Starting phenix.real_space_refine on Mon Aug 25 22:34:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kdm_37139/08_2025/8kdm_37139.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kdm_37139/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8kdm_37139/08_2025/8kdm_37139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kdm_37139/08_2025/8kdm_37139.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kdm_37139/08_2025/8kdm_37139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kdm_37139/08_2025/8kdm_37139.map" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.61, per 1000 atoms: 0.21 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: 2.80 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.51 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: 7.39 Time building geometry restraints manager: 3.52 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: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 28.990 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.210 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.65 (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 ARG 0.002 0.000 ARG A 887 TYR 0.006 0.000 TYR A 660 PHE 0.007 0.001 PHE C 360 TRP 0.012 0.001 TRP E 47 HIS 0.002 0.000 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00157 (31883) covalent geometry : angle 0.44774 (43384) SS BOND : bond 0.00090 ( 50) SS BOND : angle 0.46118 ( 100) hydrogen bonds : bond 0.23366 ( 882) hydrogen bonds : angle 8.17071 ( 2451) *********************** 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 : 0.779 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: 0.6039 time to fit residues: 518.1606 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 : 1.243 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 50.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 523 GLN A 546 GLN A 550 GLN A 599 GLN A 783 ASN A 835 GLN ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 ASN 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 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 HIS G 178 GLN F 37 GLN F 157 GLN ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN B 301 GLN B 375 ASN B 396 GLN B 546 GLN B 550 GLN B 818 GLN B 835 GLN ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 ASN B 984 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 931 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1046 HIS C1124 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.106560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.066995 restraints weight = 100694.280| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.74 r_work: 0.3106 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 31933 Z= 0.216 Angle : 0.691 15.315 43484 Z= 0.351 Chirality : 0.045 0.269 4906 Planarity : 0.005 0.061 5610 Dihedral : 4.889 70.676 4356 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.98 % Favored : 91.99 % Rotamer: Outliers : 4.30 % Allowed : 12.51 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.07 (0.12), residues: 3971 helix: 1.09 (0.20), residues: 728 sheet: -2.14 (0.15), residues: 957 loop : -3.22 (0.11), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 553 TYR 0.021 0.002 TYR B 886 PHE 0.024 0.002 PHE C1079 TRP 0.033 0.002 TRP D 94 HIS 0.009 0.001 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00488 (31883) covalent geometry : angle 0.68841 (43384) SS BOND : bond 0.00485 ( 50) SS BOND : angle 1.41278 ( 100) hydrogen bonds : bond 0.03953 ( 882) hydrogen bonds : angle 5.86778 ( 2451) *********************** 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 410 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 261 time to evaluate : 1.275 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: 0.8103 (t80) cc_final: 0.7828 (t80) REVERT: A 329 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: A 721 ASN cc_start: 0.9022 (t0) cc_final: 0.8818 (t0) REVERT: A 939 GLN cc_start: 0.8308 (tm-30) cc_final: 0.8002 (tm-30) REVERT: A 992 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8229 (mp10) REVERT: A 999 GLU cc_start: 0.9196 (tt0) cc_final: 0.8873 (tm-30) REVERT: E 31 ASP cc_start: 0.8961 (p0) cc_final: 0.8634 (p0) REVERT: E 33 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7932 (m-10) REVERT: E 45 LEU cc_start: 0.5639 (OUTLIER) cc_final: 0.5425 (tm) REVERT: E 67 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6887 (ptm160) REVERT: E 80 TYR cc_start: 0.9110 (m-80) cc_final: 0.8715 (m-10) REVERT: E 82 GLU cc_start: 0.9502 (tt0) cc_final: 0.9172 (tp30) REVERT: E 153 PHE cc_start: 0.8207 (t80) cc_final: 0.7325 (t80) REVERT: E 155 GLU cc_start: 0.6295 (pm20) cc_final: 0.5542 (pm20) REVERT: D 32 TYR cc_start: 0.8664 (m-10) cc_final: 0.8335 (m-10) REVERT: D 142 TYR cc_start: 0.7761 (t80) cc_final: 0.7249 (t80) REVERT: G 80 TYR cc_start: 0.8883 (m-80) cc_final: 0.8640 (m-80) REVERT: F 97 MET cc_start: 0.8613 (tpp) cc_final: 0.8280 (tpp) REVERT: F 110 ARG cc_start: 0.5201 (OUTLIER) cc_final: 0.4967 (ptm-80) REVERT: F 136 CYS cc_start: 0.6558 (t) cc_final: 0.5542 (p) REVERT: B 151 MET cc_start: 0.8535 (pmm) cc_final: 0.8180 (pmm) REVERT: B 222 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8819 (pp) REVERT: B 338 TYR cc_start: 0.8168 (p90) cc_final: 0.7717 (p90) REVERT: B 365 LYS cc_start: 0.9259 (mtpt) cc_final: 0.8969 (ptpp) REVERT: B 367 TYR cc_start: 0.8918 (m-80) cc_final: 0.8190 (m-80) REVERT: B 744 GLN cc_start: 0.8805 (mt0) cc_final: 0.8583 (mt0) REVERT: B 829 ARG cc_start: 0.8920 (mmm160) cc_final: 0.8701 (mmm160) REVERT: B 939 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7960 (tm-30) REVERT: B 976 ASP cc_start: 0.9091 (m-30) cc_final: 0.8871 (t0) REVERT: C 83 PHE cc_start: 0.8618 (t80) cc_final: 0.8095 (t80) REVERT: C 151 MET cc_start: 0.5228 (mmt) cc_final: 0.4438 (mmt) REVERT: C 221 LYS cc_start: 0.9290 (ttpt) cc_final: 0.9063 (tptp) REVERT: C 301 GLN cc_start: 0.9222 (OUTLIER) cc_final: 0.8918 (mm-40) REVERT: C 327 GLU cc_start: 0.9002 (mp0) cc_final: 0.8776 (mp0) REVERT: C 401 GLN cc_start: 0.7549 (mp10) cc_final: 0.7264 (mp10) REVERT: C 600 ASP cc_start: 0.8881 (m-30) cc_final: 0.8473 (m-30) REVERT: C 629 PHE cc_start: 0.7936 (t80) cc_final: 0.7676 (t80) REVERT: C 932 ASP cc_start: 0.8766 (m-30) cc_final: 0.8501 (m-30) REVERT: C 939 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8287 (tm-30) REVERT: C 1077 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6527 (m-80) outliers start: 149 outliers final: 52 residues processed: 380 average time/residue: 0.5900 time to fit residues: 273.1436 Evaluate side-chains 263 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 202 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 