Starting phenix.real_space_refine on Wed May 28 21:42:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kdm_37139/05_2025/8kdm_37139.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kdm_37139/05_2025/8kdm_37139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kdm_37139/05_2025/8kdm_37139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kdm_37139/05_2025/8kdm_37139.map" model { file = "/net/cci-nas-00/data/ceres_data/8kdm_37139/05_2025/8kdm_37139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kdm_37139/05_2025/8kdm_37139.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 158 5.16 5 C 19843 2.51 5 N 5170 2.21 5 O 5981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.79s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31152 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8190 Classifications: {'peptide': 1051} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 998} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "D" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1653 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 12, 'TRANS': 200} Chain: "G" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "F" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1653 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 12, 'TRANS': 200} Chain: "B" Number of atoms: 8190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8190 Classifications: {'peptide': 1051} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 998} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 8190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8190 Classifications: {'peptide': 1051} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 998} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 17.24, per 1000 atoms: 0.55 Number of scatterers: 31152 At special positions: 0 Unit cell: (160.304, 161.236, 226.476, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 158 16.00 O 5981 8.00 N 5170 7.00 C 19843 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 203 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 136 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " 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 Time building additional restraints: 7.40 Conformation dependent library (CDL) restraints added in 3.9 seconds 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7512 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 66 sheets defined 19.2% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'A' and resid 93 through 97 removed outlier: 4.098A pdb=" N ASN A 96 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 97 " --> pdb=" O LYS A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 93 through 97' Processing helix chain 'A' and resid 267 through 271 removed outlier: 3.597A pdb=" N THR A 271 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.780A pdb=" N VAL A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.064A pdb=" N ASP A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 728 through 736 removed outlier: 3.551A pdb=" N ALA A 732 " --> pdb=" O SER A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 740 through 765 Processing helix chain 'A' and resid 798 through 806 Processing helix chain 'A' and resid 848 through 865 Processing helix chain 'A' and resid 868 through 873 removed outlier: 3.700A pdb=" N GLY A 871 " --> pdb=" O TRP A 868 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY A 873 " --> pdb=" O PHE A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 892 Processing helix chain 'A' and resid 894 through 901 removed outlier: 4.132A pdb=" N LEU A 898 " --> pdb=" O THR A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 removed outlier: 3.674A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 949 Processing helix chain 'A' and resid 961 through 966 removed outlier: 4.219A pdb=" N ARG A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 966 " --> pdb=" O ILE A 962 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 961 through 966' Processing helix chain 'A' and resid 967 through 1015 removed outlier: 4.601A pdb=" N VAL A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1132 removed outlier: 3.596A pdb=" N GLU A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'D' and resid 123 through 130 removed outlier: 4.029A pdb=" N SER D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 removed outlier: 4.101A pdb=" N GLU D 189 " --> pdb=" O LYS D 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 196 No H-bonds generated for 'chain 'G' and resid 194 through 196' Processing helix chain 'F' and resid 123 through 128 removed outlier: 3.610A pdb=" N LEU F 127 " --> pdb=" O SER F 123 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS F 128 " --> pdb=" O ASP F 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 123 through 128' Processing helix chain 'F' and resid 184 through 189 removed outlier: 4.191A pdb=" N GLU F 189 " --> pdb=" O LYS F 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 removed outlier: 4.128A pdb=" N ASN B 96 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 97 " --> pdb=" O LYS B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 93 through 97' Processing helix chain 'B' and resid 267 through 271 removed outlier: 3.544A pdb=" N GLY B 270 " --> pdb=" O ASP B 267 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 271 " --> pdb=" O GLU B 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 267 through 271' Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 604 through 612 Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'B' and resid 728 through 738 removed outlier: 3.658A pdb=" N GLN B 737 " --> pdb=" O ASN B 733 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR B 738 " --> pdb=" O LEU B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 765 Processing helix chain 'B' and resid 798 through 806 Processing helix chain 'B' and resid 848 through 865 Processing helix chain 'B' and resid 868 through 873 removed outlier: 3.690A pdb=" N GLY B 871 " --> pdb=" O TRP B 868 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY B 873 " --> pdb=" O PHE B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 892 Processing helix chain 'B' and resid 894 through 901 removed outlier: 4.155A pdb=" N LEU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 removed outlier: 3.681A pdb=" N THR B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 949 Processing helix chain 'B' and resid 961 through 966 removed outlier: 3.766A pdb=" N ARG B 965 " --> pdb=" O ASP B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 1015 removed outlier: 4.562A pdb=" N VAL B 973 " --> pdb=" O PRO B 969 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1132 Processing helix chain 'C' and resid 267 through 271 removed outlier: 3.603A pdb=" N THR C 271 " --> pdb=" O GLU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 290 Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.605A pdb=" N LYS C 373 " --> pdb=" O SER C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 612 removed outlier: 3.855A pdb=" N THR C 608 " --> pdb=" O THR C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 724 Processing helix chain 'C' and resid 728 through 736 removed outlier: 3.790A pdb=" N ALA C 732 " --> pdb=" O SER C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 740 through 765 Processing helix chain 'C' and resid 798 through 806 Processing helix chain 'C' and resid 815 through 819 removed outlier: 4.086A pdb=" N TYR C 819 " --> pdb=" O MET C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 865 Processing helix chain 'C' and resid 868 through 873 removed outlier: 3.712A pdb=" N GLY C 871 " --> pdb=" O TRP C 868 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C 873 " --> pdb=" O PHE C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 892 Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.104A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 922 removed outlier: 3.652A pdb=" N THR C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 947 Processing helix chain 'C' and resid 967 through 1015 removed outlier: 3.950A pdb=" N VAL C 973 " --> pdb=" O PRO C 969 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 1122 through 1131 removed outlier: 3.567A pdb=" N GLU C1126 " --> pdb=" O PRO C1122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 55 removed outlier: 3.790A pdb=" N THR A 51 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.688A pdb=" N VAL A 186 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 166 removed outlier: 3.987A pdb=" N TYR A 163 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 116 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 230 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 305 removed outlier: 3.747A pdb=" N THR A 585 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 302 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 312 through 315 removed outlier: 3.556A pdb=" N GLY A 534 " --> pdb=" O PHE A 527 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 367 removed outlier: 3.806A pdb=" N LYS A 365 