Starting phenix.real_space_refine on Sun May 18 09:25:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h8c_34542/05_2025/8h8c_34542.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h8c_34542/05_2025/8h8c_34542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h8c_34542/05_2025/8h8c_34542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h8c_34542/05_2025/8h8c_34542.map" model { file = "/net/cci-nas-00/data/ceres_data/8h8c_34542/05_2025/8h8c_34542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h8c_34542/05_2025/8h8c_34542.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 24 5.16 5 C 10662 2.51 5 N 2938 2.21 5 O 3316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16940 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 7860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7860 Classifications: {'peptide': 964} Link IDs: {'PTRANS': 22, 'TRANS': 941} Chain breaks: 1 Chain: "C" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain breaks: 1 Chain: "A" Number of atoms: 7860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7860 Classifications: {'peptide': 964} Link IDs: {'PTRANS': 22, 'TRANS': 941} Chain breaks: 1 Chain: "D" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain breaks: 1 Time building chain proxies: 10.17, per 1000 atoms: 0.60 Number of scatterers: 16940 At special positions: 0 Unit cell: (93.09, 118.32, 140.07, 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 24 16.00 O 3316 8.00 N 2938 7.00 C 10662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.86 Conformation dependent library (CDL) restraints added in 2.1 seconds 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3812 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 36 sheets defined 2.0% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'C' and resid 1139 through 1148 removed outlier: 3.751A pdb=" N ALA C1145 " --> pdb=" O GLN C1141 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C1148 " --> pdb=" O LEU C1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 1154 through 1162 removed outlier: 4.596A pdb=" N GLN C1160 " --> pdb=" O GLU C1156 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C1161 " --> pdb=" O VAL C1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1166 removed outlier: 4.103A pdb=" N LYS C1166 " --> pdb=" O GLU C1163 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1163 through 1166' Processing helix chain 'D' and resid 1139 through 1148 removed outlier: 3.514A pdb=" N ALA D1145 " --> pdb=" O GLN D1141 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU D1146 " --> pdb=" O GLN D1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 1154 through 1162 removed outlier: 4.333A pdb=" N GLN D1160 " --> pdb=" O GLU D1156 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE D1161 " --> pdb=" O VAL D1157 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D1162 " --> pdb=" O CYS D1158 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 165 through 170 removed outlier: 7.164A pdb=" N TRP B 177 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 268 through 270 removed outlier: 3.755A pdb=" N LEU B 275 " --> pdb=" O VAL B 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 288 through 291 removed outlier: 6.590A pdb=" N GLN B 288 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL B 300 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG B 290 " --> pdb=" O ILE B 298 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE B 298 " --> pdb=" O CYS B 310 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU B 320 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 321 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR B 331 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 334 through 335 removed outlier: 6.657A pdb=" N ILE B 334 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 356 removed outlier: 7.022A pdb=" N GLU B 355 " --> pdb=" O ALA B 363 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA B 363 " --> pdb=" O PHE B 375 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B 390 " --> pdb=" O TYR B 374 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU B 376 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ARG B 388 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 399 through 402 removed outlier: 3.601A pdb=" N GLU B 429 " --> pdb=" O ILE B 420 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 439 through 442 removed outlier: 3.556A pdb=" N GLN B 439 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLU B 449 " --> pdb=" O TYR B 461 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASN B 464 " --> pdb=" O LEU B 469 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU B 469 " --> pdb=" O ASN B 464 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 514 through 515 removed outlier: 5.687A pdb=" N VAL B 533 " --> pdb=" O TRP B 545 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG B 544 " --> pdb=" O HIS B 556 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N HIS B 556 " --> pdb=" O ARG B 544 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP B 546 " --> pdb=" O VAL B 554 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL B 554 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ARG B 564 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE B 576 " --> pdb=" O ARG B 564 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER B 566 " --> pdb=" O ASN B 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 584 through 587 removed outlier: 4.066A pdb=" N ILE B 597 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR B 599 " --> pdb=" O TYR B 608 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR B 608 " --> pdb=" O TYR B 599 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN B 622 " --> pdb=" O ALA B 613 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ALA B 621 " --> pdb=" O TYR B 632 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.905A pdb=" N GLU B 654 " --> pdb=" O THR B 662 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 673 through 676 removed outlier: 6.627A pdb=" N GLU B 673 " --> pdb=" O THR B 685 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR B 685 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TRP B 675 " --> pdb=" O SER B 683 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 696 through 697 removed outlier: 7.295A pdb=" N LYS B 696 " --> pdb=" O ILE B 704 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 715 through 717 removed outlier: 7.422A pdb=" N SER B 716 " --> pdb=" O GLN B 724 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 724 " --> pdb=" O SER B 716 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN B 724 " --> pdb=" O PHE B 739 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 726 " --> pdb=" O ASN B 737 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS B 738 " --> pdb=" O SER B 751 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 751 " --> pdb=" O HIS B 738 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 778 through 781 removed outlier: 3.806A pdb=" N GLU B 780 " --> pdb=" O SER B 789 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N SER B 789 " --> pdb=" O GLU B 780 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL B 788 " --> pdb=" O PHE B 800 