203 ILE 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 538 LEU Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 720 CYS 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 33 TYR Chi-restraints excluded: chain E residue 45 LEU 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 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 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 124 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 635 CYS Chi-restraints excluded: chain B residue 693 THR 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 897 VAL Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 1096 ILE 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 301 GLN 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 662 THR Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 878 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 1130 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 195 optimal weight: 4.9990 chunk 152 optimal weight: 50.0000 chunk 309 optimal weight: 3.9990 chunk 180 optimal weight: 0.2980 chunk 36 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 362 optimal weight: 3.9990 chunk 236 optimal weight: 20.0000 chunk 366 optimal weight: 0.6980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN B 155 ASN B 301 GLN ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 GLN ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN C 627 ASN C 896 ASN C 904 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.105213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.064990 restraints weight = 99485.571| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.77 r_work: 0.3051 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31933 Z= 0.157 Angle : 0.614 16.722 43484 Z= 0.307 Chirality : 0.043 0.227 4906 Planarity : 0.004 0.054 5610 Dihedral : 4.586 55.839 4340 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.20 % Favored : 92.77 % Rotamer: Outliers : 3.06 % Allowed : 14.24 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.63 (0.13), residues: 3971 helix: 1.49 (0.20), residues: 730 sheet: -1.86 (0.16), residues: 983 loop : -2.96 (0.11), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 829 TYR 0.024 0.001 TYR C 886 PHE 0.021 0.001 PHE C1079 TRP 0.040 0.001 TRP E 47 HIS 0.004 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00357 (31883) covalent geometry : angle 0.61276 (43384) SS BOND : bond 0.00262 ( 50) SS BOND : angle 0.99281 ( 100) hydrogen bonds : bond 0.03617 ( 882) hydrogen bonds : angle 5.39115 ( 2451) *********************** 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 318 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 212 time to evaluate : 1.371 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 83 PHE cc_start: 0.7837 (t80) cc_final: 0.7518 (t80) REVERT: A 599 GLN cc_start: 0.9050 (tp40) cc_final: 0.8795 (mm-40) REVERT: A 601 VAL cc_start: 0.9324 (t) cc_final: 0.8910 (m) REVERT: A 721 ASN cc_start: 0.9124 (t0) cc_final: 0.8882 (t0) REVERT: A 939 GLN cc_start: 0.8371 (tm-30) cc_final: 0.8019 (tm-30) REVERT: A 992 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8235 (mp10) REVERT: A 999 GLU cc_start: 0.9218 (tt0) cc_final: 0.8891 (tm-30) REVERT: E 12 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8170 (mtpp) REVERT: E 33 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.7948 (m-10) REVERT: E 80 TYR cc_start: 0.8957 (m-80) cc_final: 0.8662 (m-10) REVERT: E 82 GLU cc_start: 0.9460 (tt0) cc_final: 0.9166 (tp30) REVERT: D 32 TYR cc_start: 0.8642 (m-10) cc_final: 0.8327 (m-10) REVERT: D 45 ARG cc_start: 0.8800 (mtp-110) cc_final: 0.8517 (mtm-85) REVERT: D 61 ARG cc_start: 0.8814 (ptt-90) cc_final: 0.8496 (ptt180) REVERT: D 87 TYR cc_start: 0.8017 (m-80) cc_final: 0.7639 (m-80) REVERT: D 142 TYR cc_start: 0.7819 (t80) cc_final: 0.7314 (t80) REVERT: G 33 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.8144 (m-10) REVERT: G 70 MET cc_start: 0.6382 (ptp) cc_final: 0.6027 (ptp) REVERT: F 136 CYS cc_start: 0.6651 (t) cc_final: 0.5628 (p) REVERT: B 222 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9019 (pp) REVERT: B 338 TYR cc_start: 0.8185 (p90) cc_final: 0.7769 (p90) REVERT: B 365 LYS cc_start: 0.9263 (mtpt) cc_final: 0.8945 (ptpt) REVERT: B 367 TYR cc_start: 0.8961 (m-80) cc_final: 0.8366 (m-80) REVERT: B 629 PHE cc_start: 0.7838 (t80) cc_final: 0.7395 (t80) REVERT: B 744 GLN cc_start: 0.8909 (mt0) cc_final: 0.8687 (mt0) REVERT: B 939 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7924 (tm-30) REVERT: B 976 ASP cc_start: 0.9098 (m-30) cc_final: 0.8897 (t0) REVERT: C 83 PHE cc_start: 0.8538 (t80) cc_final: 0.8035 (t80) REVERT: C 151 MET cc_start: 0.5168 (mmt) cc_final: 0.4483 (mmt) REVERT: C 221 LYS cc_start: 0.9315 (ttpt) cc_final: 0.9061 (tmmt) REVERT: C 301 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.9018 (mm-40) REVERT: C 327 GLU cc_start: 0.9067 (mp0) cc_final: 0.8803 (mp0) REVERT: C 365 LYS cc_start: 0.8991 (tppt) cc_final: 0.8717 (tppp) REVERT: C 629 PHE cc_start: 0.7995 (t80) cc_final: 0.7706 (t80) REVERT: C 768 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.9105 (mptt) REVERT: C 932 ASP cc_start: 0.8835 (m-30) cc_final: 0.8618 (m-30) REVERT: C 939 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8244 (tm-30) REVERT: C 992 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8196 (mp10) REVERT: C 999 GLU cc_start: 0.9210 (tt0) cc_final: 0.8941 (tm-30) REVERT: C 1077 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.6399 (m-80) outliers start: 106 outliers final: 49 residues processed: 294 average time/residue: 0.6295 time to fit residues: 223.6102 Evaluate side-chains 241 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 183 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 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 762 GLU Chi-restraints excluded: chain A residue 773 THR 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 12 LYS Chi-restraints excluded: chain E residue 33 TYR 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 33 TYR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 69 THR 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 222 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 278 CYS 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 878 ILE Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 1059 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 301 GLN Chi-restraints excluded: chain C residue 408 TYR Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 562 VAL 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 768 LYS Chi-restraints excluded: chain C residue 773 THR 