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N CYS A 419 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 499 " --> pdb=" O CYS A 419 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A 494 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 387 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AA8, first strand: chain 'A' and resid 559 through 562 removed outlier: 7.577A pdb=" N PHE A 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 640 through 641 removed outlier: 3.541A pdb=" N ALA A 676 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER A 659 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A 677 " --> pdb=" O CYS A 657 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N CYS A 657 " --> pdb=" O TYR A 677 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 683 through 684 removed outlier: 5.906A pdb=" N ALA A 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 694 through 695 Processing sheet with id=AB3, first strand: chain 'A' and resid 700 through 710 Processing sheet with id=AB4, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB5, first strand: chain 'A' and resid 769 through 770 Processing sheet with id=AB6, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AB7, first strand: chain 'A' and resid 1070 through 1072 removed outlier: 3.687A pdb=" N PHE A1071 " --> pdb=" O PHE A1103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1085 through 1086 removed outlier: 3.927A pdb=" N GLN A1095 " --> pdb=" O ILE A1086 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.560A pdb=" N VAL E 18 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.541A pdb=" N THR E 119 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL E 93 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 142 through 146 removed outlier: 3.860A pdb=" N VAL E 189 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER E 184 " --> pdb=" O ALA E 175 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA E 175 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER E 186 " --> pdb=" O PHE E 173 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.592A pdb=" N ARG D 24 " --> pdb=" O THR D 5 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 13 Processing sheet with id=AC5, first strand: chain 'D' and resid 21 through 22 removed outlier: 3.765A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER D 67 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 63 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.643A pdb=" N TYR D 49 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 47 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 116 through 120 removed outlier: 3.553A pdb=" N ASN D 139 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D 135 " --> pdb=" O PHE D 120 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL D 134 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N TYR D 175 " --> pdb=" O ASN D 140 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 149 through 150 removed outlier: 4.243A pdb=" N TYR D 194 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE D 211 " --> pdb=" O TYR D 194 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS D 209 " --> pdb=" O CYS D 196 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 207 " --> pdb=" O VAL D 198 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.523A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL G 79 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.924A pdb=" N VAL G 93 " --> pdb=" O GLN G 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 142 through 146 removed outlier: 3.894A pdb=" N VAL G 189 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER G 184 " --> pdb=" O ALA G 175 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA G 175 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER G 186 " --> pdb=" O PHE G 173 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.816A pdb=" N ARG F 24 " --> pdb=" O THR F 5 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.723A pdb=" N GLU F 107 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU F 13 " --> pdb=" O GLU F 107 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 21 through 22 removed outlier: 3.741A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER F 67 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR F 74 " --> pdb=" O SER F 63 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER F 63 " --> pdb=" O THR F 74 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.503A pdb=" N ASN F 53 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR F 49 " --> pdb=" O ASN F 53 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU F 47 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 116 through 120 removed outlier: 3.604A pdb=" N ASN F 139 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL F 134 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TYR F 175 " --> pdb=" O ASN F 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 147 through 150 removed outlier: 3.656A pdb=" N THR F 199 " --> pdb=" O LYS F 147 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN F 149 " --> pdb=" O GLU F 197 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR F 194 " --> pdb=" O PHE F 211 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE F 211 " --> pdb=" O TYR F 194 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS F 209 " --> pdb=" O CYS F 196 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL F 207 " --> pdb=" O VAL F 198 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 51 through 55 removed outlier: 3.695A pdb=" N THR B 51 " --> pdb=" O TYR B 266 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.721A pdb=" N VAL B 186 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 162 through 166 removed outlier: 3.855A pdb=" N TYR B 163 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 116 " --> pdb=" O TRP B 101 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 298 through 306 removed outlier: 3.747A pdb=" N THR B 585 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 302 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 312 through 315 removed outlier: 3.621A pdb=" N LEU B 532 " --> pdb=" O PHE B 529 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 366 through 367 removed outlier: 4.223A pdb=" N CYS B 419 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 499 " --> pdb=" O CYS B 419 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP B 423 " --> pdb=" O ARG B 495 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 366 through 367 removed outlier: 4.223A pdb=" N CYS B 419 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 499 " --> pdb=" O CYS B 419 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP B 423 " --> pdb=" O ARG B 495 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B 494 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 387 " --> pdb=" O VAL B 496 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AE8, first strand: chain 'B' and resid 551 through 553 Processing sheet with id=AE9, first strand: chain 'B' and resid 640 through 641 removed outlier: 3.520A pdb=" N ALA B 676 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 659 " --> pdb=" O VAL B 675 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR B 677 " --> pdb=" O CYS B 657 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N CYS B 657 " --> pdb=" O TYR B 677 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 694 through 695 Processing sheet with id=AF2, first strand: chain 'B' and resid 700 through 710 Processing sheet with id=AF3, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AF4, first strand: chain 'B' and resid 769 through 770 Processing sheet with id=AF5, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AF6, first strand: chain 'B' and resid 1070 through 1072 removed outlier: 3.731A pdb=" N PHE B1071 " --> pdb=" O PHE B1103 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 52 through 55 Processing sheet with id=AF8, first strand: chain 'C' and resid 217 through 220 removed outlier: 7.023A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 186 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS C 181 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 183 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C 91 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE C 87 " --> pdb=" O PHE C 187 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 163 through 166 removed outlier: 4.002A pdb=" N TYR C 163 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE C 116 " --> pdb=" O TRP C 101 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 298 through 306 removed outlier: 3.653A pdb=" N THR C 585 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR C 302 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 312 through 313 removed outlier: 3.555A pdb=" N PHE C 529 " --> pdb=" O LEU C 532 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 365 through 367 removed outlier: 3.639A pdb=" N LYS C 365 " --> pdb=" O VAL C 420 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AG5, first strand: chain 'C' and resid 551 through 553 removed outlier: 7.326A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 640 through 641 removed outlier: 3.636A pdb=" N VAL C 675 " --> pdb=" O SER C 659 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER C 659 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR C 677 " --> pdb=" O CYS C 657 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS C 657 " --> pdb=" O TYR C 677 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 694 through 695 Processing sheet with id=AG8, first strand: chain 'C' and resid 700 through 710 Processing sheet with id=AG9, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AH1, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AH2, first strand: chain 'C' and resid 1063 through 1064 removed outlier: 4.109A pdb=" N CYS C1064 " --> pdb=" O ILE C1115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'C' and resid 1071 through 1072 removed outlier: 3.509A pdb=" N PHE C1071 " --> pdb=" O PHE C1103 " (cutoff:3.500A) 887 hydrogen bonds defined for protein. 