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE B 800 " --> pdb=" O VAL B 788 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN B 790 " --> pdb=" O PHE B 798 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASP B 803 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU B 808 " --> pdb=" O ASP B 803 " (cutoff:3.500A) removed outlier: 11.290A pdb=" N ARG B 807 " --> pdb=" O TYR B 825 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N TYR B 825 " --> pdb=" O ARG B 807 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N SER B 809 " --> pdb=" O PHE B 823 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU B 822 " --> pdb=" O THR B 834 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR B 834 " --> pdb=" O GLU B 822 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLN B 824 " --> pdb=" O SER B 832 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N SER B 832 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 853 " --> pdb=" O LEU B 844 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL B 852 " --> pdb=" O TYR B 863 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N SER B 872 " --> pdb=" O TYR B 884 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 895 " --> pdb=" O SER B 902 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 926 through 927 removed outlier: 3.532A pdb=" N LYS B 942 " --> pdb=" O LYS B 933 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N VAL B 941 " --> pdb=" O ARG B 952 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 943 " --> pdb=" O GLN B 950 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 950 " --> pdb=" O ARG B 943 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B 962 " --> pdb=" O VAL B 953 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 971 through 974 removed outlier: 6.045A pdb=" N THR B 981 " --> pdb=" O PHE B 992 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 992 " --> pdb=" O THR B 981 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS B 983 " --> pdb=" O THR B 990 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR B 990 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLU B 995 " --> pdb=" O LEU B 999 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 999 " --> pdb=" O GLU B 995 " (cutoff:3.500A) removed outlier: 11.029A pdb=" N ARG B 998 " --> pdb=" O TYR B1013 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N TYR B1013 " --> pdb=" O ARG B 998 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU B1000 " --> pdb=" O TYR B1011 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B1021 " --> pdb=" O TYR B1032 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B1042 " --> pdb=" O GLU B1033 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASP B1045 " --> pdb=" O ILE B1050 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE B1050 " --> pdb=" O ASP B1045 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1087 through 1088 Processing sheet with id=AB9, first strand: chain 'B' and resid 1125 through 1126 removed outlier: 3.598A pdb=" N ILE B1126 " --> pdb=" O ASN C1188 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN C1188 " --> pdb=" O ILE B1126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 166 through 170 removed outlier: 7.077A pdb=" N TRP A 177 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 268 through 270 removed outlier: 3.853A pdb=" N LEU A 275 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 288 through 291 removed outlier: 7.783A pdb=" N ILE A 298 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU A 309 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 354 through 356 removed outlier: 7.188A pdb=" N GLU A 355 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.806A pdb=" N GLU A 376 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 399 through 403 removed outlier: 3.539A pdb=" N THR A 418 " --> pdb=" O SER A 431 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU A 428 " --> pdb=" O TRP A 440 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 450 " --> pdb=" O HIS A 441 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU A 449 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASN A 464 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A 469 " --> pdb=" O ASN A 464 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 492 through 494 Processing sheet with id=AC8, first strand: chain 'A' and resid 514 through 515 removed outlier: 5.486A pdb=" N VAL A 533 " --> pdb=" O TRP A 545 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LYS A 541 " --> pdb=" O SER A 537 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL A 554 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS A 556 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 575 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASN A 574 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 586 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR A 599 " --> pdb=" O TYR A 608 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR A 608 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 611 " --> pdb=" O GLN A 624 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 622 " --> pdb=" O ALA A 613 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ALA A 621 " --> pdb=" O TYR A 632 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 642 " --> pdb=" O GLN A 633 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.663A pdb=" N GLU A 654 " --> pdb=" O THR A 662 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 673 through 676 removed outlier: 4.657A pdb=" N GLY A 684 " --> pdb=" O TRP A 675 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 696 through 697 removed outlier: 3.904A pdb=" N ARG A 705 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 725 through 726 removed outlier: 3.612A pdb=" N ASN A 737 " --> pdb=" O ILE A 726 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 749 through 751 Processing sheet with id=AD5, first strand: chain 'A' and resid 780 through 781 removed outlier: 3.797A pdb=" N GLU A 780 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 791 through 792 removed outlier: 3.543A pdb=" N THR A 796 " --> pdb=" O LEU A 792 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N SER A 809 " --> pdb=" O PHE A 823 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 823 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER A 832 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 844 " --> pdb=" O GLU A 853 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU A 853 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL A 852 " --> pdb=" O TYR A 863 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N SER A 872 " --> pdb=" O TYR A 884 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 926 through 927 removed outlier: 6.640A pdb=" N ARG A 931 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG A 943 " --> pdb=" O ARG A 931 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS A 933 " --> pdb=" O VAL A 941 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL A 941 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU A 962 " --> pdb=" O VAL A 953 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 971 through 973 removed outlier: 3.539A pdb=" N LYS A 982 " --> pdb=" O GLU A 973 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEU A1000 " --> pdb=" O TYR A1011 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A1021 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A1042 " --> pdb=" O GLU A1033 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL A1066 " --> pdb=" O SER A1053 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 3.674A pdb=" N ILE A1126 " --> pdb=" O ASN D1188 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN D1188 " --> pdb=" O ILE A1126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 332 hydrogen bonds defined for protein. 