135313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.107834 restraints weight = 43414.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.107861 restraints weight = 42315.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.109433 restraints weight = 33975.950| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23126 Z= 0.185 Angle : 0.753 11.573 31274 Z= 0.367 Chirality : 0.047 0.432 3524 Planarity : 0.006 0.073 3810 Dihedral : 17.098 173.430 5286 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.86 % Allowed : 14.81 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.15), residues: 2636 helix: -0.01 (0.15), residues: 1204 sheet: -1.73 (0.28), residues: 256 loop : -2.01 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 392 HIS 0.010 0.002 HIS A 683 PHE 0.018 0.002 PHE D 25 TYR 0.018 0.001 TYR B 40 ARG 0.007 0.001 ARG A 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00760 ( 8) link_NAG-ASN : angle 2.40937 ( 24) link_ALPHA1-6 : bond 0.00569 ( 4) link_ALPHA1-6 : angle 2.03643 ( 12) link_BETA1-2 : bond 0.00939 ( 2) link_BETA1-2 : angle 4.74869 ( 6) link_BETA1-4 : bond 0.00975 ( 14) link_BETA1-4 : angle 3.87593 ( 42) link_ALPHA1-3 : bond 0.00968 ( 6) link_ALPHA1-3 : angle 3.82643 ( 18) hydrogen bonds : bond 0.06323 ( 994) hydrogen bonds : angle 5.18409 ( 2886) link_BETA1-6 : bond 0.00473 ( 4) link_BETA1-6 : angle 1.53716 ( 12) SS BOND : bond 0.00164 ( 6) SS BOND : angle 1.16453 ( 12) covalent geometry : bond 0.00417 (23082) covalent geometry : angle 0.72761 (31148) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 253 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7025 (pp) cc_final: 0.6739 (tp) REVERT: A 71 ILE cc_start: 0.7114 (mt) cc_final: 0.6691 (mm) REVERT: A 308 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8546 (mp) REVERT: A 351 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7713 (mtp) REVERT: B 20 SER cc_start: 0.5875 (OUTLIER) cc_final: 0.5093 (p) REVERT: B 142 ASP cc_start: 0.5984 (t0) cc_final: 0.5339 (t0) REVERT: G 13 THR cc_start: 0.8141 (m) cc_final: 0.7940 (p) REVERT: C 71 ILE cc_start: 0.7159 (mt) cc_final: 0.6671 (mm) REVERT: C 287 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6854 (mm-30) REVERT: C 313 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7858 (tt) REVERT: C 351 MET cc_start: 0.8086 (mmm) cc_final: 0.7802 (mtp) REVERT: C 470 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.6858 (mpp) REVERT: C 721 ASP cc_start: 0.8701 (m-30) cc_final: 0.8122 (m-30) REVERT: D 20 SER cc_start: 0.6317 (OUTLIER) cc_final: 0.5479 (p) REVERT: D 142 ASP cc_start: 0.5707 (t0) cc_final: 0.5391 (t0) REVERT: E 4 GLU cc_start: 0.5021 (pm20) cc_final: 0.4795 (pp20) outliers start: 110 outliers final: 63 residues processed: 340 average time/residue: 0.3210 time to fit residues: 175.7572 Evaluate side-chains 251 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 182 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 866 PHE Chi-restraints excluded: chain A residue 871 VAL 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 B residue 20 SER Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 866 PHE Chi-restraints excluded: chain C residue 871 VAL 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 D residue 20 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 37 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 147 optimal weight: 3.9990 chunk 234 optimal weight: 0.9990 chunk 164 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 44 optimal weight: 30.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 486 ASN A 557 HIS ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 GLN B 243 GLN ** C 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 ASN C1019 GLN D 243 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.126498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.098452 restraints weight = 43195.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.097908 restraints weight = 51121.