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 1130 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 392 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 chunk 180 optimal weight: 30.0000 chunk 156 optimal weight: 50.0000 chunk 4 optimal weight: 0.8980 chunk 213 optimal weight: 10.0000 chunk 304 optimal weight: 40.0000 chunk 65 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN B 409 ASN B 530 ASN B 818 GLN B 984 GLN B 993 GLN C 546 GLN C 661 HIS ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.102375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.060988 restraints weight = 98259.590| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.67 r_work: 0.2938 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 31933 Z= 0.206 Angle : 0.638 14.153 43484 Z= 0.323 Chirality : 0.044 0.205 4906 Planarity : 0.004 0.049 5610 Dihedral : 4.896 55.959 4339 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.29 % Favored : 91.64 % Rotamer: Outliers : 3.58 % Allowed : 14.21 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.43 (0.13), residues: 3971 helix: 1.43 (0.20), residues: 737 sheet: -1.70 (0.16), residues: 999 loop : -2.77 (0.12), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 38 TYR 0.026 0.001 TYR C 886 PHE 0.021 0.002 PHE C1079 TRP 0.056 0.002 TRP E 47 HIS 0.006 0.001 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00475 (31883) covalent geometry : angle 0.63653 (43384) SS BOND : bond 0.00381 ( 50) SS BOND : angle 1.08970 ( 100) hydrogen bonds : bond 0.03822 ( 882) hydrogen bonds : angle 5.13118 ( 2451) *********************** 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 329 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 205 time to evaluate : 1.289 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: 0.7977 (t80) cc_final: 0.7675 (t80) REVERT: A 601 VAL cc_start: 0.9277 (t) cc_final: 0.8755 (m) REVERT: A 629 PHE cc_start: 0.8017 (t80) cc_final: 0.7657 (t80) REVERT: A 818 GLN cc_start: 0.7667 (mm110) cc_final: 0.7424 (mp10) REVERT: A 939 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8179 (tm-30) REVERT: A 992 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8298 (mp10) REVERT: A 999 GLU cc_start: 0.9180 (tt0) cc_final: 0.8887 (tm-30) REVERT: E 12 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8174 (mtpp) REVERT: E 47 TRP cc_start: 0.7659 (OUTLIER) cc_final: 0.7188 (p-90) REVERT: E 67 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6329 (ptm160) REVERT: E 80 TYR cc_start: 0.8926 (m-80) cc_final: 0.8676 (m-10) REVERT: E 82 GLU cc_start: 0.9429 (tt0) cc_final: 0.9097 (tm-30) REVERT: E 155 GLU cc_start: 0.6927 (pm20) cc_final: 0.6712 (pm20) REVERT: D 32 TYR cc_start: 0.8632 (m-10) cc_final: 0.8333 (m-10) REVERT: D 45 ARG cc_start: 0.8825 (mtp-110) cc_final: 0.8548 (mtm-85) REVERT: D 49 TYR cc_start: 0.8729 (p90) cc_final: 0.8453 (p90) REVERT: D 87 TYR cc_start: 0.7902 (m-80) cc_final: 0.7531 (m-80) REVERT: D 142 TYR cc_start: 0.7749 (t80) cc_final: 0.7253 (t80) REVERT: G 33 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.8148 (m-10) REVERT: F 136 CYS cc_start: 0.6737 (t) cc_final: 0.5565 (p) REVERT: B 157 PHE cc_start: 0.7209 (m-80) cc_final: 0.6686 (t80) REVERT: B 338 TYR cc_start: 0.8200 (p90) cc_final: 0.7843 (p90) REVERT: B 365 LYS cc_start: 0.9311 (mtpt) cc_final: 0.9107 (pmmt) REVERT: B 367 TYR cc_start: 0.9057 (m-80) cc_final: 0.8265 (m-80) REVERT: B 692 ASN cc_start: 0.8414 (m-40) cc_final: 0.7972 (p0) REVERT: B 744 GLN cc_start: 0.8941 (mt0) cc_final: 0.8736 (mt0) REVERT: B 939 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8090 (tm-30) REVERT: C 83 PHE cc_start: 0.8463 (t80) cc_final: 0.7989 (t80) REVERT: C 151 MET cc_start: 0.5120 (mmt) cc_final: 0.4455 (mmt) REVERT: C 301 GLN cc_start: 0.9372 (OUTLIER) cc_final: 0.9031 (mm-40) REVERT: C 327 GLU cc_start: 0.9168 (mp0) cc_final: 0.8905 (mp0) REVERT: C 599 GLN cc_start: 0.8597 (tp-100) cc_final: 0.8282 (mm-40) REVERT: C 629 PHE cc_start: 0.8152 (t80) cc_final: 0.7798 (t80) REVERT: C 768 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.9116 (mptt) REVERT: C 932 ASP cc_start: 0.8912 (m-30) cc_final: 0.8635 (m-30) REVERT: C 939 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8351 (tm-30) REVERT: C 992 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8295 (mp10) REVERT: C 999 GLU cc_start: 0.9225 (tt0) cc_final: 0.8926 (tm-30) outliers start: 124 outliers final: 60 residues processed: 307 average time/residue: 0.5838 time to fit residues: 220.1220 Evaluate side-chains 248 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 180 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 278 CYS Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1111 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 12 LYS Chi-restraints excluded: chain E residue 32 HIS 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 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 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 102 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 323 CYS 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 711 VAL Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 808 VAL 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 967 ASP Chi-restraints excluded: chain B residue 1074 GLU 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 301 GLN 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 562 VAL 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 768 LYS Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1079 PHE 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 318 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 389 optimal weight: 0.9990 chunk 305 optimal weight: 20.0000 chunk 259 optimal weight: 0.5980 chunk 199 optimal weight: 3.9990 chunk 238 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 302 optimal weight: 4.9990 chunk 369 optimal weight: 0.9990 chunk 332 optimal weight: 7.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 155 ASN A 984 GLN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 GLN ** C 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1030 HIS ** 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 = 0.4029 r_free = 0.4029 target = 0.102240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.060895 restraints weight = 98175.692| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.69 r_work: 0.2933 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31933 Z= 0.168 Angle : 0.615 13.296 43484 Z= 0.307 Chirality : 0.044 0.184 4906 Planarity : 0.004 0.066 5610 Dihedral : 4.847 56.706 4334 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.16 % Favored : 91.79 % Rotamer: Outliers : 2.80 % Allowed : 15.