897 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: 6.79 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5682 1.34 - 1.46: 3863 1.46 - 1.58: 7765 1.58 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 17342 Sorted by residual: bond pdb=" CA THR B 208 " pdb=" CB THR B 208 " ideal model delta sigma weight residual 1.530 1.542 -0.011 9.80e-03 1.04e+04 1.36e+00 bond pdb=" CA PHE B 202 " pdb=" C PHE B 202 " ideal model delta sigma weight residual 1.531 1.516 0.015 1.46e-02 4.69e+03 1.12e+00 bond pdb=" C SER A 216 " pdb=" O SER A 216 " ideal model delta sigma weight residual 1.236 1.225 0.012 1.15e-02 7.56e+03 1.02e+00 bond pdb=" C ASP A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 1.340 1.368 -0.028 2.76e-02 1.31e+03 1.01e+00 bond pdb=" C ALA A 577 " pdb=" N TYR A 578 " ideal model delta sigma weight residual 1.333 1.360 -0.027 2.74e-02 1.33e+03 9.96e-01 ... (remaining 17337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 23234 1.81 - 3.62: 200 3.62 - 5.43: 22 5.43 - 7.24: 2 7.24 - 9.05: 4 Bond angle restraints: 23462 Sorted by residual: angle pdb=" N VAL A 241 " pdb=" CA VAL A 241 " pdb=" C VAL A 241 " ideal model delta sigma weight residual 110.53 115.21 -4.68 9.40e-01 1.13e+00 2.48e+01 angle pdb=" C GLU A 210 " pdb=" CA GLU A 210 " pdb=" CB GLU A 210 " ideal model delta sigma weight residual 115.89 109.32 6.57 1.32e+00 5.74e-01 2.48e+01 angle pdb=" C VAL A 241 " pdb=" CA VAL A 241 " pdb=" CB VAL A 241 " ideal model delta sigma weight residual 112.02 107.97 4.05 1.31e+00 5.83e-01 9.54e+00 angle pdb=" N ILE B 480 " pdb=" CA ILE B 480 " pdb=" C ILE B 480 " ideal model delta sigma weight residual 111.81 109.19 2.62 8.60e-01 1.35e+00 9.29e+00 angle pdb=" N HIS A 212 " pdb=" CA HIS A 212 " pdb=" C HIS A 212 " ideal model delta sigma weight residual 111.54 107.58 3.96 1.36e+00 5.41e-01 8.48e+00 ... (remaining 23457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 9280 17.70 - 35.39: 693 35.39 - 53.09: 131 53.09 - 70.79: 34 70.79 - 88.48: 14 Dihedral angle restraints: 10152 sinusoidal: 4122 harmonic: 6030 Sorted by residual: dihedral pdb=" CB GLU A 538 " pdb=" CG GLU A 538 " pdb=" CD GLU A 538 " pdb=" OE1 GLU A 538 " ideal model delta sinusoidal sigma weight residual 0.00 88.48 -88.48 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU A 355 " pdb=" CG GLU A 355 " pdb=" CD GLU A 355 " pdb=" OE1 GLU A 355 " ideal model delta sinusoidal sigma weight residual 0.00 87.74 -87.74 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU B 149 " pdb=" CG GLU B 149 " pdb=" CD GLU B 149 " pdb=" OE1 GLU B 149 " ideal model delta sinusoidal sigma weight residual 0.00 -86.99 86.99 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 10149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1474 0.027 - 0.054: 612 0.054 - 0.082: 131 0.082 - 0.109: 138 0.109 - 0.136: 47 Chirality restraints: 2402 Sorted by residual: chirality pdb=" CA ILE B 256 " pdb=" N ILE B 256 " pdb=" C ILE B 256 " pdb=" CB ILE B 256 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CB THR B 836 " pdb=" CA THR B 836 " pdb=" OG1 THR B 836 " pdb=" CG2 THR B 836 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA VAL A 342 " pdb=" N VAL A 342 " pdb=" C VAL A 342 " pdb=" CB VAL A 342 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 2399 not shown) Planarity restraints: 3092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 153 " -0.026 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 154 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 154 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 154 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 453 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.30e+00 pdb=" N PRO A 454 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 454 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 454 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 625 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 626 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 626 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 626 " 0.020 5.00e-02 4.00e+02 ... (remaining 3089 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2146 2.76 - 3.29: 14611 3.29 - 3.83: 26232 3.83 - 4.36: 30263 4.36 - 4.90: 55006 Nonbonded interactions: 128258 Sorted by model distance: nonbonded pdb=" OD2 ASP A 656 " pdb=" OG1 THR A 662 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR A 742 " pdb=" O GLY A 745 " model vdw 2.267 3.040 nonbonded pdb=" OG1 THR B 742 " pdb=" O GLY B 745 " model vdw 2.287 3.040 nonbonded pdb=" OE2 GLU B1002 " pdb=" OH TYR B1011 " model vdw 2.291 3.040 nonbonded pdb=" OG SER A1055 " pdb=" OG SER A1063 " model vdw 2.293 3.040 ... (remaining 128253 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.00 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 39.810 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 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 0.028 17342 Z= 0.100 Angle : 0.470 9.051 23462 Z= 0.288 Chirality : 0.039 0.136 2402 Planarity : 0.003 0.040 3092 Dihedral : 13.151 88.482 6340 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 1.83 % Allowed : 9.47 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.15), residues: 2062 helix: -5.11 (0.20), residues: 44 sheet: -1.28 (0.33), residues: 248 loop : -3.19 (0.12), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 417 HIS 0.002 0.000 HIS A 248 PHE 0.004 0.000 PHE B 823 TYR 0.008 0.000 TYR A 409 ARG 0.001 0.000 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.15264 ( 332) hydrogen bonds : angle 6.42212 ( 897) covalent geometry : bond 0.00161 (17342) covalent geometry : angle 0.46959 (23462) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 370 time to evaluate : 1.903 Fit side-chains REVERT: B 591 TYR cc_start: 0.6106 (m-80) cc_final: 0.5747 (m-80) REVERT: B 608 TYR cc_start: 0.7324 (t80) cc_final: 0.7116 (t80) REVERT: B 700 MET cc_start: 0.7388 (tpt) cc_final: 0.7060 (tpt) REVERT: B 973 GLU cc_start: 0.5489 (mt-10) cc_final: 0.5285 (mt-10) REVERT: B 1011 TYR cc_start: 0.8145 (m-80) cc_final: 0.7845 (m-80) REVERT: B 1086 LEU cc_start: 0.6016 (mt) cc_final: 0.5584 (mt) REVERT: A 290 ARG cc_start: 0.5837 (ttt180) cc_final: 0.5622 (tmt170) REVERT: A 353 ARG cc_start: 0.7041 (mmt90) cc_final: 0.6796 (mmt-90) REVERT: A 460 GLN cc_start: 0.7356 (tt0) cc_final: 0.6968 (tt0) REVERT: A 727 LYS cc_start: 0.7128 (ttmt) cc_final: 0.6657 (tmtt) REVERT: A 1024 LEU cc_start: 0.5745 (mt) cc_final: 0.5535 (tp) REVERT: A 1068 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6867 (tm-30) REVERT: D 1173 ASP cc_start: 0.7457 (m-30) cc_final: 0.7021 (m-30) outliers