2451 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: 13.28 Time building geometry restraints manager: 8.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10020 1.34 - 1.46: 7617 1.46 - 1.58: 14030 1.58 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 31883 Sorted by residual: bond pdb=" C SER F 7 " pdb=" N PRO F 8 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.30e-02 5.92e+03 2.67e+00 bond pdb=" C PRO B 469 " pdb=" N PRO B 470 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.43e+00 bond pdb=" C PRO A 469 " pdb=" N PRO A 470 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.35e+00 bond pdb=" C PRO C 469 " pdb=" N PRO C 470 " ideal model delta sigma weight residual 1.334 1.360 -0.027 2.34e-02 1.83e+03 1.29e+00 bond pdb=" N PRO E 14 " pdb=" CA PRO E 14 " ideal model delta sigma weight residual 1.469 1.483 -0.014 1.28e-02 6.10e+03 1.19e+00 ... (remaining 31878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 42809 1.54 - 3.07: 481 3.07 - 4.61: 64 4.61 - 6.14: 26 6.14 - 7.68: 4 Bond angle restraints: 43384 Sorted by residual: angle pdb=" N ASP B 961 " pdb=" CA ASP B 961 " pdb=" C ASP B 961 " ideal model delta sigma weight residual 114.04 109.80 4.24 1.24e+00 6.50e-01 1.17e+01 angle pdb=" C ASP B 572 " pdb=" N ILE B 573 " pdb=" CA ILE B 573 " ideal model delta sigma weight residual 121.97 126.86 -4.89 1.80e+00 3.09e-01 7.39e+00 angle pdb=" C ASP C 572 " pdb=" N ILE C 573 " pdb=" CA ILE C 573 " ideal model delta sigma weight residual 121.97 126.74 -4.77 1.80e+00 3.09e-01 7.01e+00 angle pdb=" C ASP A 572 " pdb=" N ILE A 573 " pdb=" CA ILE A 573 " ideal model delta sigma weight residual 121.97 126.50 -4.53 1.80e+00 3.09e-01 6.35e+00 angle pdb=" C LYS A 84 " pdb=" N ASP A 85 " pdb=" CA ASP A 85 " ideal model delta sigma weight residual 121.54 126.31 -4.77 1.91e+00 2.74e-01 6.25e+00 ... (remaining 43379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 18311 17.72 - 35.45: 615 35.45 - 53.17: 95 53.17 - 70.90: 9 70.90 - 88.62: 3 Dihedral angle restraints: 19033 sinusoidal: 7344 harmonic: 11689 Sorted by residual: dihedral pdb=" CA GLN A 632 " pdb=" C GLN A 632 " pdb=" N ALA A 633 " pdb=" CA ALA A 633 " ideal model delta harmonic sigma weight residual 180.00 -159.91 -20.09 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ASN A1080 " pdb=" C ASN A1080 " pdb=" N GLY A1081 " pdb=" CA GLY A1081 " ideal model delta harmonic sigma weight residual 180.00 160.90 19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ASN B1080 " pdb=" C ASN B1080 " pdb=" N GLY B1081 " pdb=" CA GLY B1081 " ideal model delta harmonic sigma weight residual 180.00 161.74 18.26 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 19030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3015 0.027 - 0.054: 1149 0.054 - 0.082: 354 0.082 - 0.109: 327 0.109 - 0.136: 61 Chirality restraints: 4906 Sorted by residual: chirality pdb=" CA ILE C1086 " pdb=" N ILE C1086 " pdb=" C ILE C1086 " pdb=" CB ILE C1086 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE C 696 " pdb=" N ILE C 696 " pdb=" C ILE C 696 " pdb=" CB ILE C 696 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA ILE A1086 " pdb=" N ILE A1086 " pdb=" C ILE A1086 " pdb=" CB ILE A1086 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 4903 not shown) Planarity restraints: 5610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 13 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO E 14 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 14 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 14 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 468 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 469 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 469 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 469 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 468 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO B 469 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 469 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 469 " -0.019 5.00e-02 4.00e+02 ... (remaining 5607 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4596 2.76 - 3.30: 29287 3.30 - 3.83: 50763 3.83 - 4.37: 56795 4.37 - 4.90: 101198 Nonbonded interactions: 242639 Sorted by model distance: nonbonded pdb=" O SER C 919 " pdb=" OG1 THR C 923 " model vdw 2.229 3.040 nonbonded pdb=" O SER A 919 " pdb=" OG1 THR A 923 " model vdw 2.254 3.040 nonbonded pdb=" O SER C 861 " pdb=" OG1 THR C 865 " model vdw 2.263 3.040 nonbonded pdb=" O SER B 919 " pdb=" OG1 THR B 923 " model vdw 2.264 3.040 nonbonded pdb=" O ALA C1069 " pdb=" OG SER C1105 " model vdw 2.265 3.040 ... (remaining 242634 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 1.400 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 66.630 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 : 0.002 0.036 31933 Z= 0.086 Angle : 0.448 7.680 43484 Z= 0.246 Chirality : 0.040 0.136 4906 Planarity : 0.003 0.034 5610 Dihedral : 8.452 88.620 11371 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.45 % Allowed : 5.55 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.12), residues: 3971 helix: 0.78 (0.19), residues: 684 sheet: -2.56 (0.16), residues: 875 loop : -3.56 (0.10), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.002 0.000 HIS C1030 PHE 0.007 0.001 PHE C 360 TYR 0.006 0.000 TYR A 660 ARG 0.002 0.000 ARG A 887 Details of bonding type rmsd hydrogen bonds : bond 0.23366 ( 882) hydrogen bonds : angle 8.17071 ( 2451) SS BOND : bond 0.00090 ( 50) SS BOND : angle 0.46118 ( 100) covalent geometry : bond 0.00157 (31883) covalent geometry : angle 0.44774 (43384) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 608 time to evaluate : 3.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 374 LEU cc_start: 0.8690 (mt) cc_final: 0.8432 (mt) REVERT: A 572 ASP cc_start: -0.0253 (OUTLIER) cc_final: -0.0458 (t70) REVERT: A 783 ASN cc_start: 0.7389 (OUTLIER) cc_final: 0.6920 (t0) REVERT: E 33 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7865 (m-10) REVERT: E 80 TYR cc_start: 0.9057 (m-80) cc_final: 0.8808 (m-10) REVERT: E 153 PHE cc_start: 0.7256 (t80) cc_final: 0.6033 (t80) REVERT: E 183 TYR cc_start: 0.8854 (m-80) cc_final: 0.8515 (m-80) REVERT: D 32 TYR cc_start: 0.8640 (m-10) cc_final: 0.8374 (m-10) REVERT: D 49 TYR cc_start: 0.9147 (p90) cc_final: 0.8897 (p90) REVERT: D 86 TYR cc_start: 0.8735 (m-80) cc_final: 0.8427 (m-80) REVERT: G 38 ARG cc_start: 0.7778 (tmm160) cc_final: 0.7425 (tmm-80) REVERT: B 338 TYR cc_start: 0.8122 (p90) cc_final: 0.7592 (p90) REVERT: B 365 LYS cc_start: 0.9073 (mtpt) cc_final: 0.8789 (ptpt) REVERT: B 367 TYR cc_start: 0.8466 (m-80) cc_final: 0.7924 (m-80) REVERT: B 600 ASP cc_start: 0.8198 (m-30) cc_final: 0.7993 (m-30) REVERT: C 83 PHE cc_start: 0.8175 (t80) cc_final: 0.7798 (t80) REVERT: C 151 MET cc_start: 0.5055 (mmt) cc_final: 0.4459 (mmt) REVERT: C 466 PRO cc_start: 0.8745 (Cg_exo) cc_final: 0.8472 (Cg_endo) REVERT: C 738 TYR cc_start: 0.8069 (m-80) cc_final: 0.7607 (m-80) REVERT: C 769 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8353 (mp10) REVERT: C 932 ASP cc_start: 0.8241 (m-30) cc_final: 0.7923 (m-30) REVERT: C 1086 ILE cc_start: 0.7676 (mt) cc_final: 0.7367 (mt) outliers start: 154 outliers final: 22 residues processed: 720 average time/residue: 1.2317 time to fit residues: 1061.6227 Evaluate side-chains 282 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 256 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 783 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 635 CYS Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 408 TYR Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain C residue 694 ILE Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 769 GLN Chi-restraints excluded: chain C residue 1077 PHE Chi-restraints excluded: chain C residue 1130 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 7.9990 chunk 302 optimal weight: 20.0000 chunk 167 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 203 optimal weight: 0.0050 chunk 161 optimal weight: 50.0000 chunk 312 optimal weight: 6.9990 chunk 121 optimal weight: 50.0000 chunk 190 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 362 optimal weight: 8.9990 overall best weight: 4.