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.099017 restraints weight = 46418.356| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23126 Z= 0.214 Angle : 0.740 11.259 31274 Z= 0.356 Chirality : 0.048 0.442 3524 Planarity : 0.005 0.055 3810 Dihedral : 15.540 154.885 5228 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.55 % Allowed : 16.45 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2636 helix: 0.70 (0.15), residues: 1184 sheet: -1.38 (0.29), residues: 268 loop : -1.34 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 890 HIS 0.008 0.001 HIS A 493 PHE 0.027 0.002 PHE A 100 TYR 0.022 0.002 TYR C 488 ARG 0.006 0.001 ARG C 430 Details of bonding type rmsd link_NAG-ASN : bond 0.01066 ( 8) link_NAG-ASN : angle 2.75194 ( 24) link_ALPHA1-6 : bond 0.00752 ( 4) link_ALPHA1-6 : angle 1.48202 ( 12) link_BETA1-2 : bond 0.00677 ( 2) link_BETA1-2 : angle 4.04932 ( 6) link_BETA1-4 : bond 0.00685 ( 14) link_BETA1-4 : angle 3.58230 ( 42) link_ALPHA1-3 : bond 0.01310 ( 6) link_ALPHA1-3 : angle 3.70364 ( 18) hydrogen bonds : bond 0.06194 ( 994) hydrogen bonds : angle 4.66258 ( 2886) link_BETA1-6 : bond 0.00337 ( 4) link_BETA1-6 : angle 1.59407 ( 12) SS BOND : bond 0.00133 ( 6) SS BOND : angle 1.99296 ( 12) covalent geometry : bond 0.00506 (23082) covalent geometry : angle 0.71584 (31148) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 216 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ILE cc_start: 0.7046 (mt) cc_final: 0.6470 (mm) REVERT: A 75 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7348 (t70) REVERT: A 100 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7856 (m-80) REVERT: A 158 MET cc_start: 0.7952 (tpp) cc_final: 0.7373 (tpt) REVERT: A 351 MET cc_start: 0.7957 (mtm) cc_final: 0.7755 (mtt) REVERT: A 675 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8223 (t) REVERT: A 719 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8726 (t) REVERT: B 20 SER cc_start: 0.6594 (OUTLIER) cc_final: 0.5527 (p) REVERT: B 94 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8262 (p) REVERT: B 142 ASP cc_start: 0.6096 (t0) cc_final: 0.5878 (t0) REVERT: B 287 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: G 13 THR cc_start: 0.8461 (m) cc_final: 0.8257 (p) REVERT: C 48 LEU cc_start: 0.6980 (tp) cc_final: 0.6467 (tp) REVERT: C 71 ILE cc_start: 0.7063 (mt) cc_final: 0.6783 (mm) REVERT: C 287 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6881 (mm-30) REVERT: C 351 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7662 (mtp) REVERT: C 466 SER cc_start: 0.7606 (t) cc_final: 0.7124 (p) REVERT: C 470 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.6980 (mpp) REVERT: C 719 VAL cc_start: 0.9092 (OUTLIER) cc_final: 0.8747 (t) REVERT: C 721 ASP cc_start: 0.8763 (m-30) cc_final: 0.8155 (m-30) REVERT: D 20 SER cc_start: 0.6508 (OUTLIER) cc_final: 0.5587 (p) REVERT: D 142 ASP cc_start: 0.6198 (t0) cc_final: 0.5555 (t0) REVERT: D 287 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.7919 (m-80) outliers start: 103 outliers final: 58 residues processed: 302 average time/residue: 0.3236 time to fit residues: 159.8466 Evaluate side-chains 250 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 180 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 866 PHE Chi-restraints excluded: chain A residue 871 VAL 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 1000 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 782 SER Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 866 PHE Chi-restraints excluded: chain C residue 871 VAL 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 1000 LEU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 37 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 233 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 chunk 224 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 184 optimal weight: 20.0000 chunk 241 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.126961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.099025 restraints weight = 43837.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.098133 restraints weight = 51335.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.099668 restraints weight = 44322.235| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23126 Z= 0.154 Angle : 0.627 10.649 31274 Z= 0.298 Chirality : 0.045 0.471 3524 Planarity : 0.004 0.049 3810 Dihedral : 14.612 154.152 5208 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.98 % Allowed : 18.13 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2636 helix: 1.06 (0.15), residues: 1198 sheet: -1.12 (0.30), residues: 268 loop : -1.17 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 988 HIS 0.004 0.001 HIS A 493 PHE 0.019 0.002 PHE A 793 TYR 0.013 0.001 TYR C 869 ARG 0.003 0.000 ARG A 473 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 8) link_NAG-ASN : angle 1.78369 ( 24) link_ALPHA1-6 : bond 0.00665 ( 4) link_ALPHA1-6 : angle 1.58591 ( 12) link_BETA1-2 : bond 0.00643 ( 2) link_BETA1-2 : angle 4.04122 ( 6) link_BETA1-4 : bond 0.00655 ( 14) link_BETA1-4 : angle 3.26501 ( 42) link_ALPHA1-3 : bond 0.01234 ( 6) link_ALPHA1-3 : angle 3.78624 ( 18) hydrogen bonds : bond 0.05226 ( 994) hydrogen bonds : angle 4.34994 ( 2886) link_BETA1-6 : bond 0.00144 ( 4) link_BETA1-6 : angle 1.61014 ( 12) SS BOND : bond 0.00077 ( 6) SS BOND : angle 1.44425 ( 12) covalent geometry : bond 0.00362 (23082) covalent geometry : angle 0.60331 (31148) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 194 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7174 (t70) REVERT: A 158 MET cc_start: 0.7926 (tpp) cc_final: 0.7702 (tpp) REVERT: A 351 MET cc_start: 0.7979 (mtm) cc_final: 0.7669 (mtt) REVERT: A 675 THR cc_start: 0.8588 (p) cc_final: 0.8154 (t) REVERT: A 719 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8574 (t) REVERT: B 20 SER cc_start: 0.6540 (OUTLIER) cc_final: 0.5467 (p) REVERT: B 142 ASP cc_start: 0.6122 (t0) cc_final: 0.5863 (t0) REVERT: B 287 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: C 64 THR cc_start: 0.6206 (OUTLIER) cc_final: 0.5839 (p) REVERT: C 71 ILE cc_start: 0.6964 (mt) cc_final: 0.6735 (mm) REVERT: C 158 MET cc_start: 0.7997 (tpp) cc_final: 0.7796 (tpp) REVERT: C 287 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6657 (mm-30) REVERT: C 351 MET cc_start: 0.8109 (mmm) cc_final: 0.7728 (mtp) REVERT: C 466 SER cc_start: 0.7622 (t) cc_final: 0.7236 (p) REVERT: C 470 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7250 (mpp) REVERT: C 719 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8659 (t) REVERT: D 142 ASP cc_start: 0.6234 (t0) cc_final: 0.5634 (t0) outliers start: 90 outliers final: 61 residues processed: 266 average time/residue: 0.3248 time to fit residues: 143.6587 Evaluate side-chains 243 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 175 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 866 PHE Chi-restraints excluded: chain A residue 871 VAL 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 1000 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 782 SER Chi-restraints excluded: chain C residue 866 PHE Chi-restraints excluded: chain C residue 871 VAL 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 D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 35 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 198 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 chunk 15 optimal weight: 0.0970 chunk 226 optimal weight: 4.9990 chunk 178 optimal weight: 0.0010 chunk 169 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.125070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.095451 restraints weight = 42393.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.095249 restraints weight = 43294.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.096318 restraints weight = 36163.594| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23126 Z= 0.117 Angle : 0.587 9.722 31274 Z= 0.278 Chirality : 0.044 0.480 3524 Planarity : 0.004 0.044 3810 Dihedral : 13.972 149.296 5203 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.67 % Allowed : 18.57 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.16), residues: 2636 helix: 1.28 (0.15), residues: 1200 sheet: -0.96 (0.30), residues: 276 loop : -1.08 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 988 HIS 0.012 0.001 HIS C 683 PHE 0.019 0.001 PHE A 184 TYR 0.012 0.001 TYR A 869 ARG 0.004 0.000 ARG A 473 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 8) link_NAG-ASN : angle 1.53358 ( 24) link_ALPHA1-6 : bond 0.00748 ( 4) link_ALPHA1-6 : angle 1.56901 ( 12) link_BETA1-2 : bond 0.00685 ( 2) link_BETA1-2 : angle 4.22351 ( 6) link_BETA1-4 : bond 0.00610 ( 14) link_BETA1-4 : angle 3.08168 ( 42) link_ALPHA1-3 : bond 0.01227 ( 6) link_ALPHA1-3 : angle 3.77067 ( 18) hydrogen bonds : bond 0.04737 ( 994) hydrogen bonds : angle 4.16334 ( 2886) link_BETA1-6 : bond 0.00060 ( 4) link_BETA1-6 : angle 1.57644 ( 12) SS BOND : bond 0.00054 ( 6) SS BOND : angle 1.00621 ( 12) covalent geometry : bond 0.00260 (23082) covalent geometry : angle 0.56370 (31148) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 197 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8019 (tpp) cc_final: 0.7631 (tpp) REVERT: A 391 MET cc_start: 0.6958 (mtm) cc_final: 0.6756 (mtm) REVERT: A 675 