start: 33 outliers final: 21 residues processed: 399 average time/residue: 0.3225 time to fit residues: 186.4632 Evaluate side-chains 249 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain B residue 1089 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain D residue 1175 VAL Chi-restraints excluded: chain D residue 1212 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 0.0270 chunk 156 optimal weight: 6.9990 chunk 86 optimal weight: 0.2980 chunk 53 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 161 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 187 optimal weight: 0.6980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 ASN B 198 HIS B 278 GLN B 294 ASN B 373 HIS B 510 GLN B 551 GLN B 585 GLN B 658 GLN B 724 GLN B 733 ASN B 738 HIS B 740 ASN ** B 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 766 HIS B 772 GLN B 937 GLN B 971 HIS B1071 ASN ** B1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1103 GLN B1117 GLN B1121 ASN C1185 ASN C1213 ASN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 ASN A 303 ASN A 373 HIS ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN A 510 GLN A 550 GLN A 585 GLN A 658 GLN A 692 HIS A 725 HIS A 740 ASN A 755 GLN A 772 GLN A 786 GLN A 940 GLN A 950 GLN A1026 ASN D1148 GLN D1160 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.203206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.174315 restraints weight = 22198.298| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.16 r_work: 0.3883 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17342 Z= 0.085 Angle : 0.481 15.457 23462 Z= 0.250 Chirality : 0.041 0.141 2402 Planarity : 0.003 0.046 3092 Dihedral : 3.901 57.914 2373 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 2.93 % Allowed : 14.12 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.15), residues: 2062 helix: -4.13 (0.47), residues: 42 sheet: -0.39 (0.34), residues: 256 loop : -2.96 (0.12), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 177 HIS 0.003 0.000 HIS B 766 PHE 0.017 0.001 PHE A 839 TYR 0.011 0.001 TYR B 396 ARG 0.004 0.000 ARG B 280 Details of bonding type rmsd hydrogen bonds : bond 0.02593 ( 332) hydrogen bonds : angle 5.14963 ( 897) covalent geometry : bond 0.00173 (17342) covalent geometry : angle 0.48080 (23462) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 241 time to evaluate : 1.933 Fit side-chains REVERT: B 159 THR cc_start: 0.5747 (p) cc_final: 0.5251 (t) REVERT: B 290 ARG cc_start: 0.6449 (ttp-170) cc_final: 0.6170 (ttm-80) REVERT: B 411 ASP cc_start: 0.6946 (m-30) cc_final: 0.6613 (t0) REVERT: B 460 GLN cc_start: 0.7820 (mt0) cc_final: 0.7475 (mt0) REVERT: B 591 TYR cc_start: 0.6240 (m-80) cc_final: 0.5809 (m-80) REVERT: B 1033 GLU cc_start: 0.5334 (mt-10) cc_final: 0.4607 (mt-10) REVERT: B 1061 PHE cc_start: 0.6147 (t80) cc_final: 0.5946 (t80) REVERT: A 290 ARG cc_start: 0.6035 (ttt180) cc_final: 0.5765 (tpt-90) REVERT: A 291 TYR cc_start: 0.5997 (m-80) cc_final: 0.5688 (m-80) REVERT: A 353 ARG cc_start: 0.7366 (mmt90) cc_final: 0.6991 (mmt-90) REVERT: A 719 ASP cc_start: 0.6313 (t0) cc_final: 0.6102 (t0) REVERT: A 727 LYS cc_start: 0.7331 (ttmt) cc_final: 0.6884 (tmtt) REVERT: A 790 GLN cc_start: 0.6951 (tm-30) cc_final: 0.6395 (tp40) REVERT: A 866 ASN cc_start: 0.8273 (p0) cc_final: 0.8017 (p0) REVERT: A 1024 LEU cc_start: 0.6027 (mt) cc_final: 0.5458 (tp) REVERT: A 1068 GLU cc_start: 0.7356 (tm-30) cc_final: 0.6864 (tm-30) REVERT: D 1173 ASP cc_start: 0.7366 (m-30) cc_final: 0.6984 (m-30) outliers start: 53 outliers final: 33 residues processed: 281 average time/residue: 0.2744 time to fit residues: 116.8828 Evaluate side-chains 234 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 992 PHE Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain B residue 1089 ASN Chi-restraints excluded: chain C residue 1185 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain D residue 1175 VAL Chi-restraints excluded: chain D residue 1177 SER Chi-restraints excluded: chain D residue 1212 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 171 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 198 optimal weight: 0.3980 chunk 70 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 chunk 203 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 HIS ** B 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 HIS B 740 ASN ** B 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 ASN B1089 ASN B1103 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 GLN A 288 GLN A 421 HIS A 506 ASN A 574 ASN A 640 GLN A 657 GLN A 738 HIS A 799 ASN A 855 GLN A 885 GLN A1026 ASN ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.175189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.146523 restraints weight = 22540.989| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.39 r_work: 0.3504 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 17342 Z= 0.320 Angle : 0.803 13.686 23462 Z= 0.430 Chirality : 0.050 0.186 2402 Planarity : 0.006 0.055 3092 Dihedral : 5.918 51.529 2364 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.02 % Favored : 85.79 % Rotamer: Outliers : 4.76 % Allowed : 16.50 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.15), residues: 2062 helix: -3.78 (0.59), residues: 44 sheet: -0.79 (0.28), residues: 356 loop : -3.25 (0.12), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 546 HIS 0.023 0.002 HIS B 198 PHE 0.019 0.003 PHE B1131 TYR 0.025 0.003 TYR B1018 ARG 0.006 0.001 ARG B 280 Details of bonding type rmsd hydrogen bonds : bond 0.05405 ( 332) hydrogen bonds : angle 5.88773 ( 897) covalent geometry : bond 0.00774 (17342) covalent geometry : angle 0.80332 (23462) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 221 time to evaluate : 2.252 Fit side-chains REVERT: B 249 PHE cc_start: 0.6687 (OUTLIER) cc_final: 0.6118 (t80) REVERT: B 290 ARG cc_start: 0.6978 (ttp-170) cc_final: 0.6397 (ttm-80) REVERT: B 312 TYR cc_start: 0.5252 (m-80) cc_final: 0.4990 (m-80) REVERT: B 320 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6504 (mm-30) REVERT: B 355 GLU cc_start: 0.7222 (tp30) cc_final: 0.6875 (tp30) REVERT: B 409 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7162 (p90) REVERT: B 411 ASP cc_start: 0.7668 (m-30) cc_final: 0.7154 (m-30) REVERT: B 460 GLN cc_start: 0.7675 (mt0) cc_final: 0.7454 (mt0) REVERT: B 666 ARG cc_start: 0.8234 (ptm160) cc_final: 0.7608 (ptm160) REVERT: B 886 TYR cc_start: 0.8265 (m-80) cc_final: 0.7807 (m-80) REVERT: A 240 GLN cc_start: 0.5751 (OUTLIER) cc_final: 0.5294 (tt0) REVERT: A 290 ARG cc_start: 0.6565 (ttt180) cc_final: 0.5998 (tpt-90) REVERT: A 353 ARG cc_start: 0.7560 (mmt90) cc_final: 0.6962 (mmt90) REVERT: A 414 ASP cc_start: 0.7096 (m-30) cc_final: 0.6812 (m-30) REVERT: A 445 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6752 (tt) REVERT: A 482 TYR cc_start: 0.9307 (m-80) cc_final: 0.9101 (m-80) REVERT: A 586 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8612 (mm) REVERT: A 611 GLU cc_start: 0.8024 (mp0) cc_final: 0.7745 (mp0) REVERT: A 719 ASP cc_start: 0.7098 (t0) cc_final: 0.6880 (t0) REVERT: A 727 LYS cc_start: 0.7434 (ttmt) cc_final: 0.7228 (tmtt) REVERT: A 1024 LEU cc_start: 0.6653 (mt) cc_final: 0.5988 (tp) REVERT: A 1068 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7464 (tm-30) REVERT: D 1180 LYS cc_start: 0.7232 (pttt) cc_final: 0.6912 (ptpt) REVERT: D 1212 ILE cc_start: 0.5821 (OUTLIER) cc_final: 0.5296 (pt) outliers start: 86 outliers final: 50 residues processed: 293 average time/residue: 0.3040 time to fit residues: 131.9821 Evaluate side-chains 242 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 186 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 981 THR Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1049 ASN Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain B residue 1089 ASN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain D residue 1167 GLU Chi-restraints excluded: chain D residue 1177 SER Chi-restraints excluded: chain D residue 1179 VAL Chi-restraints excluded: chain D residue 1207 THR Chi-restraints excluded: chain D residue 1212 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 91 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 171 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 115 optimal weight: 30.