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 201 GLN A 318 ASN A 396 GLN A 546 GLN A 550 GLN A 599 GLN A 783 ASN A 835 GLN A 904 GLN A1046 HIS A1124 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN D 90 HIS D 102 GLN D 157 GLN D 191 HIS ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 HIS G 178 GLN F 37 GLN F 157 GLN F 191 HIS B 118 ASN B 155 ASN B 201 GLN B 301 GLN B 396 GLN B 409 ASN B 546 GLN B 550 GLN B 818 GLN B 835 GLN B 896 ASN B 904 GLN B 917 GLN B 984 GLN B 993 GLN B1046 HIS B1124 GLN C 201 GLN C 281 ASN ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN C 550 GLN C 599 GLN C 661 HIS C 769 GLN C 877 GLN C 904 GLN C 931 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1046 HIS C1124 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.102633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.061408 restraints weight = 98360.933| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.69 r_work: 0.2944 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 31933 Z= 0.329 Angle : 0.804 17.907 43484 Z= 0.414 Chirality : 0.049 0.331 4906 Planarity : 0.005 0.059 5610 Dihedral : 5.490 63.235 4356 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.89 % Favored : 90.98 % Rotamer: Outliers : 4.74 % Allowed : 12.22 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.18 (0.12), residues: 3971 helix: 0.66 (0.19), residues: 735 sheet: -2.14 (0.15), residues: 970 loop : -3.20 (0.11), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 94 HIS 0.018 0.002 HIS B1030 PHE 0.027 0.003 PHE A 764 TYR 0.025 0.002 TYR G 183 ARG 0.016 0.001 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.04834 ( 882) hydrogen bonds : angle 5.93569 ( 2451) SS BOND : bond 0.01416 ( 50) SS BOND : angle 1.91348 ( 100) covalent geometry : bond 0.00748 (31883) covalent geometry : angle 0.79949 (43384) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 258 time to evaluate : 3.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8127 (t80) cc_final: 0.7852 (t80) REVERT: A 101 TRP cc_start: 0.8292 (OUTLIER) cc_final: 0.6898 (p90) REVERT: A 151 MET cc_start: 0.5967 (OUTLIER) cc_final: 0.5759 (tpt) REVERT: A 329 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7810 (m-80) REVERT: A 992 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.8369 (mp10) REVERT: A 999 GLU cc_start: 0.9238 (tt0) cc_final: 0.8873 (tm-30) REVERT: E 12 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8195 (mtpp) REVERT: E 67 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6867 (ptm160) REVERT: E 80 TYR cc_start: 0.9082 (m-80) cc_final: 0.8685 (m-10) REVERT: E 153 PHE cc_start: 0.8281 (t80) cc_final: 0.7594 (t80) REVERT: D 32 TYR cc_start: 0.8631 (m-10) cc_final: 0.8332 (m-10) REVERT: D 50 ASP cc_start: 0.9301 (m-30) cc_final: 0.9014 (m-30) REVERT: D 62 PHE cc_start: 0.7548 (m-80) cc_final: 0.6985 (m-80) REVERT: D 142 TYR cc_start: 0.7729 (t80) cc_final: 0.7242 (t80) REVERT: G 34 MET cc_start: 0.7630 (tpt) cc_final: 0.6759 (tpt) REVERT: F 97 MET cc_start: 0.8734 (tpp) cc_final: 0.8498 (tpp) REVERT: F 136 CYS cc_start: 0.6597 (t) cc_final: 0.5526 (p) REVERT: F 142 TYR cc_start: 0.8369 (t80) cc_final: 0.8124 (t80) REVERT: B 151 MET cc_start: 0.8537 (pmm) cc_final: 0.8219 (pmm) REVERT: B 157 PHE cc_start: 0.6619 (m-80) cc_final: 0.6414 (t80) REVERT: B 222 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9117 (pp) REVERT: B 338 TYR cc_start: 0.8132 (p90) cc_final: 0.7703 (p90) REVERT: B 365 LYS cc_start: 0.9321 (mtpt) cc_final: 0.8973 (ptpt) REVERT: B 367 TYR cc_start: 0.9042 (m-80) cc_final: 0.8389 (m-80) REVERT: B 744 GLN cc_start: 0.8871 (mt0) cc_final: 0.8600 (mt0) REVERT: B 939 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8107 (tm-30) REVERT: C 83 PHE cc_start: 0.8568 (t80) cc_final: 0.8096 (t80) REVERT: C 151 MET cc_start: 0.5169 (mmt) cc_final: 0.4458 (mmt) REVERT: C 327 GLU cc_start: 0.9139 (mp0) cc_final: 0.8917 (mp0) REVERT: C 629 PHE cc_start: 0.8284 (t80) cc_final: 0.7911 (t80) REVERT: C 932 ASP cc_start: 0.8862 (m-30) cc_final: 0.8578 (m-30) REVERT: C 939 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8415 (tm-30) REVERT: C 992 GLN cc_start: 0.9290 (OUTLIER) cc_final: 0.8410 (mp10) REVERT: C 999 GLU cc_start: 0.9267 (tt0) cc_final: 0.8935 (tm-30) REVERT: C 1077 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.6990 (m-80) outliers start: 164 outliers final: 56 residues processed: 384 average time/residue: 1.1340 time to fit residues: 535.0585 Evaluate side-chains 249 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 184 time to evaluate : 3.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1130 PHE Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 47 TRP Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 635 CYS Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 408 TYR Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1077 PHE Chi-restraints excluded: chain C residue 1079 PHE Chi-restraints excluded: chain C residue 1105 SER Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1130 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 95 optimal weight: 1.9990 chunk 246 optimal weight: 0.9990 chunk 249 optimal weight: 5.9990 chunk 394 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 228 optimal weight: 30.0000 chunk 18 optimal weight: 1.9990 chunk 272 optimal weight: 0.8980 chunk 263 optimal weight: 9.9990 chunk 132 optimal weight: 50.0000 chunk 284 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 GLN A 896 ASN A 904 GLN A 939 GLN A1005 ASN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN B 301 GLN B 409 ASN B 984 GLN C 396 GLN C 401 GLN C 546 GLN C 661 HIS C 896 ASN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.104223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.063533 restraints weight = 98863.454| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.73 r_work: 0.3009 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31933 Z= 0.128 Angle : 0.620 18.324 43484 Z= 0.308 Chirality : 0.043 0.208 4906 Planarity : 0.004 0.054 5610 Dihedral : 4.775 56.548 4338 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.33 % Favored : 92.65 % Rotamer: Outliers : 3.29 % Allowed : 14.30 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.13), residues: 3971 helix: 1.32 (0.20), residues: 727 sheet: -1.94 (0.15), residues: 988 loop : -2.96 (0.11), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 47 HIS 0.004 0.001 HIS C1046 PHE 0.021 0.001 PHE C1079 TYR 0.052 0.001 TYR G 201 ARG 0.009 0.001 ARG C 829 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 882) hydrogen bonds : angle 5.40547 ( 2451) SS BOND : bond 0.00245 ( 50) SS BOND : angle 0.90926 ( 100) covalent geometry : bond 0.00293 (31883) covalent geometry : angle 0.61875 (43384) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 209 time to evaluate : 3.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.7804 (t80) cc_final: 0.7480 (t80) REVERT: A 101 TRP cc_start: 0.8209 (OUTLIER) cc_final: 0.6290 (p90) REVERT: A 601 VAL cc_start: 0.9301 (t) cc_final: 0.8930 (m) REVERT: A 992 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8213 (mp10) REVERT: A 999 GLU cc_start: 0.9189 (tt0) cc_final: 0.8865 (tm-30) REVERT: E 31 ASP cc_start: 0.8901 (p0) cc_final: 0.8700 (p0) REVERT: E 33 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.8044 (m-10) REVERT: E 54 ASP cc_start: 0.9193 (OUTLIER) cc_final: 0.8786 (p0) REVERT: E 80 TYR cc_start: 0.9033 (m-80) cc_final: 0.8766 (m-10) REVERT: D 32 TYR cc_start: 0.8607 (m-10) cc_final: 0.8268 (m-10) REVERT: D 49 TYR cc_start: 0.8591 (p90) cc_final: 0.8383 (p90) REVERT: D 50 ASP cc_start: 0.9311 (m-30) cc_final: 0.9076 (m-30) REVERT: D 61 ARG cc_start: 0.8807 (ptt-90) cc_final: 0.8462 (ptt180) REVERT: D 87 TYR cc_start: 0.7993 (m-80) cc_final: 0.7653 (m-80) REVERT: D 142 TYR cc_start: 0.7801 (t80) cc_final: 0.7288 (t80) REVERT: G 33 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.8091 (m-10) REVERT: G 34 MET cc_start: 0.7175 (tpt) cc_final: 0.6875 (tpt) REVERT: G 45 LEU cc_start: 0.0862 (OUTLIER) cc_final: -0.0294 (tm) REVERT: G 70 MET cc_start: 0.7353 (ptp) cc_final: 0.6806 (ptp) REVERT: F 136 CYS cc_start: 0.6688 (t) cc_final: 0.5619 (p) REVERT: B 157 PHE cc_start: 0.6752 (m-80) cc_final: 0.6496 (t80) REVERT: B 338 TYR cc_start: 0.8205 (p90) cc_final: 0.7790 (p90) REVERT: B 365 LYS cc_start: 0.9291 (mtpt) cc_final: 0.8983 (ptpt) REVERT: B 367 TYR cc_start: 0.8985 (m-80) cc_final: 0.8377 (m-80) REVERT: B 629 PHE cc_start: 0.7882 (t80) cc_final: 0.7679 (t80) REVERT: B 744 GLN cc_start: 0.8960 (mt0) cc_final: 0.8756 (mt0) REVERT: B 939 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7953 (tm-30) REVERT: C 83 PHE cc_start: 0.8480 (t80) cc_final: 0.7968 (t80) REVERT: C 151 MET cc_start: 0.5332 (mmt) cc_final: 0.4545 (mmt) REVERT: C 327 GLU cc_start: 0.9112 (mp0) cc_final: 0.8846 (mp0) REVERT: C 365 LYS cc_start: 0.8962 (tppt) cc_final: 0.8685 (tppp) REVERT: C 629 PHE cc_start: 0.8026 (t80) cc_final: 0.7720 (t80) REVERT: C 932 ASP cc_start: 0.8858 (m-30) cc_final: 0.8634 (m-30) REVERT: C 939 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8263 (tm-30) REVERT: C 992 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8236 (mp10) REVERT: C 999 GLU cc_start: 0.9237 (tt0) cc_final: 0.8952 (tm-30) REVERT: C 1077 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6905 (m-80) outliers start: 114 outliers final: 49 residues processed: 298 average time/residue: 1.1535 time to fit residues: 421.7331 Evaluate side-chains 236 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 179 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1130 PHE Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 635 CYS Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 408 TYR Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1077 PHE Chi-restraints excluded: chain C residue 1079 PHE Chi-restraints excluded: chain C residue 1105 SER Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1130 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 339 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 103 optimal weight: 0.4980 chunk 382 optimal weight: 10.0000 chunk 184 optimal weight: 50.0000 chunk 153 optimal weight: 20.0000 chunk 358 optimal weight: 0.9980 chunk 128 optimal weight: 30.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 GLN A 904 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN B 409 ASN B 530 ASN B 818 GLN ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN ** C 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN C 951 ASN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.101525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.059789 restraints weight = 99458.305| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.71 r_work: 0.2904 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 31933 Z= 0.213 Angle : 0.653 19.270 43484 Z= 0.329 Chirality : 0.044 0.182 4906 Planarity : 0.004 0.060 5610 Dihedral : 4.960 57.149 4337 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.36 % Favored : 91.59 % Rotamer: Outliers : 3.76 % Allowed : 14.36 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.13), residues: 3971 helix: 1.40 (0.20), residues: 735 sheet: -1.77 (0.16), residues: 1003 loop : -2.75 (0.12), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP E 47 HIS 0.005 0.001 HIS B1030 PHE 0.020 0.002 PHE C1079 TYR 0.027 0.001 TYR D 49 ARG 0.008 0.001 ARG C1089 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 882) hydrogen bonds : angle 5.17473 ( 2451) SS BOND : bond 0.00398 ( 50) SS BOND : angle 1.15245 ( 100) covalent geometry : bond 0.00493 (31883) covalent geometry : angle 0.65151 (43384) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 193 time to evaluate : 3.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 83 PHE cc_start: 0.7937 (t80) cc_final: 0.7654 (t80) REVERT: A 601 VAL cc_start: 0.9240 (t) cc_final: 0.8865 (m) REVERT: A 818 GLN cc_start: 0.7954 (mm110) cc_final: 0.7569 (mp10) REVERT: A 992 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8296 (mp10) REVERT: A 999 GLU cc_start: 0.9169 (tt0) cc_final: 0.8893 (tm-30) REVERT: E 12 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8202 (mtpp) REVERT: E 54 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8838 (p0) REVERT: E 81 MET cc_start: 0.7694 (ttp) cc_final: 0.7469 (tmt) REVERT: D 32 TYR cc_start: 0.8616 (m-10) cc_final: 0.8296 (m-10) REVERT: D 61 ARG cc_start: 0.8850 (ptt-90) cc_final: 0.8520 (ptt180) REVERT: D 87 TYR cc_start: 0.7946 (m-80) cc_final: 0.7569 (m-80) REVERT: D 142 TYR cc_start: 0.7742 (t80) cc_final: 0.7226 (t80) REVERT: G 33 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.8088 (m-10) REVERT: G 34 MET cc_start: 0.7157 (tpt) cc_final: 0.6889 (tpt) REVERT: G 45 LEU cc_start: 0.1116 (OUTLIER) cc_final: -0.0073 (tm) REVERT: G 70 MET cc_start: 0.7529 (ptp) cc_final: 0.7141 (ptp) REVERT: F 136 CYS cc_start: 0.6747 (t) cc_final: 0.5567 (p) REVERT: B 157 PHE cc_start: 0.7478 (m-80) cc_final: 0.7118 (t80) REVERT: B 338 TYR cc_start: 0.8209 (p90) cc_final: 0.7867 (p90) REVERT: B 365 LYS cc_start: 0.9334 (mtpt) cc_final: 0.9112 (pmmt) REVERT: B 367 TYR cc_start: 0.9071 (m-80) cc_final: 0.8279 (m-80) REVERT: B 692 ASN cc_start: 0.8489 (m-40) cc_final: 0.8212 (p0) REVERT: B 744 GLN cc_start: 0.8973 (mt0) cc_final: 0.8743 (mt0) REVERT: B 848 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8668 (p) REVERT: B 939 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8101 (tm-30) REVERT: C 83 PHE cc_start: 0.8407 (t80) cc_final: 0.7938 (t80) REVERT: C 151 MET cc_start: 0.5227 (mmt) cc_final: 0.4549 (mmt) REVERT: C 327 GLU cc_start: 0.9168 (mp0) cc_final: 0.8882 (mp0) REVERT: C 629 PHE cc_start: 0.8162 (t80) cc_final: 0.7813 (t80) REVERT: C 632 GLN cc_start: 0.8837 (tp-100) cc_final: 0.8583 (tp-100) REVERT: C 932 ASP cc_start: 0.8919 (m-30) cc_final: 0.8639 (m-30) REVERT: C 939 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8338 (tm-30) REVERT: C 951 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8314 (OUTLIER) REVERT: C 992 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8325 (mp10) REVERT: C 999 GLU cc_start: 0.9257 (tt0) cc_final: 0.8943 (tm-30) outliers start: 130 outliers final: 69 residues processed: 302 average time/residue: 1.1138 time to fit residues: 415.5679 Evaluate side-chains 248 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 172 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1130 PHE Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 833 CYS Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 408 TYR Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain C residue 951 ASN Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1079 PHE Chi-restraints excluded: chain C residue 1105 SER Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain C residue 1130 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 164 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 370 optimal weight: 10.0000 chunk 293 optimal weight: 1.9990 chunk 35 optimal weight: 30.0000 chunk 236 optimal weight: 5.9990 chunk 381 optimal weight: 0.5980 chunk 373 optimal weight: 0.5980 chunk 397 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN B 737 GLN ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN ** C 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 ASN C 951 ASN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.102826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.061649 restraints weight = 98076.661| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.69 r_work: 0.2951 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31933 Z= 0.122 Angle : 0.603 17.128 43484 Z= 0.299 Chirality : 0.043 0.186 4906 Planarity : 0.004 0.057 5610 Dihedral : 4.814 57.604 4334 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.76 % Favored : 92.22 % Rotamer: Outliers : 3.21 % Allowed : 15.22 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.13), residues: 3971 helix: 1.60 (0.20), residues: 737 sheet: -1.66 (0.16), residues: 1018 loop : -2.59 (0.12), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 47 HIS 0.003 0.001 HIS C1046 PHE 0.019 0.001 PHE C1079 TYR 0.021 0.001 TYR C 886 ARG 0.013 0.000 ARG C 829 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 882) hydrogen bonds : angle 4.95392 ( 2451) SS BOND : bond 0.00241 ( 50) SS BOND : angle 0.91730 ( 100) covalent geometry : bond 0.00281 (31883) covalent geometry : angle 0.60243 (43384) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 186 time to evaluate : 3.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 83 PHE cc_start: 0.7970 (t80) cc_final: 0.7661 (t80) REVERT: A 101 TRP cc_start: 0.8377 (OUTLIER) cc_final: 0.6063 (p90) REVERT: A 601 VAL cc_start: 0.9256 (t) cc_final: 0.9009 (m) REVERT: A 818 GLN cc_start: 0.7702 (mm110) cc_final: 0.7482 (mp10) REVERT: A 992 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8236 (mp10) REVERT: A 999 GLU cc_start: 0.9157 (tt0) cc_final: 0.8893 (tm-30) REVERT: A 1076 VAL cc_start: 0.7482 (OUTLIER) cc_final: 0.6886 (m) REVERT: E 33 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.8136 (m-10) REVERT: E 47 TRP cc_start: 0.7365 (OUTLIER) cc_final: 0.7123 (p-90) REVERT: E 54 ASP cc_start: 0.9188 (OUTLIER) cc_final: 0.8974 (p0) REVERT: D 32 TYR cc_start: 0.8602 (m-10) cc_final: 0.8228 (m-10) REVERT: D 87 TYR cc_start: 0.7893 (m-80) cc_final: 0.7531 (m-80) REVERT: D 142 TYR cc_start: 0.7823 (t80) cc_final: 0.7312 (t80) REVERT: G 33 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.8135 (m-10) REVERT: G 34 MET cc_start: 0.7178 (tpt) cc_final: 0.6899 (tpt) REVERT: G 45 LEU cc_start: 0.1168 (OUTLIER) cc_final: 0.0015 (tm) REVERT: G 63 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7298 (pmtt) REVERT: G 70 MET cc_start: 0.7528 (ptp) cc_final: 0.6866 (ptp) REVERT: F 110 ARG cc_start: 0.4816 (OUTLIER) cc_final: 0.4455 (tmm160) REVERT: F 136 CYS cc_start: 0.6806 (t) cc_final: 0.5567 (p) REVERT: B 157 PHE cc_start: 0.7550 (m-80) cc_final: 0.6937 (t80) REVERT: B 338 TYR cc_start: 0.8201 (p90) cc_final: 0.7878 (p90) REVERT: B 365 LYS cc_start: 0.9340 (mtpt) cc_final: 0.9114 (pmmt) REVERT: B 367 TYR cc_start: 0.9090 (m-80) cc_final: 0.8338 (m-80) REVERT: B 629 PHE cc_start: 0.7735 (t80) cc_final: 0.7505 (t80) REVERT: B 692 ASN cc_start: 0.8353 (m-40) cc_final: 0.8016 (p0) REVERT: B 744 GLN cc_start: 0.8966 (mt0) cc_final: 0.8748 (mt0) REVERT: B 939 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8046 (tm-30) REVERT: B 977 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8539 (ptp90) REVERT: C 83 PHE cc_start: 0.8427 (t80) cc_final: 0.7946 (t80) REVERT: C 151 MET cc_start: 0.5183 (mmt) cc_final: 0.4547 (mmt) REVERT: C 327 GLU cc_start: 0.9171 (mp0) cc_final: 0.8890 (mp0) REVERT: C 629 PHE cc_start: 0.8067 (t80) cc_final: 0.7776 (t80) REVERT: C 932 ASP cc_start: 0.8920 (m-30) cc_final: 0.8685 (m-30) REVERT: C 937 ASN cc_start: 0.9238 (OUTLIER) cc_final: 0.8934 (t0) REVERT: C 939 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8342 (tm-30) REVERT: C 999 GLU cc_start: 0.9236 (tt0) cc_final: 0.8936 (tm-30) REVERT: C 1076 VAL cc_start: 0.7820 (OUTLIER) cc_final: 0.7435 (t) outliers start: 111 outliers final: 59 residues processed: 284 average time/residue: 1.1407 time to fit residues: 399.7611 Evaluate side-chains 239 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 167 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1130 PHE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 47 TRP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 833 CYS Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 977 ARG Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 408 TYR Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain C residue 937 ASN Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1079 PHE Chi-restraints excluded: chain C residue 1105 SER Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain C residue 1130 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 197 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 181 optimal weight: 20.0000 chunk 382 optimal weight: 0.0470 chunk 374 optimal weight: 1.9990 chunk 230 optimal weight: 30.0000 chunk 20 optimal weight: 0.9980 chunk 394 optimal weight: 6.9990 chunk 270 optimal weight: 3.9990 chunk 313 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN ** C 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 ASN C 992 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.102513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.061369 restraints weight = 98430.643| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.69 r_work: 0.2943 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31933 Z= 0.133 Angle : 0.606 16.076 43484 Z= 0.298 Chirality : 0.043 0.188 4906 Planarity : 0.004 0.052 5610 Dihedral : 4.767 58.493 4334 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.93 % Favored : 92.04 % Rotamer: Outliers : 3.44 % Allowed : 15.37 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.13), residues: 3971 helix: 1.65 (0.20), residues: 737 sheet: -1.54 (0.16), residues: 1012 loop : -2.49 (0.12), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP E 47 HIS 0.003 0.000 HIS C1046 PHE 0.018 0.001 PHE C1079 TYR 0.025 0.001 TYR D 49 ARG 0.008 0.000 ARG B 829 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 882) hydrogen bonds : angle 4.82532 ( 2451) SS BOND : bond 0.00263 ( 50) SS BOND : angle 0.91988 ( 100) covalent geometry : bond 0.00307 (31883) covalent geometry : angle 0.60555 (43384) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 183 time to evaluate : 3.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 83 PHE cc_start: 0.8010 (t80) cc_final: 0.7705 (t80) REVERT: A 101 TRP cc_start: 0.8416 (OUTLIER) cc_final: 0.6133 (p90) REVERT: A 818 GLN cc_start: 0.7766 (mm110) cc_final: 0.7565 (mp10) REVERT: A 992 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8245 (mp10) REVERT: A 999 GLU cc_start: 0.9156 (tt0) cc_final: 0.8903 (tm-30) REVERT: A 1076 VAL cc_start: 0.7709 (OUTLIER) cc_final: 0.7436 (m) REVERT: A 1092 PHE cc_start: 0.7980 (t80) cc_final: 0.7661 (t80) REVERT: E 33 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.8120 (m-10) REVERT: E 54 ASP cc_start: 0.9199 (OUTLIER) cc_final: 0.8982 (p0) REVERT: D 24 ARG cc_start: 0.7751 (mpp80) cc_final: 0.7517 (mpp80) REVERT: D 32 TYR cc_start: 0.8593 (m-10) cc_final: 0.8233 (m-10) REVERT: D 87 TYR cc_start: 0.7919 (m-80) cc_final: 0.7491 (m-80) REVERT: D 142 TYR cc_start: 0.7833 (t80) cc_final: 0.7337 (t80) REVERT: G 33 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.8235 (m-10) REVERT: G 34 MET cc_start: 0.7197 (tpt) cc_final: 0.6905 (tpt) REVERT: G 45 LEU cc_start: 0.1083 (OUTLIER) cc_final: -0.0104 (tm) REVERT: G 70 MET cc_start: 0.7259 (ptp) cc_final: 0.6995 (ptp) REVERT: F 97 MET cc_start: 0.8575 (tpt) cc_final: 0.8145 (tpp) REVERT: F 136 CYS cc_start: 0.6842 (t) cc_final: 0.5607 (p) REVERT: B 45 GLU cc_start: 0.8588 (tp30) cc_final: 0.8295 (mm-30) REVERT: B 157 PHE cc_start: 0.7449 (m-80) cc_final: 0.6966 (t80) REVERT: B 338 TYR cc_start: 0.8288 (p90) cc_final: 0.8012 (p90) REVERT: B 365 LYS cc_start: 0.9369 (mtpt) cc_final: 0.9034 (pttt) REVERT: B 367 TYR cc_start: 0.9113 (m-80) cc_final: 0.8607 (m-80) REVERT: B 476 TRP cc_start: 0.9093 (m100) cc_final: 0.8774 (t-100) REVERT: B 629 PHE cc_start: 0.7741 (t80) cc_final: 0.7414 (t80) REVERT: B 692 ASN cc_start: 0.8360 (m-40) cc_final: 0.8062 (p0) REVERT: B 744 GLN cc_start: 0.8957 (mt0) cc_final: 0.8730 (mt0) REVERT: B 939 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8073 (tm-30) REVERT: B 977 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8544 (ptp90) REVERT: C 83 PHE cc_start: 0.8431 (t80) cc_final: 0.7950 (t80) REVERT: C 151 MET cc_start: 0.5241 (mmt) cc_final: 0.4547 (mmt) REVERT: C 327 GLU cc_start: 0.9176 (mp0) cc_final: 0.8882 (mp0) REVERT: C 629 PHE cc_start: 0.8091 (t80) cc_final: 0.7797 (t80) REVERT: C 932 ASP cc_start: 0.8914 (m-30) cc_final: 0.8681 (m-30) REVERT: C 939 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8361 (tm-30) REVERT: C 999 GLU cc_start: 0.9228 (tt0) cc_final: 0.8935 (tm-30) outliers start: 119 outliers final: 64 residues processed: 284 average time/residue: 1.1043 time to fit residues: 388.1608 Evaluate side-chains 240 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 168 time to evaluate : 3.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1130 PHE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 833 CYS Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 977 ARG Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 408 TYR Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain C residue 1130 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 174 optimal weight: 50.0000 chunk 255 optimal weight: 0.9990 chunk 138 optimal weight: 30.0000 chunk 313 optimal weight: 6.9990 chunk 322 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 16 optimal weight: 0.0030 chunk 215 optimal weight: 0.6980 chunk 9 optimal weight: 20.0000 chunk 28 optimal weight: 50.0000 chunk 11 optimal weight: 20.0000 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN B 877 GLN ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN ** C 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1030 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.103555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.062924 restraints weight = 98482.931| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.72 r_work: 0.2995 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 31933 Z= 0.107 Angle : 0.604 14.483 43484 Z= 0.294 Chirality : 0.043 0.188 4906 Planarity : 0.004 0.052 5610 Dihedral : 4.676 57.062 4334 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.50 % Favored : 92.47 % Rotamer: Outliers : 2.95 % Allowed : 16.12 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.13), residues: 3971 helix: 1.70 (0.20), residues: 739 sheet: -1.41 (0.16), residues: 1008 loop : -2.39 (0.12), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP E 47 HIS 0.004 0.000 HIS C1046 PHE 0.028 0.001 PHE C1077 TYR 0.024 0.001 TYR D 49 ARG 0.009 0.000 ARG B 829 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 882) hydrogen bonds : angle 4.67594 ( 2451) SS BOND : bond 0.00212 ( 50) SS BOND : angle 0.81421 ( 100) covalent geometry : bond 0.00244 (31883) covalent geometry : angle 0.60352 (43384) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 190 time to evaluate : 3.