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.13), residues: 3971 helix: 1.60 (0.20), residues: 731 sheet: -1.58 (0.16), residues: 1015 loop : -2.60 (0.12), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 829 TYR 0.022 0.001 TYR C 886 PHE 0.020 0.001 PHE C1079 TRP 0.038 0.001 TRP E 47 HIS 0.005 0.001 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00386 (31883) covalent geometry : angle 0.61349 (43384) SS BOND : bond 0.00311 ( 50) SS BOND : angle 1.02896 ( 100) hydrogen bonds : bond 0.03553 ( 882) hydrogen bonds : angle 4.97616 ( 2451) *********************** 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 293 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 196 time to evaluate : 1.289 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: A 83 PHE cc_start: 0.7952 (t80) cc_final: 0.7496 (t80) REVERT: A 601 VAL cc_start: 0.9216 (t) cc_final: 0.8759 (m) REVERT: A 629 PHE cc_start: 0.8017 (t80) cc_final: 0.7595 (t80) REVERT: A 939 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8168 (tm-30) REVERT: A 992 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8256 (mp10) REVERT: A 999 GLU cc_start: 0.9171 (tt0) cc_final: 0.8896 (tm-30) REVERT: A 1076 VAL cc_start: 0.7472 (OUTLIER) cc_final: 0.6838 (m) REVERT: E 82 GLU cc_start: 0.9452 (tt0) cc_final: 0.9114 (tm-30) REVERT: D 24 ARG cc_start: 0.7750 (mpp80) cc_final: 0.7516 (mpp80) REVERT: D 32 TYR cc_start: 0.8631 (m-10) cc_final: 0.8282 (m-10) REVERT: D 45 ARG cc_start: 0.8881 (mtp-110) cc_final: 0.8596 (mtm-85) REVERT: D 61 ARG cc_start: 0.8820 (ptt-90) cc_final: 0.8526 (ptt180) REVERT: D 87 TYR cc_start: 0.7931 (m-80) cc_final: 0.7561 (m-80) REVERT: D 142 TYR cc_start: 0.7834 (t80) cc_final: 0.7338 (t80) REVERT: G 33 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.8263 (m-10) REVERT: G 34 MET cc_start: 0.7629 (tpt) cc_final: 0.7387 (tpt) REVERT: G 70 MET cc_start: 0.6815 (mtm) cc_final: 0.6134 (ptm) REVERT: B 83 PHE cc_start: 0.8518 (m-80) cc_final: 0.8291 (m-80) REVERT: B 157 PHE cc_start: 0.7279 (m-80) cc_final: 0.6815 (t80) REVERT: B 338 TYR cc_start: 0.8242 (p90) cc_final: 0.7934 (p90) REVERT: B 365 LYS cc_start: 0.9330 (mtpt) cc_final: 0.9111 (pmmt) REVERT: B 367 TYR cc_start: 0.9095 (m-80) cc_final: 0.8347 (m-80) REVERT: B 692 ASN cc_start: 0.8436 (m-40) cc_final: 0.8075 (p0) REVERT: B 744 GLN cc_start: 0.8936 (mt0) cc_final: 0.8716 (mt0) REVERT: B 939 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8079 (tm-30) REVERT: B 977 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8501 (ptp90) REVERT: C 83 PHE cc_start: 0.8438 (t80) cc_final: 0.7976 (t80) REVERT: C 151 MET cc_start: 0.5107 (mmt) cc_final: 0.4467 (mmt) REVERT: C 301 GLN cc_start: 0.9379 (OUTLIER) cc_final: 0.9067 (mm-40) REVERT: C 327 GLU cc_start: 0.9167 (mp0) cc_final: 0.8881 (mp0) REVERT: C 629 PHE cc_start: 0.8110 (t80) cc_final: 0.7814 (t80) REVERT: C 768 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.9116 (mptt) REVERT: C 886 TYR cc_start: 0.8019 (m-10) cc_final: 0.7817 (m-80) REVERT: C 932 ASP cc_start: 0.8944 (m-30) cc_final: 0.8696 (m-30) REVERT: C 939 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8374 (tm-30) REVERT: C 992 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8266 (mp10) REVERT: C 999 GLU cc_start: 0.9231 (tt0) cc_final: 0.8931 (tm-30) REVERT: C 1076 VAL cc_start: 0.7831 (OUTLIER) cc_final: 0.7477 (t) outliers start: 97 outliers final: 58 residues processed: 279 average time/residue: 0.6326 time to fit residues: 213.7640 Evaluate side-chains 240 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 174 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 278 CYS Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1130 PHE Chi-restraints excluded: chain E residue 69 THR 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 119 ILE 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 254 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 278 CYS 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 831 LEU 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 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 301 GLN 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 562 VAL Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 616 THR 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 768 LYS Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 992 GLN 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 1130 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 157 optimal weight: 8.9990 chunk 195 optimal weight: 4.9990 chunk 356 optimal weight: 4.9990 chunk 41 optimal weight: 30.0000 chunk 236 optimal weight: 3.9990 chunk 173 optimal weight: 0.0070 chunk 5 optimal weight: 0.1980 chunk 226 optimal weight: 30.0000 chunk 276 optimal weight: 2.9990 chunk 74 optimal weight: 0.0870 chunk 72 optimal weight: 0.4980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 984 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** ** C 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.103419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.062567 restraints weight = 97828.428| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.69 r_work: 0.2986 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31933 Z= 0.110 Angle : 0.593 11.518 43484 Z= 0.293 Chirality : 0.043 0.193 4906 Planarity : 0.004 0.050 5610 Dihedral : 4.714 57.819 4334 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.66 % Favored : 92.32 % Rotamer: Outliers : 2.83 % Allowed : 15.54 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.13), residues: 3971 helix: 1.67 (0.20), residues: 739 sheet: -1.39 (0.16), residues: 978 loop : -2.50 (0.12), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 829 TYR 0.014 0.001 TYR C 886 PHE 0.024 0.001 PHE C1077 TRP 0.041 0.001 TRP E 47 HIS 0.003 0.000 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00252 (31883) covalent geometry : angle 0.59237 (43384) SS BOND : bond 0.00249 ( 50) SS BOND : angle 0.87235 ( 100) hydrogen bonds : bond 0.03203 ( 882) hydrogen bonds : angle 4.80486 ( 2451) *********************** 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 289 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 191 time to evaluate : 1.226 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: symmetry clash REVERT: A 57 ASP cc_start: 0.8110 (t0) cc_final: 0.7787 (t0) REVERT: A 83 PHE cc_start: 0.7940 (t80) cc_final: 0.7645 (t80) REVERT: A 601 VAL cc_start: 0.9229 (t) cc_final: 0.8837 (m) REVERT: A 629 PHE cc_start: 0.7921 (t80) cc_final: 0.7551 (t80) REVERT: A 939 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8134 (tm-30) REVERT: A 961 