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS A1026 ASN ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.177103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149082 restraints weight = 22384.500| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.55 r_work: 0.3519 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17342 Z= 0.184 Angle : 0.633 13.787 23462 Z= 0.339 Chirality : 0.045 0.162 2402 Planarity : 0.004 0.059 3092 Dihedral : 5.127 46.053 2359 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.66 % Favored : 87.34 % Rotamer: Outliers : 4.32 % Allowed : 18.16 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.15), residues: 2062 helix: -3.62 (0.59), residues: 44 sheet: -1.07 (0.29), residues: 348 loop : -3.08 (0.12), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 196 HIS 0.009 0.001 HIS B 198 PHE 0.016 0.002 PHE B1075 TYR 0.024 0.002 TYR A1079 ARG 0.006 0.000 ARG B 280 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 332) hydrogen bonds : angle 5.62446 ( 897) covalent geometry : bond 0.00435 (17342) covalent geometry : angle 0.63346 (23462) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 203 time to evaluate : 2.018 Fit side-chains revert: symmetry clash REVERT: B 181 TYR cc_start: 0.8336 (t80) cc_final: 0.7992 (t80) REVERT: B 249 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.6238 (t80) REVERT: B 284 PHE cc_start: 0.8025 (m-10) cc_final: 0.7802 (m-80) REVERT: B 290 ARG cc_start: 0.6867 (ttp-170) cc_final: 0.6335 (ttm-80) REVERT: B 355 GLU cc_start: 0.7362 (tp30) cc_final: 0.6975 (tp30) REVERT: B 409 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.7227 (p90) REVERT: B 411 ASP cc_start: 0.7667 (m-30) cc_final: 0.7251 (m-30) REVERT: B 886 TYR cc_start: 0.8294 (m-80) cc_final: 0.7941 (m-80) REVERT: B 923 ARG cc_start: 0.7179 (ptt180) cc_final: 0.6930 (ptt180) REVERT: C 1163 GLU cc_start: 0.7961 (tt0) cc_final: 0.7746 (tt0) REVERT: A 290 ARG cc_start: 0.6672 (ttt180) cc_final: 0.6033 (tpt-90) REVERT: A 353 ARG cc_start: 0.7612 (mmt90) cc_final: 0.6954 (mmt90) REVERT: A 414 ASP cc_start: 0.7505 (m-30) cc_final: 0.7231 (m-30) REVERT: A 445 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6865 (tt) REVERT: A 586 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8529 (mm) REVERT: A 611 GLU cc_start: 0.7980 (mp0) cc_final: 0.7613 (mt-10) REVERT: A 719 ASP cc_start: 0.7084 (t0) cc_final: 0.6826 (t0) REVERT: A 790 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: A 1068 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7467 (tm-30) REVERT: D 1173 ASP cc_start: 0.7959 (m-30) cc_final: 0.7567 (m-30) REVERT: D 1180 LYS cc_start: 0.7085 (pttt) cc_final: 0.6745 (ptpt) REVERT: D 1212 ILE cc_start: 0.5765 (OUTLIER) cc_final: 0.5324 (pt) outliers start: 78 outliers final: 61 residues processed: 267 average time/residue: 0.3103 time to fit residues: 122.0429 Evaluate side-chains 247 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 180 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 903 THR Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain B residue 1089 ASN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1084 THR Chi-restraints excluded: chain D residue 1156 GLU Chi-restraints excluded: chain D residue 1167 GLU Chi-restraints excluded: chain D residue 1175 VAL Chi-restraints excluded: chain D residue 1177 SER Chi-restraints excluded: chain D residue 1179 VAL Chi-restraints excluded: chain D residue 1206 ILE Chi-restraints excluded: chain D residue 1207 THR Chi-restraints excluded: chain D residue 1212 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 102 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 96 optimal weight: 0.0270 chunk 157 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 574 ASN B 639 GLN B 885 GLN A 201 GLN A 288 GLN ** A1078 GLN ** 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 = 0.3999 r_free = 0.3999 target = 0.177711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.149624 restraints weight = 22338.111| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.64 r_work: 0.3529 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17342 Z= 0.146 Angle : 0.589 13.929 23462 Z= 0.314 Chirality : 0.043 0.161 2402 Planarity : 0.004 0.057 3092 Dihedral : 4.817 44.784 2359 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.43 % Favored : 86.57 % Rotamer: Outliers : 4.54 % Allowed : 19.66 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.16), residues: 2062 helix: -3.25 (0.62), residues: 44 sheet: -1.02 (0.28), residues: 368 loop : -3.01 (0.13), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 177 HIS 0.004 0.001 HIS A1059 PHE 0.012 0.001 PHE B1075 TYR 0.017 0.001 TYR A1018 ARG 0.006 0.000 ARG B 280 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 332) hydrogen bonds : angle 5.48051 ( 897) covalent geometry : bond 0.00340 (17342) covalent geometry : angle 0.58931 (23462) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 201 time to evaluate : 1.943 Fit side-chains revert: symmetry clash REVERT: B 181 TYR cc_start: 0.8315 (t80) cc_final: 0.7946 (t80) REVERT: B 249 PHE cc_start: 0.6888 (OUTLIER) cc_final: 0.6238 (t80) REVERT: B 263 ASP cc_start: 0.6729 (t70) cc_final: 0.6380 (p0) REVERT: B 290 ARG cc_start: 0.6856 (ttp-170) cc_final: 0.6299 (ttm-80) REVERT: B 312 TYR cc_start: 0.5331 (m-80) cc_final: 0.5053 (m-80) REVERT: B 353 ARG cc_start: 0.7755 (mmm-85) cc_final: 0.7460 (mmm-85) REVERT: B 411 ASP cc_start: 0.7610 (m-30) cc_final: 0.7131 (m-30) REVERT: B 460 GLN cc_start: 0.7790 (mt0) cc_final: 0.7521 (mt0) REVERT: B 658 GLN cc_start: 0.8403 (mm-40) cc_final: 0.7946 (mm-40) REVERT: B 689 ASP cc_start: 0.7558 (p0) cc_final: 0.7161 (p0) REVERT: B 886 TYR cc_start: 0.8296 (m-80) cc_final: 0.8034 (m-80) REVERT: B 923 ARG cc_start: 0.7102 (ptt180) cc_final: 0.6820 (ptt180) REVERT: B 1076 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7180 (tp40) REVERT: C 1163 GLU cc_start: 0.7901 (tt0) cc_final: 0.7683 (tt0) REVERT: A 290 ARG cc_start: 0.6799 (ttt180) cc_final: 0.5960 (tpt90) REVERT: A 353 ARG cc_start: 0.7514 (mmt90) cc_final: 0.6815 (mmt90) REVERT: A 414 ASP cc_start: 0.7687 (m-30) cc_final: 0.7443 (m-30) REVERT: A 445 