THR cc_start: 0.8574 (p) cc_final: 0.8102 (t) REVERT: A 719 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8593 (t) REVERT: B 20 SER cc_start: 0.6703 (OUTLIER) cc_final: 0.5783 (p) REVERT: B 142 ASP cc_start: 0.6209 (t0) cc_final: 0.5873 (t0) REVERT: B 287 TYR cc_start: 0.8228 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: C 64 THR cc_start: 0.6224 (OUTLIER) cc_final: 0.5906 (p) REVERT: C 158 MET cc_start: 0.7921 (tpp) cc_final: 0.7573 (tpp) REVERT: C 287 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6585 (mm-30) REVERT: C 351 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7750 (mtp) REVERT: C 391 MET cc_start: 0.7153 (mtm) cc_final: 0.6937 (mtm) REVERT: C 466 SER cc_start: 0.7715 (t) cc_final: 0.7335 (p) REVERT: C 470 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7336 (mpp) REVERT: C 719 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8705 (t) REVERT: D 111 ASP cc_start: 0.7812 (t70) cc_final: 0.6973 (t70) REVERT: D 142 ASP cc_start: 0.6284 (t0) cc_final: 0.5644 (t0) outliers start: 83 outliers final: 56 residues processed: 265 average time/residue: 0.2955 time to fit residues: 130.2824 Evaluate side-chains 232 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 169 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 866 PHE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 866 PHE Chi-restraints excluded: chain C residue 871 VAL 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 D residue 26 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 35 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 15 optimal weight: 0.6980 chunk 120 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 212 optimal weight: 0.5980 chunk 18 optimal weight: 9.9990 chunk 230 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 172 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 HIS A 826 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.123254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.093400 restraints weight = 42594.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.092897 restraints weight = 43739.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.094551 restraints weight = 36708.907| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23126 Z= 0.163 Angle : 0.619 9.574 31274 Z= 0.296 Chirality : 0.045 0.486 3524 Planarity : 0.004 0.043 3810 Dihedral : 13.621 150.582 5199 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.29 % Allowed : 18.44 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2636 helix: 1.31 (0.16), residues: 1186 sheet: -0.96 (0.30), residues: 276 loop : -1.03 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 89 HIS 0.023 0.002 HIS C 683 PHE 0.021 0.002 PHE A 793 TYR 0.027 0.001 TYR C 488 ARG 0.003 0.000 ARG A 473 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 8) link_NAG-ASN : angle 1.56774 ( 24) link_ALPHA1-6 : bond 0.00713 ( 4) link_ALPHA1-6 : angle 1.46095 ( 12) link_BETA1-2 : bond 0.00644 ( 2) link_BETA1-2 : angle 4.16697 ( 6) link_BETA1-4 : bond 0.00572 ( 14) link_BETA1-4 : angle 3.00752 ( 42) link_ALPHA1-3 : bond 0.01135 ( 6) link_ALPHA1-3 : angle 3.86013 ( 18) hydrogen bonds : bond 0.05144 ( 994) hydrogen bonds : angle 4.21472 ( 2886) link_BETA1-6 : bond 0.00165 ( 4) link_BETA1-6 : angle 1.62865 ( 12) SS BOND : bond 0.00121 ( 6) SS BOND : angle 1.04624 ( 12) covalent geometry : bond 0.00385 (23082) covalent geometry : angle 0.59697 (31148) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 181 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.7962 (tpp) cc_final: 0.7590 (tpp) REVERT: A 351 MET cc_start: 0.8022 (mtm) cc_final: 0.7719 (mtp) REVERT: A 675 THR cc_start: 0.8593 (p) cc_final: 0.8141 (t) REVERT: A 719 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8568 (t) REVERT: B 142 ASP cc_start: 0.6322 (t0) cc_final: 0.6019 (t0) REVERT: B 287 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: C 100 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7462 (m-10) REVERT: C 158 MET cc_start: 0.8013 (tpp) cc_final: 0.7588 (tpp) REVERT: C 287 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6677 (mm-30) REVERT: C 351 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7666 (mtp) REVERT: C 466 SER cc_start: 0.7778 (t) cc_final: 0.7425 (p) REVERT: C 470 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7368 (mpp) REVERT: C 719 VAL cc_start: 0.9062 (OUTLIER) cc_final: 0.8629 (t) REVERT: D 111 ASP cc_start: 