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.7945 (t80) cc_final: 0.7635 (t80) REVERT: A 151 MET cc_start: 0.5837 (OUTLIER) cc_final: 0.5622 (tpt) REVERT: A 573 ILE cc_start: 0.6456 (OUTLIER) cc_final: 0.6202 (pt) REVERT: A 992 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8226 (mp10) REVERT: A 999 GLU cc_start: 0.9147 (tt0) cc_final: 0.8913 (tm-30) REVERT: A 1076 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7544 (m) REVERT: A 1092 PHE cc_start: 0.7802 (t80) cc_final: 0.7462 (t80) REVERT: E 33 TYR cc_start: 0.8489 (OUTLIER) cc_final: 0.8210 (m-10) REVERT: E 54 ASP cc_start: 0.9229 (OUTLIER) cc_final: 0.9026 (p0) REVERT: D 24 ARG cc_start: 0.7771 (mpp80) cc_final: 0.7528 (mpp80) REVERT: D 32 TYR cc_start: 0.8572 (m-10) cc_final: 0.8202 (m-10) REVERT: D 87 TYR cc_start: 0.7917 (m-80) cc_final: 0.7483 (m-80) REVERT: D 142 TYR cc_start: 0.7849 (t80) cc_final: 0.7352 (t80) REVERT: G 33 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.8219 (m-10) REVERT: G 34 MET cc_start: 0.7256 (tpt) cc_final: 0.6904 (tpt) REVERT: G 45 LEU cc_start: 0.1008 (OUTLIER) cc_final: -0.0127 (tm) REVERT: G 63 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7435 (pmtt) REVERT: F 136 CYS cc_start: 0.6883 (t) cc_final: 0.5577 (p) REVERT: B 129 ASN cc_start: 0.7139 (OUTLIER) cc_final: 0.6934 (t0) REVERT: B 157 PHE cc_start: 0.7389 (m-80) cc_final: 0.6900 (t80) REVERT: B 338 TYR cc_start: 0.8360 (p90) cc_final: 0.8078 (p90) REVERT: B 365 LYS cc_start: 0.9356 (mtpt) cc_final: 0.9032 (pttt) REVERT: B 367 TYR cc_start: 0.9125 (m-80) cc_final: 0.8652 (m-80) REVERT: B 476 TRP cc_start: 0.9085 (m100) cc_final: 0.8779 (t-100) REVERT: B 629 PHE cc_start: 0.7590 (t80) cc_final: 0.7375 (t80) REVERT: B 692 ASN cc_start: 0.8262 (m-40) cc_final: 0.7942 (p0) REVERT: B 744 GLN cc_start: 0.8948 (mt0) cc_final: 0.8712 (mt0) REVERT: B 929 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8071 (mmmm) REVERT: B 939 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8050 (tm-30) REVERT: C 83 PHE cc_start: 0.8416 (t80) cc_final: 0.7936 (t80) REVERT: C 151 MET cc_start: 0.5283 (mmt) cc_final: 0.4601 (mmt) REVERT: C 327 GLU cc_start: 0.9185 (mp0) cc_final: 0.8900 (mp0) REVERT: C 629 PHE cc_start: 0.7964 (t80) cc_final: 0.7717 (t80) REVERT: C 932 ASP cc_start: 0.8899 (m-30) cc_final: 0.8680 (m-30) REVERT: C 939 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8368 (tm-30) REVERT: C 999 GLU cc_start: 0.9210 (tt0) cc_final: 0.8945 (tm-30) REVERT: C 1076 VAL cc_start: 0.7962 (OUTLIER) cc_final: 0.7524 (t) REVERT: C 1077 PHE cc_start: 0.8074 (m-80) cc_final: 0.7779 (m-80) outliers start: 102 outliers final: 63 residues processed: 278 average time/residue: 1.1174 time to fit residues: 384.4524 Evaluate side-chains 252 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 177 time to evaluate : 3.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1130 PHE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 833 CYS Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 408 TYR Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1079 PHE Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain C residue 1130 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 275 optimal weight: 3.9990 chunk 301 optimal weight: 5.9990 chunk 232 optimal weight: 0.2980 chunk 192 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 253 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 118 optimal weight: 50.0000 chunk 175 optimal weight: 50.0000 chunk 368 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 917 GLN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN ** C 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.101619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.060056 restraints weight = 99019.597| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.71 r_work: 0.2915 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31933 Z= 0.184 Angle : 0.643 14.560 43484 Z= 0.315 Chirality : 0.044 0.207 4906 Planarity : 0.004 0.074 5610 Dihedral : 4.818 54.614 4334 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.11 % Favored : 91.82 % Rotamer: Outliers : 2.89 % Allowed : 16.44 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.13), residues: 3971 helix: 1.64 (0.20), residues: 748 sheet: -1.36 (0.16), residues: 1029 loop : -2.33 (0.12), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP E 47 HIS 0.003 0.001 HIS A1040 PHE 0.023 0.001 PHE B1057 TYR 0.020 0.001 TYR C 356 ARG 0.016 0.001 ARG C 829 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 882) hydrogen bonds : angle 4.73575 ( 2451) SS BOND : bond 0.00319 ( 50) SS BOND : angle 0.99524 ( 100) covalent geometry : bond 0.00427 (31883) covalent geometry : angle 0.64196 (43384) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 180 time to evaluate : 3.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8025 (t80) cc_final: 0.7719 (t80) REVERT: A 151 MET cc_start: 0.5976 (OUTLIER) cc_final: 0.5740 (tpt) REVERT: A 992 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8284 (mp10) REVERT: A 999 GLU cc_start: 0.9151 (tt0) cc_final: 0.8910 (tm-30) REVERT: A 1077 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7707 (t80) REVERT: E 33 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.8142 (m-10) REVERT: E 153 PHE cc_start: 0.8238 (t80) cc_final: 0.8027 (t80) REVERT: E 155 GLU cc_start: 0.6348 (pm20) cc_final: 0.6124 (pm20) REVERT: D 24 ARG cc_start: 0.7810 (mpp80) cc_final: 0.7548 (mpp80) REVERT: D 32 TYR cc_start: 0.8586 (m-10) cc_final: 0.8248 (m-10) REVERT: D 142 TYR cc_start: 0.7864 (t80) cc_final: 0.7374 (t80) REVERT: G 33 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8251 (m-10) REVERT: G 34 MET cc_start: 0.7293 (tpt) cc_final: 0.6943 (tpt) REVERT: G 45 LEU cc_start: 0.1269 (OUTLIER) cc_final: 0.0078 (tm) REVERT: G 63 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7457 (pmtt) REVERT: B 129 ASN cc_start: 0.7308 (OUTLIER) cc_final: 0.7062 (t0) REVERT: B 157 PHE cc_start: 0.7514 (m-80) cc_final: 0.7034 (t80) REVERT: B 338 TYR cc_start: 0.8367 (p90) cc_final: 0.8079 (p90) REVERT: B 365 LYS cc_start: 0.9442 (mtpt) cc_final: 0.9172 (pmmt) REVERT: B 367 TYR cc_start: 0.9234 (m-80) cc_final: 0.8546 (m-80) REVERT: B 629 PHE cc_start: 0.7763 (t80) cc_final: 0.7461 (t80) REVERT: B 744 GLN cc_start: 0.8926 (mt0) cc_final: 0.8680 (mt0) REVERT: B 929 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8175 (mmmm) REVERT: B 939 GLN cc_start: 0.8480 (tm-30) cc_final: 0.8159 (tm-30) REVERT: B 977 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8563 (ptp90) REVERT: C 83 PHE cc_start: 0.8375 (t80) cc_final: 0.7928 (t80) REVERT: C 151 MET cc_start: 0.5162 (mmt) cc_final: 0.4570 (mmt) REVERT: C 327 GLU cc_start: 0.9203 (mp0) cc_final: 0.8906 (mp0) REVERT: C 629 PHE cc_start: 0.8113 (t80) cc_final: 0.7820 (t80) REVERT: C 632 GLN cc_start: 0.8757 (tp-100) cc_final: 0.8500 (tp-100) REVERT: C 932 ASP cc_start: 0.8959 (m-30) cc_final: 0.8703 (m-30) REVERT: C 939 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8351 (tm-30) REVERT: C 999 GLU cc_start: 0.9235 (tt0) cc_final: 0.8953 (tm-30) REVERT: C 1077 PHE cc_start: 0.8040 (m-80) cc_final: 0.7744 (m-80) outliers start: 100 outliers final: 64 residues processed: 267 average time/residue: 1.1172 time to fit residues: 368.5440 Evaluate side-chains 243 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 169 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1077 PHE Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1130 PHE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 833 CYS Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 977 ARG Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 408 TYR Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1079 PHE Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 152 optimal weight: 20.0000 chunk 285 optimal weight: 2.9990 chunk 398 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 367 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 274 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 ASN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 947 GLN B 984 GLN ** B1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.099395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.057099 restraints weight = 98802.586| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.72 r_work: 0.2828 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.5880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 31933 Z= 0.277 Angle : 0.723 15.569 43484 Z= 0.361 Chirality : 0.046 0.229 4906 Planarity : 0.004 0.064 5610 Dihedral : 5.280 56.502 4330 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.37 % Favored : 90.56 % Rotamer: Outliers : 2.74 % Allowed : 16.61 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.87 (0.13), residues: 3971 helix: 1.51 (0.20), residues: 731 sheet: -1.33 (0.16), residues: 1029 loop : -2.25 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 47 HIS 0.005 0.001 HIS A1040 PHE 0.033 0.002 PHE C 551 TYR 0.026 0.001 TYR D 49 ARG 0.012 0.001 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 882) hydrogen bonds : angle 4.94796 ( 2451) SS BOND : bond 0.00432 ( 50) SS BOND : angle 1.33313 ( 100) covalent geometry : bond 0.00637 (31883) covalent geometry : angle 0.72069 (43384) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 184 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8014 (t80) cc_final: 0.7564 (t80) REVERT: A 107 MET cc_start: 0.8394 (mpp) cc_final: 0.8148 (mmp) REVERT: A 157 PHE cc_start: 0.7962 (m-80) cc_final: 0.7724 (m-80) REVERT: A 992 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8299 (mp10) REVERT: A 999 GLU cc_start: 0.9177 (tt0) cc_final: 0.8926 (tm-30) REVERT: A 1077 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7625 (t80) REVERT: E 155 GLU cc_start: 0.6177 (pm20) cc_final: 0.5942 (pm20) REVERT: D 32 TYR cc_start: 0.8553 (m-10) cc_final: 0.8203 (m-10) REVERT: D 142 TYR cc_start: 0.7824 (t80) cc_final: 0.7328 (t80) REVERT: G 33 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.8249 (m-10) REVERT: G 34 MET cc_start: 0.7399 (tpt) cc_final: 0.7070 (tpt) REVERT: G 45 LEU cc_start: 0.1815 (OUTLIER) cc_final: 0.0627 (tm) REVERT: G 63 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7439 (pmtt) REVERT: B 157 PHE cc_start: 0.7945 (m-80) cc_final: 0.7318 (t80) REVERT: B 338 TYR cc_start: 0.8393 (p90) cc_final: 0.8108 (p90) REVERT: B 365 LYS cc_start: 0.9551 (mtpt) cc_final: 0.9281 (pmmt) REVERT: B 367 TYR cc_start: 0.9279 (m-80) cc_final: 0.8602 (m-80) REVERT: B 744 GLN cc_start: 0.8931 (mt0) cc_final: 0.8713 (mt0) REVERT: B 815 PHE cc_start: 0.8238 (m-10) cc_final: 0.7946 (m-10) REVERT: B 816 MET cc_start: 0.7671 (tmm) cc_final: 0.7392 (tmm) REVERT: B 929 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8278 (mmmm) REVERT: B 939 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8238 (tm-30) REVERT: B 977 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8517 (ptp90) REVERT: B 1077 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7669 (t80) REVERT: C 83 PHE cc_start: 0.8254 (t80) cc_final: 0.8009 (t80) REVERT: C 151 MET cc_start: 0.5177 (mmt) cc_final: 0.4555 (mmt) REVERT: C 327 GLU cc_start: 0.9201 (mp0) cc_final: 0.8867 (mp0) REVERT: C 629 PHE cc_start: 0.8264 (t80) cc_final: 0.7932 (t80) REVERT: C 632 GLN cc_start: 0.8814 (tp-100) cc_final: 0.8545 (tp-100) REVERT: C 932 ASP cc_start: 0.9001 (m-30) cc_final: 0.8688 (m-30) REVERT: C 939 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8445 (tm-30) REVERT: C 999 GLU cc_start: 0.9267 (tt0) cc_final: 0.8967 (tm-30) REVERT: C 1077 PHE cc_start: 0.8028 (m-80) cc_final: 0.7727 (m-80) outliers start: 95 outliers final: 59 residues processed: 265 average time/residue: 1.1413 time to fit residues: 375.2412 Evaluate side-chains 237 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 170 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1077 PHE Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1130 PHE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 833 CYS Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 977 ARG Chi-restraints excluded: chain B residue 1077 PHE Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 408 TYR Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain C residue 1064 CYS Chi-restraints excluded: chain C residue 1079 PHE Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 48 optimal weight: 0.0770 chunk 81 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 348 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 chunk 240 optimal weight: 0.6980 chunk 110 optimal weight: 40.0000 chunk 92 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN B 301 GLN B 984 GLN ** B1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 984 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.101935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.060837 restraints weight = 98099.080| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.67 r_work: 0.2940 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31933 Z= 0.117 Angle : 0.663 13.778 43484 Z= 0.323 Chirality : 0.044 0.192 4906 Planarity : 0.004 0.060 5610 Dihedral : 5.004 57.953 4328 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.01 % Favored : 91.94 % Rotamer: Outliers : 2.37 % Allowed : 17.04 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.73 (0.13), residues: 3971 helix: 1.60 (0.20), residues: 743 sheet: -1.12 (0.16), residues: 993 loop : -2.22 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 47 HIS 0.003 0.000 HIS C1046 PHE 0.023 0.001 PHE E 153 TYR 0.013 0.001 TYR G 183 ARG 0.014 0.001 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.03297 ( 882) hydrogen bonds : angle 4.68851 ( 2451) SS BOND : bond 0.00306 ( 50) SS BOND : angle 1.02015 ( 100) covalent geometry : bond 0.00269 (31883) covalent geometry : angle 0.66237 (43384) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 180 time to evaluate : 3.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8021 (t80) cc_final: 0.7688 (t80) REVERT: A 152 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8060 (tt) REVERT: A 992 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8219 (mp10) REVERT: A 999 GLU cc_start: 0.9125 (tt0) cc_final: 0.8916 (tm-30) REVERT: A 1077 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7637 (t80) REVERT: A 1092 PHE cc_start: 0.8048 (t80) cc_final: 0.7645 (t80) REVERT: D 24 ARG cc_start: 0.7900 (mpp80) cc_final: 0.7582 (mpp80) REVERT: D 32 TYR cc_start: 0.8551 (m-10) cc_final: 0.8200 (m-10) REVERT: D 50 ASP cc_start: 0.9592 (m-30) cc_final: 0.9357 (m-30) REVERT: D 53 ASN cc_start: 0.9040 (t0) cc_final: 0.8839 (p0) REVERT: D 142 TYR cc_start: 0.7865 (t80) cc_final: 0.7364 (t80) REVERT: G 33 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8359 (m-10) REVERT: G 34 MET cc_start: 0.7405 (tpt) cc_final: 0.7075 (tpt) REVERT: G 45 LEU cc_start: 0.1561 (OUTLIER) cc_final: 0.0429 (tm) REVERT: G 63 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7448 (pmtt) REVERT: G 70 MET cc_start: 0.6405 (ptm) cc_final: 0.6143 (ptt) REVERT: F 136 CYS cc_start: 0.6988 (t) cc_final: 0.5629 (p) REVERT: B 157 PHE cc_start: 0.7840 (m-80) cc_final: 0.7199 (t80) REVERT: B 338 TYR cc_start: 0.8379 (p90) cc_final: 0.8074 (p90) REVERT: B 365 LYS cc_start: 0.9524 (mtpt) cc_final: 0.9274 (pmmt) REVERT: B 367 TYR cc_start: 0.9257 (m-80) cc_final: 0.8613 (m-80) REVERT: B 476 TRP cc_start: 0.9102 (m100) cc_final: 0.8783 (t-100) REVERT: B 744 GLN cc_start: 0.8903 (mt0) cc_final: 0.8689 (mt0) REVERT: B 929 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8103 (mmmm) REVERT: B 939 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8109 (tm-30) REVERT: B 1077 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7585 (t80) REVERT: B 1092 PHE cc_start: 0.8208 (t80) cc_final: 0.7901 (t80) REVERT: C 83 PHE cc_start: 0.8258 (t80) cc_final: 0.7836 (t80) REVERT: C 151 MET cc_start: 0.5270 (mmt) cc_final: 0.4641 (mmt) REVERT: C 327 GLU cc_start: 0.9203 (mp0) cc_final: 0.8899 (mp0) REVERT: C 629 PHE cc_start: 0.8035 (t80) cc_final: 0.7761 (t80) REVERT: C 632 GLN cc_start: 0.8724 (tp-100) cc_final: 0.8313 (tp-100) REVERT: C 932 ASP cc_start: 0.8964 (m-30) cc_final: 0.8726 (m-30) REVERT: C 939 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8362 (tm-30) REVERT: C 999 GLU cc_start: 0.9236 (tt0) cc_final: 0.8927 (tm-30) REVERT: C 1077 PHE cc_start: 0.7987 (m-80) cc_final: 0.7588 (m-80) outliers start: 82 outliers final: 52 residues processed: 249 average time/residue: 1.1740 time to fit residues: 359.8831 Evaluate side-chains 227 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 167 time to evaluate : 3.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 833 CYS Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1077 PHE Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1130 PHE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 833 CYS Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 1077 PHE Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 984 GLN Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 293 optimal weight: 0.5980 chunk 104 optimal weight: 0.0770 chunk 221 optimal weight: 0.0870 chunk 232 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 124 optimal weight: 50.0000 chunk 70 optimal weight: 0.0010 chunk 329 optimal weight: 10.0000 chunk 316 optimal weight: 3.9990 overall best weight: 0.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN B 984 GLN B 993 GLN C 530 ASN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.102750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.062016 restraints weight = 98058.726| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.70 r_work: 0.2975 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31933 Z= 0.111 Angle : 0.662 14.211 43484 Z= 0.319 Chirality : 0.044 0.212 4906 Planarity : 0.004 0.050 5610 Dihedral : 4.827 57.095 4326 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.03 % Favored : 91.94 % Rotamer: Outliers : 2.14 % Allowed : 17.50 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.59 (0.13), residues: 3971 helix: 1.67 (0.20), residues: 739 sheet: -0.95 (0.17), residues: 958 loop : -2.15 (0.12), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP E 47 HIS 0.004 0.000 HIS C1046 PHE 0.033 0.001 PHE B 815 TYR 0.014 0.001 TYR B1049 ARG 0.015 0.001 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.03117 ( 882) hydrogen bonds : angle 4.57111 ( 2451) SS BOND : bond 0.00275 ( 50) SS BOND : angle 0.92476 ( 100) covalent geometry : bond 0.00254 (31883) covalent geometry : angle 0.66133 (43384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28912.90 seconds wall clock time: 497 minutes 0.37 seconds (29820.37 seconds total)