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6745 (tt) REVERT: A 516 ASP cc_start: 0.8731 (p0) cc_final: 0.8515 (p0) REVERT: A 586 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8414 (mm) REVERT: A 611 GLU cc_start: 0.7878 (mp0) cc_final: 0.7541 (mt-10) REVERT: A 654 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: A 719 ASP cc_start: 0.7069 (t0) cc_final: 0.6867 (t0) REVERT: A 727 LYS cc_start: 0.7462 (tmtt) cc_final: 0.6892 (ttmt) REVERT: A 790 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: A 855 GLN cc_start: 0.7139 (pt0) cc_final: 0.6892 (pt0) REVERT: A 942 LYS cc_start: 0.7821 (mttp) cc_final: 0.7051 (tttp) REVERT: A 1068 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7397 (tm-30) REVERT: D 1173 ASP cc_start: 0.7860 (m-30) cc_final: 0.7490 (m-30) REVERT: D 1180 LYS cc_start: 0.7055 (pttt) cc_final: 0.6666 (ptpt) outliers start: 82 outliers final: 58 residues processed: 266 average time/residue: 0.2997 time to fit residues: 119.5245 Evaluate side-chains 250 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 186 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 903 THR Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain B residue 1076 GLN Chi-restraints excluded: chain B residue 1089 ASN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1084 THR Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain D residue 1156 GLU Chi-restraints excluded: chain D residue 1167 GLU Chi-restraints excluded: chain D residue 1175 VAL Chi-restraints excluded: chain D residue 1177 SER Chi-restraints excluded: chain D residue 1179 VAL Chi-restraints excluded: chain D residue 1206 ILE Chi-restraints excluded: chain D residue 1207 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 72 optimal weight: 0.0270 chunk 179 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 885 GLN A 248 HIS A 288 GLN A 401 HIS ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.179531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.151307 restraints weight = 22232.272| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.63 r_work: 0.3545 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17342 Z= 0.119 Angle : 0.558 13.713 23462 Z= 0.297 Chirality : 0.043 0.196 2402 Planarity : 0.004 0.057 3092 Dihedral : 4.449 35.255 2354 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.32 % Favored : 87.68 % Rotamer: Outliers : 4.04 % Allowed : 20.76 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.16), residues: 2062 helix: -2.93 (0.67), residues: 44 sheet: -0.85 (0.29), residues: 360 loop : -2.90 (0.13), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 177 HIS 0.003 0.001 HIS A 421 PHE 0.021 0.001 PHE B1080 TYR 0.015 0.001 TYR D1214 ARG 0.005 0.000 ARG B 280 Details of bonding type rmsd hydrogen bonds : bond 0.03179 ( 332) hydrogen bonds : angle 5.32909 ( 897) covalent geometry : bond 0.00268 (17342) covalent geometry : angle 0.55831 (23462) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 197 time to evaluate : 1.880 Fit side-chains revert: symmetry clash REVERT: B 181 TYR cc_start: 0.8315 (t80) cc_final: 0.7893 (t80) REVERT: B 242 TYR cc_start: 0.6048 (OUTLIER) cc_final: 0.5430 (t80) REVERT: B 249 PHE cc_start: 0.6878 (t80) cc_final: 0.6278 (t80) REVERT: B 263 ASP cc_start: 0.6706 (t70) cc_final: 0.6381 (p0) REVERT: B 290 ARG cc_start: 0.6852 (ttp-170) cc_final: 0.6287 (ttm-80) REVERT: B 312 TYR cc_start: 0.5290 (m-80) cc_final: 0.5019 (m-80) REVERT: B 353 ARG cc_start: 0.7769 (mmm-85) cc_final: 0.7488 (mmm-85) REVERT: B 411 ASP cc_start: 0.7550 (m-30) cc_final: 0.7161 (m-30) REVERT: B 460 GLN cc_start: 0.7783 (mt0) cc_final: 0.7495 (mt0) REVERT: B 470 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8328 (tp) REVERT: B 658 GLN cc_start: 0.8404 (mm-40) cc_final: 0.7962 (mm-40) REVERT: B 677 ASP cc_start: 0.8408 (p0) cc_final: 0.8206 (p0) REVERT: B 689 ASP cc_start: 0.7623 (p0) cc_final: 0.7406 (p0) REVERT: B 923 ARG cc_start: 0.7125 (ptt180) cc_final: 0.6893 (ptt180) REVERT: C 1163 GLU cc_start: 0.7889 (tt0) cc_final: 0.7675 (tt0) REVERT: A 200 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.6210 (t80) REVERT: A 290 ARG cc_start: 0.6825 (ttt180) cc_final: 0.6002 (tpt90) REVERT: A 353 ARG cc_start: 0.7458 (mmt90) cc_final: 0.6769 (mmt-90) REVERT: A 445 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6755 (tt) REVERT: A 516 ASP cc_start: 0.8733 (p0) cc_final: 0.8492 (p0) REVERT: A 586 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8397 (mm) REVERT: A 611 GLU cc_start: 0.7858 (mp0) cc_final: 0.7532 (mt-10) REVERT: A 727 LYS cc_start: 0.7476 (tmtt) cc_final: 0.6928 (ttmt) REVERT: A 790 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: A 855 GLN cc_start: 0.7080 (pt0) cc_final: 0.6851 (pt0) REVERT: A 942 LYS cc_start: 0.7810 (mttp) cc_final: 0.7038 (tttp) REVERT: A 1068 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7396 (tm-30) REVERT: D 1173 ASP cc_start: 0.7825 (m-30) cc_final: 0.7416 (m-30) REVERT: D 1180 LYS cc_start: 0.7055 (pttt) cc_final: 0.6670 (ptpt) outliers start: 73 outliers final: 54 residues processed: 254 average time/residue: 0.3050 time to fit residues: 115.8478 Evaluate side-chains 249 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 189 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 903 THR Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain B residue 1089 ASN Chi-restraints excluded: chain C residue 1196 LEU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1084 THR Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain D residue 1167 GLU Chi-restraints excluded: chain D residue 1175 VAL Chi-restraints excluded: chain D residue 1177 SER Chi-restraints excluded: chain D residue 1179 VAL Chi-restraints excluded: chain D residue 1192 TYR Chi-restraints excluded: chain D residue 1207 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 142 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 164 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 113 optimal weight: 0.2980 chunk 147 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 885 GLN A 288 GLN ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.183076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.154283 restraints weight = 22247.030| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.37 r_work: 0.3608 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17342 Z= 0.092 Angle : 0.523 13.685 23462 Z= 0.276 Chirality : 0.042 0.180 2402 Planarity : 0.003 0.056 3092 Dihedral : 4.084 34.557 2354 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % Rotamer: Outliers : 3.49 % Allowed : 21.48 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.16), residues: 2062 helix: -2.72 (0.68), residues: 46 sheet: -0.23 (0.29), residues: 356 loop : -2.80 (0.13), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 177 HIS 0.002 0.000 HIS B 373 PHE 0.016 0.001 PHE B1080 TYR 0.011 0.001 TYR B 409 ARG 0.005 0.000 ARG B 280 Details of bonding type rmsd hydrogen bonds : bond 0.02665 ( 332) hydrogen bonds : angle 5.12694 ( 897) covalent geometry : bond 0.00194 (17342) covalent geometry : angle 0.52292 (23462) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 214 time to evaluate : 1.984 Fit side-chains revert: symmetry clash REVERT: B 242 TYR