0.7817 (t70) cc_final: 0.6980 (t70) REVERT: D 142 ASP cc_start: 0.6316 (t0) cc_final: 0.5681 (t0) REVERT: D 287 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7859 (m-80) outliers start: 97 outliers final: 65 residues processed: 264 average time/residue: 0.2806 time to fit residues: 123.9935 Evaluate side-chains 240 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 168 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 871 VAL 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 D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain E residue 33 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 244 optimal weight: 8.9990 chunk 177 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 199 optimal weight: 1.9990 chunk 75 optimal weight: 0.1980 chunk 67 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 204 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 HIS C 683 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.124350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.094284 restraints weight = 42919.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.093580 restraints weight = 39484.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.094847 restraints weight = 34208.263| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23126 Z= 0.112 Angle : 0.575 9.256 31274 Z= 0.272 Chirality : 0.043 0.488 3524 Planarity : 0.004 0.041 3810 Dihedral : 13.129 144.157 5193 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.14 % Allowed : 20.20 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 2636 helix: 1.48 (0.16), residues: 1196 sheet: -0.94 (0.30), residues: 278 loop : -0.99 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 89 HIS 0.014 0.001 HIS A 683 PHE 0.022 0.001 PHE B 25 TYR 0.024 0.001 TYR A 488 ARG 0.003 0.000 ARG A 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 8) link_NAG-ASN : angle 1.36435 ( 24) link_ALPHA1-6 : bond 0.00781 ( 4) link_ALPHA1-6 : angle 1.54878 ( 12) link_BETA1-2 : bond 0.00647 ( 2) link_BETA1-2 : angle 4.25458 ( 6) link_BETA1-4 : bond 0.00578 ( 14) link_BETA1-4 : angle 2.82617 ( 42) link_ALPHA1-3 : bond 0.01208 ( 6) link_ALPHA1-3 : angle 3.78722 ( 18) hydrogen bonds : bond 0.04510 ( 994) hydrogen bonds : angle 4.03473 ( 2886) link_BETA1-6 : bond 0.00058 ( 4) link_BETA1-6 : angle 1.56454 ( 12) SS BOND : bond 0.00127 ( 6) SS BOND : angle 0.86365 ( 12) covalent geometry : bond 0.00243 (23082) covalent geometry : angle 0.55251 (31148) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 186 time to evaluate : 2.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.7960 (tpp) cc_final: 0.7606 (tpp) REVERT: A 351 MET cc_start: 0.7972 (mtm) cc_final: 0.7626 (mtp) REVERT: A 675 THR cc_start: 0.8548 (p) cc_final: 0.8021 (t) REVERT: A 719 VAL cc_start: 0.8976 (OUTLIER) cc_final: 0.8549 (t) REVERT: B 111 ASP cc_start: 0.7743 (t70) cc_final: 0.6905 (t70) REVERT: B 142 ASP cc_start: 0.6279 (t0) cc_final: 0.5980 (t0) REVERT: B 234 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8282 (tm) REVERT: B 287 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7712 (m-80) REVERT: C 158 MET cc_start: 0.7960 (tpp) cc_final: 0.7621 (tpp) REVERT: C 287 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6582 (mm-30) REVERT: C 351 MET cc_start: 0.8113 (mmm) cc_final: 0.7545 (mtp) REVERT: C 466 SER cc_start: 0.7855 (t) cc_final: 0.7467 (p) REVERT: C 470 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7392 (mpp) REVERT: C 719 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8647 (t) REVERT: D 111 ASP cc_start: 0.7766 (t70) cc_final: 0.6933 (t70) REVERT: D 142 ASP cc_start: 0.6289 (t0) cc_final: 0.5599 (t0) REVERT: D 234 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8260 (tm) REVERT: D 287 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7675 (m-80) outliers start: 71 outliers final: 53 residues processed: 247 average time/residue: 0.2886 time to fit residues: 119.0676 Evaluate side-chains 230 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 170 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 184 PHE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 871 VAL 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 998 ILE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain E residue 33 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 35 optimal weight: 9.9990 chunk 110 optimal weight: 0.5980 chunk 180 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 245 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 195 optimal weight: 9.9990 chunk 262 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 HIS B 118 GLN B 270 GLN C 946 GLN D 270 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.120962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.090911 restraints weight = 42801.