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8607 (OUTLIER) REVERT: A 992 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8224 (mp10) REVERT: A 1092 PHE cc_start: 0.7863 (t80) cc_final: 0.7588 (t80) REVERT: E 33 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.8065 (m-10) REVERT: E 47 TRP cc_start: 0.7628 (OUTLIER) cc_final: 0.7417 (p-90) REVERT: E 82 GLU cc_start: 0.9452 (tt0) cc_final: 0.9106 (tm-30) REVERT: E 87 ARG cc_start: 0.7907 (mmm-85) cc_final: 0.7644 (mmm-85) REVERT: E 155 GLU cc_start: 0.6425 (pm20) cc_final: 0.6157 (pm20) REVERT: D 32 TYR cc_start: 0.8621 (m-10) cc_final: 0.8266 (m-10) REVERT: D 45 ARG cc_start: 0.8910 (mtp-110) cc_final: 0.8624 (mtm-85) REVERT: D 87 TYR cc_start: 0.7914 (m-80) cc_final: 0.7520 (m-80) REVERT: D 142 TYR cc_start: 0.7837 (t80) cc_final: 0.7340 (t80) REVERT: G 33 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8303 (m-10) REVERT: G 34 MET cc_start: 0.7750 (tpt) cc_final: 0.7543 (tpt) REVERT: G 70 MET cc_start: 0.6937 (mtm) cc_final: 0.6264 (ptm) REVERT: F 97 MET cc_start: 0.8557 (tpt) cc_final: 0.8278 (tpp) REVERT: F 136 CYS cc_start: 0.6991 (t) cc_final: 0.5792 (p) REVERT: B 83 PHE cc_start: 0.8457 (m-80) cc_final: 0.8215 (m-80) REVERT: B 157 PHE cc_start: 0.7236 (m-80) cc_final: 0.6785 (t80) REVERT: B 338 TYR cc_start: 0.8274 (p90) cc_final: 0.7988 (p90) REVERT: B 365 LYS cc_start: 0.9329 (mtpt) cc_final: 0.9111 (pmmt) REVERT: B 367 TYR cc_start: 0.9096 (m-80) cc_final: 0.8351 (m-80) REVERT: B 692 ASN cc_start: 0.8328 (m-40) cc_final: 0.7965 (p0) REVERT: B 744 GLN cc_start: 0.8933 (mt0) cc_final: 0.8720 (mt0) REVERT: B 939 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8047 (tm-30) REVERT: C 83 PHE cc_start: 0.8441 (t80) cc_final: 0.7948 (t80) REVERT: C 151 MET cc_start: 0.5217 (mmt) cc_final: 0.4528 (mmt) REVERT: C 327 GLU cc_start: 0.9174 (mp0) cc_final: 0.8891 (mp0) REVERT: C 629 PHE cc_start: 0.7986 (t80) cc_final: 0.7727 (t80) REVERT: C 768 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9098 (mptt) REVERT: C 932 ASP cc_start: 0.8894 (m-30) cc_final: 0.8667 (m-30) REVERT: C 939 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8329 (tm-30) REVERT: C 1076 VAL cc_start: 0.7826 (OUTLIER) cc_final: 0.7404 (t) outliers start: 98 outliers final: 63 residues processed: 271 average time/residue: 0.5887 time to fit residues: 195.0490 Evaluate side-chains 245 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 176 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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 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 762 GLU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 992 GLN 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 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 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 33 TYR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 68 VAL 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 267 ASP Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 323 CYS 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 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 1105 SER 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 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 768 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 378 optimal weight: 0.0570 chunk 63 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 246 optimal weight: 2.9990 chunk 351 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 238 optimal weight: 4.9990 chunk 397 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 344 optimal weight: 0.0020 chunk 17 optimal weight: 9.9990 overall best weight: 2.6112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 GLN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN B 947 GLN ** C 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 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 = 0.4011 r_free = 0.4011 target = 0.101312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.059698 restraints weight = 98956.259| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.74 r_work: 0.2904 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 31933 Z= 0.191 Angle : 0.630 11.071 43484 Z= 0.316 Chirality : 0.044 0.251 4906 Planarity : 0.004 0.049 5610 Dihedral : 4.908 54.930 4334 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.49 % Favored : 91.46 % Rotamer: Outliers : 3.18 % Allowed : 15.83 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.13), residues: 3971 helix: 1.56 (0.20), residues: 748 sheet: -1.27 (0.16), residues: 1004 loop : -2.40 (0.12), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 110 TYR 0.027 0.001 TYR D 49 PHE 0.021 0.001 PHE A1057 TRP 0.034 0.001 TRP E 47 HIS 0.004 0.001 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00435 (31883) covalent geometry : angle 0.62878 (43384) SS BOND : bond 0.00327 ( 50) SS BOND : angle 1.06208 ( 100) hydrogen bonds : bond 0.03679 ( 882) hydrogen bonds : angle 4.81100 ( 2451) *********************** 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 300 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 190 time to evaluate : 1.379 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: 0.8058 (t80) cc_final: 0.7741 (t80) REVERT: A 151 MET cc_start: 0.5936 (OUTLIER) cc_final: 0.5728 (tpt) REVERT: A 301 GLN cc_start: 0.9358 (OUTLIER) cc_final: 0.9141 (mm-40) REVERT: A 601 VAL cc_start: 0.9205 (t) cc_final: 0.8706 (m) REVERT: A 629 PHE cc_start: 0.8071 (t80) cc_final: 0.7562 (t80) REVERT: A 961 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8595 (t0) REVERT: A 992 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8285 (mp10) REVERT: A 1076 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7533 (m) REVERT: E 33 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.8215 (m-10) REVERT: E 47 TRP cc_start: 0.7890 (OUTLIER) cc_final: 0.7544 (p-90) REVERT: E 82 GLU cc_start: 0.9463 (tt0) cc_final: 0.9068 (tm-30) REVERT: D 24 ARG cc_start: 0.7808 (mpp80) cc_final: 0.7535 (mpp80) REVERT: D 32 TYR cc_start: 0.8647 (m-10) cc_final: 0.8316 (m-10) REVERT: D 61 ARG cc_start: 0.8911 (ptt180) cc_final: 0.8671 (ptt180) REVERT: D 87 TYR cc_start: 0.8037 (m-80) cc_final: 0.7592 (m-80) REVERT: D 142 TYR cc_start: 0.7831 (t80) cc_final: 0.7340 (t80) REVERT: G 33 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.8238 (m-10) REVERT: G 34 MET cc_start: 0.7748 (tpt) cc_final: 0.7513 (tpt) REVERT: G 70 MET cc_start: 0.7061 (mtm) cc_final: 0.6647 (ptm) REVERT: B 45 GLU cc_start: 0.8547 (tp30) cc_final: 0.8345 (mm-30) REVERT: B 157 PHE cc_start: 0.7586 (m-80) cc_final: 0.7090 (t80) REVERT: B 338 TYR cc_start: 0.8316 (p90) cc_final: 