cc_start: 0.6036 (OUTLIER) cc_final: 0.5396 (t80) REVERT: B 249 PHE cc_start: 0.7001 (t80) cc_final: 0.6550 (t80) REVERT: B 263 ASP cc_start: 0.6787 (t70) cc_final: 0.6502 (p0) REVERT: B 290 ARG cc_start: 0.6810 (ttp-170) cc_final: 0.6250 (ttm-80) REVERT: B 312 TYR cc_start: 0.5366 (m-80) cc_final: 0.5099 (m-80) REVERT: B 353 ARG cc_start: 0.7824 (mmm-85) cc_final: 0.7558 (mmm-85) REVERT: B 411 ASP cc_start: 0.7494 (m-30) cc_final: 0.7185 (m-30) REVERT: B 460 GLN cc_start: 0.7783 (mt0) cc_final: 0.7497 (mt0) REVERT: B 658 GLN cc_start: 0.8356 (mm-40) cc_final: 0.7959 (mm-40) REVERT: B 923 ARG cc_start: 0.7181 (ptt180) cc_final: 0.6958 (ptt180) REVERT: C 1135 GLU cc_start: 0.4859 (mp0) cc_final: 0.4616 (mp0) REVERT: A 200 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.6208 (t80) REVERT: A 290 ARG cc_start: 0.6737 (ttt180) cc_final: 0.5938 (tmt170) REVERT: A 353 ARG cc_start: 0.7543 (mmt90) cc_final: 0.6869 (mmt-90) REVERT: A 414 ASP cc_start: 0.7910 (m-30) cc_final: 0.7671 (m-30) REVERT: A 445 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6554 (tt) REVERT: A 482 TYR cc_start: 0.8917 (m-80) cc_final: 0.8713 (m-80) REVERT: A 516 ASP cc_start: 0.8653 (p0) cc_final: 0.8433 (p0) REVERT: A 551 GLN cc_start: 0.7625 (mm110) cc_final: 0.7415 (mm110) REVERT: A 586 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8365 (mm) REVERT: A 654 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7595 (mt-10) REVERT: A 727 LYS cc_start: 0.7209 (tmtt) cc_final: 0.6812 (ttmt) REVERT: A 790 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7421 (tm-30) REVERT: A 835 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.7668 (pm20) REVERT: A 868 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8471 (mt0) REVERT: A 905 GLU cc_start: 0.8057 (tp30) cc_final: 0.7771 (tt0) REVERT: A 1068 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7325 (tm-30) REVERT: D 1173 ASP cc_start: 0.7777 (m-30) cc_final: 0.7398 (m-30) REVERT: D 1180 LYS cc_start: 0.6953 (pttt) cc_final: 0.6506 (ptpt) outliers start: 63 outliers final: 45 residues processed: 266 average time/residue: 0.2985 time to fit residues: 120.3239 Evaluate side-chains 249 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 197 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain B residue 1089 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 868 GLN Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain D residue 1175 VAL Chi-restraints excluded: chain D residue 1177 SER Chi-restraints excluded: chain D residue 1192 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 117 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 574 ASN B 885 GLN A 288 GLN D1188 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.175662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.147648 restraints weight = 22284.536| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.44 r_work: 0.3506 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17342 Z= 0.208 Angle : 0.648 13.576 23462 Z= 0.345 Chirality : 0.045 0.187 2402 Planarity : 0.004 0.056 3092 Dihedral : 4.853 38.510 2354 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.99 % Favored : 85.01 % Rotamer: Outliers : 4.82 % Allowed : 20.65 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.16), residues: 2062 helix: -3.01 (0.63), residues: 46 sheet: -0.94 (0.28), residues: 380 loop : -2.89 (0.13), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 177 HIS 0.005 0.001 HIS A1059 PHE 0.018 0.002 PHE A1101 TYR 0.021 0.002 TYR A1018 ARG 0.004 0.001 ARG B 280 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 332) hydrogen bonds : angle 5.39254 ( 897) covalent geometry : bond 0.00500 (17342) covalent geometry : angle 0.64773 (23462) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 198 time to evaluate : 1.815 Fit side-chains REVERT: B 159 THR cc_start: 0.6643 (p) cc_final: 0.6218 (t) REVERT: B 242 TYR cc_start: 0.6038 (OUTLIER) cc_final: 0.5234 (t80) REVERT: B 249 PHE cc_start: 0.6950 (OUTLIER) cc_final: 0.6414 (t80) REVERT: B 263 ASP cc_start: 0.7120 (t70) cc_final: 0.6820 (p0) REVERT: B 290 ARG cc_start: 0.7024 (ttp-170) cc_final: 0.6318 (ttm-80) REVERT: B 353 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7736 (mmm-85) REVERT: B 388 ARG cc_start: 0.7252 (tpt170) cc_final: 0.6895 (tpt-90) REVERT: B 411 ASP cc_start: 0.7700 (m-30) cc_final: 0.7210 (m-30) REVERT: B 470 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8458 (tp) REVERT: B 658 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8015 (mm-40) REVERT: B 666 ARG cc_start: 0.8302 (ptm160) cc_final: 0.7788 (ptm160) REVERT: B 689 ASP cc_start: 0.7659 (p0) cc_final: 0.7360 (p0) REVERT: B 1076 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7353 (tp40) REVERT: B 1107 ILE cc_start: 0.8312 (mt) cc_final: 0.8099 (mt) REVERT: A 200 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.6340 (t80) REVERT: A 290 ARG cc_start: 0.6998 (ttt180) cc_final: 0.6136 (tpt90) REVERT: A 353 ARG cc_start: 0.7751 (mmt90) cc_final: 0.7007 (mmt90) REVERT: A 445 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.6920 (tt) REVERT: A 586 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8538 (mm) REVERT: A 627 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8313 (mp0) REVERT: A 654 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7731 (mt-10) REVERT: A 790 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: A 835 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.7813 (pm20) REVERT: A 868 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8476 (mt0) REVERT: A 942 LYS cc_start: 0.7939 (mttp) cc_final: 0.7117 (tttp) REVERT: A 1068 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7484 (tm-30) REVERT: D 1173 ASP cc_start: 0.7819 (m-30) cc_final: 0.7581 (m-30) REVERT: D 1180 LYS cc_start: 0.7287 (pttt) cc_final: 0.6939 (ptpt) outliers start: 87 outliers final: 64 residues processed: 267 average time/residue: 0.2911 time to fit residues: 116.2519 Evaluate side-chains 259 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 184 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 903 THR Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain B residue 1076 GLN Chi-restraints excluded: chain B residue 1089 ASN Chi-restraints excluded: chain C residue 1196 LEU Chi-restraints excluded: chain C residue 1206 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 868 GLN Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1084 THR Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain D residue 1167 GLU Chi-restraints excluded: chain D residue 1175 VAL Chi-restraints excluded: chain D residue 1177 SER Chi-restraints excluded: chain D residue 1206 ILE Chi-restraints excluded: chain D residue 1207 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.7980 chunk 7 optimal weight: 0.0980 chunk 157 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 574 ASN B 885 GLN A 288 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.177439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.148898 restraints weight = 22410.013| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.37 r_work: 0.3539 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17342 Z= 0.147 Angle : 0.605 13.666 23462 Z= 0.323 Chirality : 0.044 