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.088895 restraints weight = 43970.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.090095 restraints weight = 41061.598| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23126 Z= 0.222 Angle : 0.683 9.362 31274 Z= 0.329 Chirality : 0.047 0.480 3524 Planarity : 0.004 0.041 3810 Dihedral : 13.238 149.627 5189 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.16 % Allowed : 19.63 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.16), residues: 2636 helix: 1.24 (0.15), residues: 1182 sheet: -0.97 (0.31), residues: 266 loop : -1.03 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 392 HIS 0.034 0.002 HIS C 683 PHE 0.024 0.002 PHE A 967 TYR 0.034 0.002 TYR A 488 ARG 0.003 0.000 ARG B 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00611 ( 8) link_NAG-ASN : angle 2.10667 ( 24) link_ALPHA1-6 : bond 0.00699 ( 4) link_ALPHA1-6 : angle 1.41639 ( 12) link_BETA1-2 : bond 0.00650 ( 2) link_BETA1-2 : angle 4.07449 ( 6) link_BETA1-4 : bond 0.00608 ( 14) link_BETA1-4 : angle 2.74135 ( 42) link_ALPHA1-3 : bond 0.01282 ( 6) link_ALPHA1-3 : angle 3.89389 ( 18) hydrogen bonds : bond 0.05640 ( 994) hydrogen bonds : angle 4.30851 ( 2886) link_BETA1-6 : bond 0.00085 ( 4) link_BETA1-6 : angle 1.72649 ( 12) SS BOND : bond 0.01124 ( 6) SS BOND : angle 1.46309 ( 12) covalent geometry : bond 0.00532 (23082) covalent geometry : angle 0.66325 (31148) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 177 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8106 (tpp) cc_final: 0.7778 (tpp) REVERT: A 351 MET cc_start: 0.8102 (mtm) cc_final: 0.7709 (mtt) REVERT: A 507 MET cc_start: 0.7708 (tpt) cc_final: 0.7447 (tpt) REVERT: A 675 THR cc_start: 0.8668 (p) cc_final: 0.8229 (t) REVERT: B 142 ASP cc_start: 0.6476 (t0) cc_final: 0.6230 (t0) REVERT: B 203 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8065 (mp10) REVERT: B 234 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8357 (tm) REVERT: B 287 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: C 100 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7517 (m-10) REVERT: C 158 MET cc_start: 0.8124 (tpp) cc_final: 0.7751 (tpp) REVERT: C 287 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6727 (mm-30) REVERT: C 351 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7559 (mtp) REVERT: C 466 SER cc_start: 0.7962 (t) cc_final: 0.7583 (p) REVERT: C 470 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7473 (mpp) REVERT: C 675 THR cc_start: 0.8579 (p) cc_final: 0.8064 (t) REVERT: C 719 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8652 (t) REVERT: D 111 ASP cc_start: 0.7829 (t70) cc_final: 0.7042 (t70) REVERT: D 142 ASP cc_start: 0.6435 (t0) cc_final: 0.5768 (t0) REVERT: D 234 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8282 (tm) REVERT: D 287 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7669 (m-80) outliers start: 94 outliers final: 73 residues processed: 253 average time/residue: 0.2947 time to fit residues: 124.6236 Evaluate side-chains 252 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 170 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 782 SER Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 871 VAL 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 998 ILE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 36 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 109 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 214 optimal weight: 0.9990 chunk 221 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 211 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 HIS A 946 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.123523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.3249 r_free = 0.3249 target = 0.091196 restraints weight = 42678.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.093069 restraints weight = 32446.