0.8010 (p90) REVERT: B 365 LYS cc_start: 0.9348 (mtpt) cc_final: 0.9103 (pmmt) REVERT: B 367 TYR cc_start: 0.9114 (m-80) cc_final: 0.8434 (m-80) REVERT: B 476 TRP cc_start: 0.9065 (m100) cc_final: 0.8769 (t-100) REVERT: B 744 GLN cc_start: 0.8926 (mt0) cc_final: 0.8670 (mt0) REVERT: B 939 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8172 (tm-30) REVERT: B 977 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8486 (ptp90) REVERT: C 83 PHE cc_start: 0.8371 (t80) cc_final: 0.7931 (t80) REVERT: C 151 MET cc_start: 0.5058 (mmt) cc_final: 0.4413 (mmt) REVERT: C 327 GLU cc_start: 0.9208 (mp0) cc_final: 0.8913 (mp0) REVERT: C 629 PHE cc_start: 0.8135 (t80) cc_final: 0.7830 (t80) REVERT: C 632 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8530 (tp-100) REVERT: C 768 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.9097 (mptt) REVERT: C 932 ASP cc_start: 0.8954 (m-30) cc_final: 0.8686 (m-30) REVERT: C 937 ASN cc_start: 0.9270 (OUTLIER) cc_final: 0.8973 (t0) REVERT: C 939 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8432 (tm-30) REVERT: C 999 GLU cc_start: 0.9231 (tt0) cc_final: 0.8928 (tm-30) outliers start: 110 outliers final: 66 residues processed: 283 average time/residue: 0.5400 time to fit residues: 186.7169 Evaluate side-chains 247 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 170 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 278 CYS Chi-restraints excluded: chain A residue 301 GLN 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 961 ASP 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 1111 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 47 TRP 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 E residue 202 ILE Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 68 VAL 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 278 CYS Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 325 PHE 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 585 THR 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 958 VAL Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 977 ARG Chi-restraints excluded: chain B residue 1105 SER Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 92 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 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 768 LYS 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 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 78 optimal weight: 0.9990 chunk 361 optimal weight: 0.9990 chunk 339 optimal weight: 0.8980 chunk 308 optimal weight: 6.9990 chunk 247 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 269 optimal weight: 0.9980 chunk 211 optimal weight: 0.1980 chunk 209 optimal weight: 1.9990 chunk 303 optimal weight: 7.9990 chunk 351 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN A 984 GLN ** 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** G 3 GLN ** C 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 ASN C1030 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.103048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.062329 restraints weight = 98006.348| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.59 r_work: 0.2973 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31933 Z= 0.113 Angle : 0.618 11.807 43484 Z= 0.303 Chirality : 0.044 0.196 4906 Planarity : 0.004 0.060 5610 Dihedral : 4.794 55.941 4334 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.83 % Favored : 92.14 % Rotamer: Outliers : 2.72 % Allowed : 16.70 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.13), residues: 3971 helix: 1.56 (0.20), residues: 757 sheet: -1.24 (0.16), residues: 1008 loop : -2.33 (0.12), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 829 TYR 0.021 0.001 TYR C 886 PHE 0.023 0.001 PHE D 118 TRP 0.036 0.001 TRP E 47 HIS 0.003 0.000 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00254 (31883) covalent geometry : angle 0.61764 (43384) SS BOND : bond 0.00274 ( 50) SS BOND : angle 0.88850 ( 100) hydrogen bonds : bond 0.03171 ( 882) hydrogen bonds : angle 4.67575 ( 2451) *********************** 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 282 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 188 time to evaluate : 1.028 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 57 ASP cc_start: 0.8158 (t0) cc_final: 0.7829 (t0) REVERT: A 83 PHE cc_start: 0.8030 (t80) cc_final: 0.7710 (t80) REVERT: A 301 GLN cc_start: 0.9352 (OUTLIER) cc_final: 0.9125 (mm-40) REVERT: A 601 VAL cc_start: 0.9198 (t) cc_final: 0.8867 (m) REVERT: A 629 PHE cc_start: 0.8028 (t80) cc_final: 0.7689 (t80) REVERT: A 992 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8230 (mp10) REVERT: A 1092 PHE cc_start: 0.7772 (t80) cc_final: 0.7398 (t80) REVERT: E 33 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.8054 (m-10) REVERT: E 47 TRP cc_start: 0.7753 (OUTLIER) cc_final: 0.7505 (p-90) REVERT: E 82 GLU cc_start: 0.9453 (tt0) cc_final: 0.9058 (tm-30) REVERT: D 32 TYR cc_start: 0.8593 (m-10) cc_final: 0.8264 (m-10) REVERT: D 61 ARG cc_start: 0.8863 (ptt180) cc_final: 0.8573 (ptt180) REVERT: D 97 MET cc_start: 0.8410 (tpp) cc_final: 0.7809 (tpp) REVERT: D 142 TYR cc_start: 0.7876 (t80) cc_final: 0.7386 (t80) REVERT: G 33 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.8244 (m-10) REVERT: G 34 MET cc_start: 0.7683 (tpt) cc_final: 0.7452 (tpt) REVERT: G 45 LEU cc_start: 0.1056 (OUTLIER) cc_final: -0.0052 (tm) REVERT: G 70 MET cc_start: 0.6971 (mtm) cc_final: 0.6523 (ptm) REVERT: B 45 GLU cc_start: 0.8603 (tp30) cc_final: 0.8382 (mm-30) REVERT: B 157 PHE cc_start: 0.7477 (m-80) cc_final: 0.6916 (t80) REVERT: B 338 TYR cc_start: 0.8358 (p90) cc_final: 0.8063 (p90) REVERT: B 365 LYS cc_start: 0.9392 (mtpt) cc_final: 0.9122 (pmmt) REVERT: B 367 TYR cc_start: 0.9163 (m-80) cc_final: 0.8473 (m-80) REVERT: B 744 GLN cc_start: 0.8912 (mt0) cc_final: 0.8685 (mt0) REVERT: B 815 PHE cc_start: 0.8093 (m-10) cc_final: 0.7870 (m-10) REVERT: B 816 MET cc_start: 0.7698 (tmm) cc_final: 0.7457 (tmm) REVERT: B 939 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8079 (tm-30) REVERT: C 83 PHE cc_start: 0.8386 (t80) cc_final: 0.7925 (t80) REVERT: C 151 MET cc_start: 0.5241 (mmt) cc_final: 0.4551 (mmt) REVERT: C 327 GLU cc_start: 0.9204 (mp0) cc_final: 0.8920 (mp0) REVERT: C 629 PHE cc_start: 0.7974 (t80) cc_final: 0.7705 (t80) REVERT: C 932 ASP cc_start: 0.8925 (m-30) cc_final: 0.8694 (m-30) REVERT: C 937 ASN cc_start: 0.9192 (OUTLIER) cc_final: 0.8928 (t0) REVERT: C 939 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8396 (tm-30) REVERT: C 999 GLU cc_start: 0.9191 (tt0) cc_final: 0.8935 (tm-30) REVERT: C 1076 VAL cc_start: 0.7845 (OUTLIER) cc_final: 0.7386 (t) outliers start: 94 outliers final: 56 residues processed: 264 average time/residue: 0.4764 time to fit residues: 153.9184 Evaluate side-chains 239 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 175 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 278 CYS Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 992 GLN 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 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 56 THR Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 68 VAL 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 267 ASP Chi-restraints excluded: chain B residue 278 CYS 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 958 VAL Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 92 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 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 768 LYS 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 1111 VAL Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain C residue 1130 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 250 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 363 optimal weight: 0.0020 chunk 220 optimal weight: 20.0000 chunk 229 optimal weight: 4.9990 chunk 183 optimal weight: 0.0040 chunk 17 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 984 GLN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 ASN C 937 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.102934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.062166 restraints weight = 98211.268| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.70 r_work: 0.2974 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31933 Z= 0.117 Angle : 0.628 12.527 43484 Z= 0.306 Chirality : 0.043 0.209 4906 Planarity : 0.004 0.049 5610 Dihedral : 4.717 56.697 4332 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.76 % Favored : 92.19 % Rotamer: Outliers : 2.46 % Allowed : 17.19 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.13), residues: 3971 helix: 1.63 (0.20), residues: 757 sheet: -1.18 (0.16), residues: 1008 loop : -2.26 (0.12), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 829 TYR 0.027 0.001 TYR D 49 PHE 0.022 0.001 PHE F 118 TRP 0.040 0.001 TRP E 47 HIS 0.003 0.000 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00270 (31883) covalent geometry : angle 0.62762 (43384) SS BOND : bond 0.00265 ( 50) SS BOND : angle 0.85418 ( 100) hydrogen bonds : bond 0.03141 ( 882) hydrogen bonds : angle 4.62000 ( 2451) *********************** 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 271 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 186 time to evaluate : 1.198 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 57 ASP cc_start: 0.8154 (t0) cc_final: 0.7810 (t0) REVERT: A 83 PHE cc_start: 0.8060 (t80) cc_final: 0.7735 (t80) REVERT: A 152 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8147 (mp) REVERT: A 601 VAL cc_start: 0.9206 (t) cc_final: 0.8858 (m) REVERT: A 629 PHE cc_start: 0.8056 (t80) cc_final: 0.7785 (t80) REVERT: A 992 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8228 (mp10) REVERT: A 1092 PHE cc_start: 0.7825 (t80) cc_final: 0.7420 (t80) REVERT: E 33 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.8046 (m-10) REVERT: E 82 GLU cc_start: 0.9397 (tt0) cc_final: 0.9025 (tm-30) REVERT: E 155 GLU cc_start: 0.6394 (pm20) cc_final: 0.6156 (pm20) REVERT: D 32 TYR cc_start: 0.8544 (m-10) cc_final: 0.8232 (m-10) REVERT: D 96 ARG cc_start: 0.8100 (mmp80) cc_final: 0.7900 (mmp80) REVERT: D 142 TYR cc_start: 0.7864 (t80) cc_final: 0.7391 (t80) REVERT: G 33 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8347 (m-10) REVERT: G 34 MET cc_start: 0.7737 (tpt) cc_final: 0.7510 (tpt) REVERT: G 45 LEU cc_start: 0.1271 (OUTLIER) cc_final: 0.0156 (tm) REVERT: G 70 MET cc_start: 0.6905 (mtm) cc_final: 0.6591 (ptm) REVERT: B 45 GLU cc_start: 0.8642 (tp30) cc_final: 0.8418 (mm-30) REVERT: B 157 PHE cc_start: 0.7512 (m-80) cc_final: 0.6965 (t80) REVERT: B 338 TYR cc_start: 0.8358 (p90) cc_final: 0.8072 (p90) REVERT: B 365 LYS cc_start: 0.9422 (mtpt) cc_final: 0.9166 (pmmt) REVERT: B 367 TYR cc_start: 0.9195 (m-80) cc_final: 0.8491 (m-80) REVERT: B 476 TRP cc_start: 0.9107 (m100) cc_final: 0.8786 (t-100) REVERT: B 744 GLN cc_start: 0.8905 (mt0) cc_final: 0.8673 (mt0) REVERT: B 815 PHE cc_start: 0.8141 (m-10) cc_final: 0.7916 (m-10) REVERT: B 886 TYR cc_start: 0.8890 (t80) cc_final: 0.8677 (t80) REVERT: B 939 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8114 (tm-30) REVERT: B 1092 PHE cc_start: 0.7965 (t80) cc_final: 0.7726 (t80) REVERT: C 83 PHE cc_start: 0.8373 (t80) cc_final: 0.7906 (t80) REVERT: C 151 MET cc_start: 0.5329 (mmt) cc_final: 0.4609 (mmt) REVERT: C 327 GLU cc_start: 0.9204 (mp0) cc_final: 0.8913 (mp0) REVERT: C 629 PHE cc_start: 0.7984 (t80) cc_final: 0.7738 (t80) REVERT: C 932 ASP cc_start: 0.8905 (m-30) cc_final: 0.8650 (m-30) REVERT: C 937 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8807 (m-40) REVERT: C 939 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8215 (tm-30) REVERT: C 999 GLU cc_start: 0.9190 (tt0) cc_final: 0.8914 (tm-30) REVERT: C 1032 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8192 (ttp) REVERT: C 1076 VAL cc_start: 0.7851 (OUTLIER) cc_final: 0.7387 (t) outliers start: 85 outliers final: 61 residues processed: 257 average time/residue: 0.5178 time to fit residues: 163.2664 Evaluate side-chains 248 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 179 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 278 CYS Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 833 CYS Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 992 GLN 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 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 33 TYR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 68 VAL 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 278 CYS 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 773 THR Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 833 CYS Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 92 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 724 ILE Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 768 LYS Chi-restraints excluded: chain C residue 937 ASN Chi-restraints excluded: chain C residue 1032 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 339 optimal weight: 0.7980 chunk 122 optimal weight: 40.0000 chunk 71 optimal weight: 0.0980 chunk 44 optimal weight: 5.9990 chunk 352 optimal weight: 7.9990 chunk 390 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 317 optimal weight: 2.9990 chunk 348 optimal weight: 0.1980 chunk 321 optimal weight: 2.9990 chunk 383 