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.093283 restraints weight = 25539.221| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23126 Z= 0.122 Angle : 0.598 9.421 31274 Z= 0.285 Chirality : 0.044 0.478 3524 Planarity : 0.004 0.060 3810 Dihedral : 12.841 143.169 5189 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.18 % Allowed : 20.56 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2636 helix: 1.48 (0.16), residues: 1182 sheet: -0.90 (0.31), residues: 266 loop : -0.98 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 392 HIS 0.029 0.001 HIS A 683 PHE 0.029 0.001 PHE B 25 TYR 0.030 0.001 TYR A 488 ARG 0.004 0.000 ARG A 473 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 8) link_NAG-ASN : angle 1.77258 ( 24) link_ALPHA1-6 : bond 0.00774 ( 4) link_ALPHA1-6 : angle 1.54112 ( 12) link_BETA1-2 : bond 0.00672 ( 2) link_BETA1-2 : angle 4.21470 ( 6) link_BETA1-4 : bond 0.00541 ( 14) link_BETA1-4 : angle 2.57248 ( 42) link_ALPHA1-3 : bond 0.01044 ( 6) link_ALPHA1-3 : angle 3.73708 ( 18) hydrogen bonds : bond 0.04793 ( 994) hydrogen bonds : angle 4.09162 ( 2886) link_BETA1-6 : bond 0.00067 ( 4) link_BETA1-6 : angle 1.60073 ( 12) SS BOND : bond 0.00163 ( 6) SS BOND : angle 1.21092 ( 12) covalent geometry : bond 0.00274 (23082) covalent geometry : angle 0.57793 (31148) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 193 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8051 (tpp) cc_final: 0.7735 (tpp) REVERT: A 351 MET cc_start: 0.8020 (mtm) cc_final: 0.7675 (mtp) REVERT: A 675 THR cc_start: 0.8647 (p) cc_final: 0.8160 (t) REVERT: A 719 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8587 (t) REVERT: B 142 ASP cc_start: 0.6335 (t0) cc_final: 0.6014 (t0) REVERT: B 203 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8254 (mp10) REVERT: B 234 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8323 (tm) REVERT: B 287 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.7712 (m-80) REVERT: C 70 GLU cc_start: 0.7782 (tp30) cc_final: 0.6875 (mt-10) REVERT: C 158 MET cc_start: 0.8067 (tpp) cc_final: 0.7729 (tpp) REVERT: C 287 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6615 (mm-30) REVERT: C 351 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7662 (mtp) REVERT: C 466 SER cc_start: 0.8016 (t) cc_final: 0.7600 (p) REVERT: C 470 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7256 (mpp) REVERT: C 675 THR cc_start: 0.8571 (p) cc_final: 0.8074 (t) REVERT: C 719 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8627 (t) REVERT: D 111 ASP cc_start: 0.7837 (t70) cc_final: 0.7028 (t70) REVERT: D 142 ASP cc_start: 0.6327 (t0) cc_final: 0.5712 (t0) REVERT: D 234 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8290 (tm) REVERT: D 287 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7690 (m-80) outliers start: 72 outliers final: 58 residues processed: 250 average time/residue: 0.3215 time to fit residues: 133.4552 Evaluate side-chains 242 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 175 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 871 VAL 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 998 ILE Chi-restraints excluded: chain C residue 1002 ASP Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 36 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 54 optimal weight: 0.0870 chunk 145 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 168 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.123291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 122)---------------| | r_work = 0.3292 r_free = 0.3292 target = 0.092506 restraints weight = 42635.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.091919 restraints weight = 36404.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.092866 restraints weight = 32779.313| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23126 Z= 0.131 Angle : 0.600 9.500 31274 Z= 0.287 Chirality : 0.044 0.471 3524 Planarity : 0.004 0.047 3810 Dihedral : 12.561 137.758 5189 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.96 % Allowed : 20.95 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.16), residues: 2636 helix: 1.53 (0.16), residues: 1182 sheet: -0.90 (0.31), residues: 266 loop : -0.94 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 392 HIS 0.028 0.002 HIS A 683 PHE 0.031 0.002 PHE B 25 TYR 0.030 0.001 TYR C 488 ARG 0.004 0.000 ARG A 473 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 8) link_NAG-ASN : angle 1.76676 ( 24) link_ALPHA1-6 : bond 0.00762 ( 4) link_ALPHA1-6 : angle 1.54195 ( 12) link_BETA1-2 : bond 0.00679 ( 2) link_BETA1-2 : angle 