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 984 GLN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.102647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.061778 restraints weight = 98562.580| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.70 r_work: 0.2959 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31933 Z= 0.132 Angle : 0.647 13.518 43484 Z= 0.314 Chirality : 0.044 0.208 4906 Planarity : 0.004 0.078 5610 Dihedral : 4.752 56.726 4332 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.86 % Favored : 92.09 % Rotamer: Outliers : 2.40 % Allowed : 17.39 % Favored : 80.21 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.13), residues: 3971 helix: 1.68 (0.20), residues: 751 sheet: -1.14 (0.16), residues: 1013 loop : -2.22 (0.13), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 829 TYR 0.031 0.001 TYR D 49 PHE 0.021 0.001 PHE C 551 TRP 0.054 0.001 TRP E 47 HIS 0.002 0.000 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00307 (31883) covalent geometry : angle 0.64608 (43384) SS BOND : bond 0.00305 ( 50) SS BOND : angle 0.96833 ( 100) hydrogen bonds : bond 0.03175 ( 882) hydrogen bonds : angle 4.60475 ( 2451) ********************** 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 266 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 183 time to evaluate : 0.821 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 57 ASP cc_start: 0.8121 (t0) cc_final: 0.7777 (t0) REVERT: A 83 PHE cc_start: 0.8055 (t80) cc_final: 0.7725 (t80) REVERT: A 152 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8012 (tt) REVERT: A 601 VAL cc_start: 0.9221 (t) cc_final: 0.8868 (m) REVERT: A 629 PHE cc_start: 0.8093 (t80) cc_final: 0.7815 (t80) REVERT: A 992 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8223 (mp10) REVERT: A 1092 PHE cc_start: 0.7876 (t80) cc_final: 0.7476 (t80) REVERT: E 81 MET cc_start: 0.7900 (ttp) cc_final: 0.7686 (tmm) REVERT: E 82 GLU cc_start: 0.9386 (tt0) cc_final: 0.9044 (tm-30) REVERT: E 155 GLU cc_start: 0.6517 (pm20) cc_final: 0.6280 (pm20) REVERT: D 32 TYR cc_start: 0.8540 (m-10) cc_final: 0.8210 (m-10) REVERT: D 142 TYR cc_start: 0.7861 (t80) cc_final: 0.7430 (t80) REVERT: G 33 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.8318 (m-10) REVERT: G 34 MET cc_start: 0.7748 (tpt) cc_final: 0.7534 (tpt) REVERT: G 45 LEU cc_start: 0.1338 (OUTLIER) cc_final: 0.0213 (tm) REVERT: G 70 MET cc_start: 0.6898 (mtm) cc_final: 0.6101 (ptm) REVERT: B 45 GLU cc_start: 0.8636 (tp30) cc_final: 0.8431 (mm-30) REVERT: B 157 PHE cc_start: 0.7581 (m-80) cc_final: 0.7036 (t80) REVERT: B 338 TYR cc_start: 0.8363 (p90) cc_final: 0.8033 (p90) REVERT: B 365 LYS cc_start: 0.9461 (mtpt) cc_final: 0.9193 (pmmt) REVERT: B 367 TYR cc_start: 0.9239 (m-80) cc_final: 0.8555 (m-80) REVERT: B 476 TRP cc_start: 0.9121 (m100) cc_final: 0.8806 (t-100) REVERT: B 744 GLN cc_start: 0.8903 (mt0) cc_final: 0.8668 (mt0) REVERT: B 939 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8123 (tm-30) REVERT: B 1077 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7742 (t80) REVERT: B 1092 PHE cc_start: 0.7826 (t80) cc_final: 0.7549 (t80) REVERT: B 1130 PHE cc_start: 0.8327 (t80) cc_final: 0.8106 (t80) REVERT: C 83 PHE cc_start: 0.8377 (t80) cc_final: 0.7933 (t80) REVERT: C 151 MET cc_start: 0.5320 (mmt) cc_final: 0.4587 (mmt) REVERT: C 327 GLU cc_start: 0.9200 (mp0) cc_final: 0.8913 (mp0) REVERT: C 629 PHE cc_start: 0.8002 (t80) cc_final: 0.7752 (t80) REVERT: C 932 ASP cc_start: 0.8913 (m-30) cc_final: 0.8658 (m-30) REVERT: C 937 ASN cc_start: 0.9193 (OUTLIER) cc_final: 0.8897 (t0) REVERT: C 939 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8209 (tm-30) REVERT: C 999 GLU cc_start: 0.9194 (tt0) cc_final: 0.8921 (tm-30) REVERT: C 1076 VAL cc_start: 0.7860 (OUTLIER) cc_final: 0.7387 (t) outliers start: 83 outliers final: 60 residues processed: 253 average time/residue: 0.5393 time to fit residues: 165.6857 Evaluate side-chains 244 residues out of total 3465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 177 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 278 CYS Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 833 CYS Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1077 PHE Chi-restraints excluded: chain A residue 1111 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 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 56 THR 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 G residue 68 VAL 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 128 CYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 278 CYS 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 773 THR Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 833 CYS 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 92 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 585 THR 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 768 LYS 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 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 362 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 317 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 chunk 246 optimal weight: 0.2980 chunk 88 optimal weight: 4.9990 chunk 275 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 368 optimal weight: 8.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- 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** A 984 GLN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN C 937 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.100846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.059209 restraints weight = 98674.811| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.70 r_work: 0.2889 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 31933 Z= 0.194 Angle : 0.676 12.944 43484 Z= 0.335 Chirality : 0.044 0.242 4906 Planarity : 0.004 0.081 5610 Dihedral : 4.969 56.175 4330 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.51 % Favored : 91.41 % Rotamer: Outliers : 2.31 % Allowed : 17.45 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.13), residues: 3971 helix: 1.68 (0.20), residues: 736 sheet: -1.07 (0.16), residues: 1023 loop : -2.16 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 829 TYR 0.032 0.001 TYR D 49 PHE 0.036 0.002 PHE B 815 TRP 0.056 0.002 TRP E 47 HIS 0.004 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00452 (31883) covalent geometry : angle 0.67469 (43384) SS BOND : bond 0.00369 ( 50) SS BOND : angle 1.12180 ( 100) hydrogen bonds : bond 0.03693 ( 882) hydrogen bonds : angle 4.71135 ( 2451) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15066.19 seconds wall clock time: 256 minutes 32.80 seconds (15392.80 seconds total)