4.15252 ( 6) link_BETA1-4 : bond 0.00532 ( 14) link_BETA1-4 : angle 2.55176 ( 42) link_ALPHA1-3 : bond 0.01064 ( 6) link_ALPHA1-3 : angle 3.74526 ( 18) hydrogen bonds : bond 0.04692 ( 994) hydrogen bonds : angle 4.06229 ( 2886) link_BETA1-6 : bond 0.00030 ( 4) link_BETA1-6 : angle 1.59460 ( 12) SS BOND : bond 0.00161 ( 6) SS BOND : angle 1.14558 ( 12) covalent geometry : bond 0.00303 (23082) covalent geometry : angle 0.58026 (31148) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 179 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8083 (tpp) cc_final: 0.7778 (tpp) REVERT: A 351 MET cc_start: 0.7977 (mtm) cc_final: 0.7736 (mtp) REVERT: A 507 MET cc_start: 0.7682 (tpt) cc_final: 0.7478 (tpt) REVERT: A 675 THR cc_start: 0.8587 (p) cc_final: 0.8047 (t) REVERT: A 684 TYR cc_start: 0.7968 (m-10) cc_final: 0.7650 (m-10) REVERT: A 719 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8584 (t) REVERT: B 142 ASP cc_start: 0.6459 (t0) cc_final: 0.6069 (t0) REVERT: B 234 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8291 (tm) REVERT: B 287 TYR cc_start: 0.8230 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: C 70 GLU cc_start: 0.7682 (tp30) cc_final: 0.6980 (mt-10) REVERT: C 158 MET cc_start: 0.8069 (tpp) cc_final: 0.7744 (tpp) REVERT: C 287 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6607 (mm-30) REVERT: C 351 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7899 (mtp) REVERT: C 466 SER cc_start: 0.7881 (t) cc_final: 0.7440 (p) REVERT: C 470 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7341 (mpp) REVERT: C 675 THR cc_start: 0.8565 (p) cc_final: 0.8073 (t) REVERT: C 719 VAL cc_start: 0.9002 (OUTLIER) cc_final: 0.8592 (t) REVERT: D 111 ASP cc_start: 0.7855 (t70) cc_final: 0.6966 (t70) REVERT: D 142 ASP cc_start: 0.6453 (t0) cc_final: 0.5794 (t0) REVERT: D 234 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8276 (tm) REVERT: D 287 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7696 (m-80) outliers start: 67 outliers final: 56 residues processed: 231 average time/residue: 0.3012 time to fit residues: 117.0651 Evaluate side-chains 236 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 172 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 871 VAL 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 998 ILE Chi-restraints excluded: chain C residue 1002 ASP Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 36 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 247 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 242 optimal weight: 0.7980 chunk 153 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 221 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 HIS D 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.121816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.092151 restraints weight = 43095.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.090822 restraints weight = 43609.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.092352 restraints weight = 40561.311| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.6034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23126 Z= 0.143 Angle : 0.608 9.455 31274 Z= 0.291 Chirality : 0.044 0.457 3524 Planarity : 0.004 0.044 3810 Dihedral : 12.247 133.048 5189 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.23 % Allowed : 20.95 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2636 helix: 1.47 (0.16), residues: 1192 sheet: -0.96 (0.31), residues: 266 loop : -0.89 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 392 HIS 0.013 0.001 HIS A 683 PHE 0.040 0.002 PHE A 231 TYR 0.027 0.001 TYR A 488 ARG 0.003 0.000 ARG D 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 8) link_NAG-ASN : angle 1.81994 ( 24) link_ALPHA1-6 : bond 0.00719 ( 4) link_ALPHA1-6 : angle 1.53788 ( 12) link_BETA1-2 : bond 0.00724 ( 2) link_BETA1-2 : angle 4.09969 ( 6) link_BETA1-4 : bond 0.00527 ( 14) link_BETA1-4 : angle 2.50516 ( 42) link_ALPHA1-3 : bond 0.01006 ( 6) link_ALPHA1-3 : angle 3.69450 ( 18) hydrogen bonds : bond 0.04797 ( 994) hydrogen bonds : angle 4.08294 ( 2886) link_BETA1-6 : bond 0.00200 ( 4) link_BETA1-6 : angle 1.65488 ( 12) SS BOND : bond 0.00165 ( 6) SS BOND : angle 1.34716 ( 12) covalent geometry : bond 0.00337 (23082) covalent geometry : angle 0.58817 (31148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6868.65 seconds wall clock time: 120 minutes 36.44 seconds (7236.44 seconds total)