0.171 2402 Planarity : 0.004 0.056 3092 Dihedral : 4.703 37.061 2354 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.05 % Favored : 86.95 % Rotamer: Outliers : 3.99 % Allowed : 21.65 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.16), residues: 2062 helix: -2.94 (0.64), residues: 46 sheet: -0.89 (0.28), residues: 380 loop : -2.86 (0.13), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 177 HIS 0.004 0.001 HIS A 421 PHE 0.017 0.001 PHE A1101 TYR 0.023 0.001 TYR A1079 ARG 0.004 0.000 ARG B 280 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 332) hydrogen bonds : angle 5.35221 ( 897) covalent geometry : bond 0.00341 (17342) covalent geometry : angle 0.60540 (23462) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 192 time to evaluate : 1.786 Fit side-chains REVERT: B 159 THR cc_start: 0.6668 (p) cc_final: 0.6256 (t) REVERT: B 242 TYR cc_start: 0.6077 (OUTLIER) cc_final: 0.5169 (t80) REVERT: B 249 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.6635 (t80) REVERT: B 263 ASP cc_start: 0.7118 (t70) cc_final: 0.6828 (p0) REVERT: B 290 ARG cc_start: 0.7042 (ttp-170) cc_final: 0.6362 (ttm-80) REVERT: B 312 TYR cc_start: 0.5321 (m-80) cc_final: 0.5098 (m-80) REVERT: B 353 ARG cc_start: 0.8021 (mmm-85) cc_final: 0.7793 (mmm-85) REVERT: B 411 ASP cc_start: 0.7733 (m-30) cc_final: 0.7332 (m-30) REVERT: B 460 GLN cc_start: 0.7961 (mt0) cc_final: 0.7684 (mt0) REVERT: B 470 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8448 (tp) REVERT: B 658 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8014 (mm-40) REVERT: B 666 ARG cc_start: 0.8294 (ptm160) cc_final: 0.7834 (ptm160) REVERT: B 1076 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7416 (tp40) REVERT: A 200 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.6338 (t80) REVERT: A 290 ARG cc_start: 0.6974 (ttt180) cc_final: 0.6124 (tpt90) REVERT: A 328 GLN cc_start: 0.7092 (mp10) cc_final: 0.6653 (mp10) REVERT: A 353 ARG cc_start: 0.7815 (mmt90) cc_final: 0.7105 (mmt90) REVERT: A 445 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.6972 (tt) REVERT: A 482 TYR cc_start: 0.9163 (m-80) cc_final: 0.8944 (m-80) REVERT: A 586 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8608 (mm) REVERT: A 611 GLU cc_start: 0.8096 (mp0) cc_final: 0.7736 (mt-10) REVERT: A 627 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8347 (mp0) REVERT: A 654 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7705 (mt-10) REVERT: A 727 LYS cc_start: 0.7670 (tmtt) cc_final: 0.7043 (tttt) REVERT: A 790 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: A 835 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.7832 (pm20) REVERT: A 868 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8602 (mt0) REVERT: A 942 LYS cc_start: 0.7919 (mttp) cc_final: 0.7143 (tttp) REVERT: A 1068 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7486 (tm-30) REVERT: D 1173 ASP cc_start: 0.7896 (m-30) cc_final: 0.7563 (m-30) REVERT: D 1180 LYS cc_start: 0.7231 (pttt) cc_final: 0.6889 (ptpt) outliers start: 72 outliers final: 56 residues processed: 251 average time/residue: 0.3049 time to fit residues: 114.7328 Evaluate side-chains 251 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 184 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain B residue 1076 GLN Chi-restraints excluded: chain B residue 1089 ASN Chi-restraints excluded: chain C residue 1196 LEU Chi-restraints excluded: chain C residue 1206 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 868 GLN Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1084 THR Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain D residue 1167 GLU Chi-restraints excluded: chain D residue 1175 VAL Chi-restraints excluded: chain D residue 1177 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 54 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 185 optimal weight: 0.4980 chunk 22 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 6 optimal weight: 0.4980 chunk 51 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 639 GLN A 288 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.175624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.147142 restraints weight = 22192.998| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.32 r_work: 0.3511 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17342 Z= 0.187 Angle : 0.647 13.744 23462 Z= 0.346 Chirality : 0.045 0.177 2402 Planarity : 0.004 0.056 3092 Dihedral : 4.923 38.297 2354 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.18 % Favored : 84.82 % Rotamer: Outliers : 4.37 % Allowed : 21.48 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.16), residues: 2062 helix: -2.96 (0.65), residues: 46 sheet: -0.99 (0.28), residues: 380 loop : -2.91 (0.13), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 177 HIS 0.005 0.001 HIS A1059 PHE 0.018 0.002 PHE B1080 TYR 0.025 0.002 TYR A1079 ARG 0.004 0.000 ARG B1074 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 332) hydrogen bonds : angle 5.45044 ( 897) covalent geometry : bond 0.00442 (17342) covalent geometry : angle 0.64666 (23462) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4124 Ramachandran restraints generated. 2062 Oldfield, 0 Emsley, 2062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 189 time to evaluate : 1.834 Fit side-chains REVERT: B 159 THR cc_start: 0.6630 (p) cc_final: 0.6231 (t) REVERT: B 242 TYR cc_start: 0.6195 (OUTLIER) cc_final: 0.5362 (t80) REVERT: B 249 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6531 (t80) REVERT: B 263 ASP cc_start: 0.7240 (t70) cc_final: 0.6939 (p0) REVERT: B 290 ARG cc_start: 0.7087 (ttp-170) cc_final: 0.6361 (ttm-80) REVERT: B 353 ARG cc_start: 0.8023 (mmm-85) cc_final: 0.7805 (mmm-85) REVERT: B 388 ARG cc_start: 0.7261 (tpt170) cc_final: 0.6916 (tpt-90) REVERT: B 411 ASP cc_start: 0.7709 (m-30) cc_final: 0.7312 (m-30) REVERT: B 460 GLN cc_start: 0.7919 (mt0) cc_final: 0.7643 (mt0) REVERT: B 470 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8433 (tp) REVERT: B 658 GLN cc_start: 0.8486 (mm-40) cc_final: 0.7997 (mm-40) REVERT: B 666 ARG cc_start: 0.8295 (ptm160) cc_final: 0.7804 (ptm160) REVERT: B 1076 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7365 (tp40) REVERT: A 200 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.6351 (t80) REVERT: A 290 ARG cc_start: 0.7136 (ttt180) cc_final: 0.6245 (tpt90) REVERT: A 353 ARG cc_start: 0.7869 (mmt90) cc_final: 0.7159 (mmt90) REVERT: A 445 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7026 (tt) REVERT: A 586 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8533 (mm) REVERT: A 654 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: A 727 LYS cc_start: 0.7934 (tmtt) cc_final: 0.7312 (tttt) REVERT: A 790 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: A 835 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.7846 (pm20) REVERT: A 868 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8573 (mt0) REVERT: A 920 MET cc_start: 0.7326 (tpp) cc_final: 0.7098 (tpt) REVERT: A 942 LYS cc_start: 0.7935 (mttp) cc_final: 0.7134 (tttp) REVERT: A 1068 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7468 (tm-30) REVERT: D 1173 ASP cc_start: 0.7868 (m-30) cc_final: 0.7626 (m-30) REVERT: D 1180 LYS cc_start: 0.7231 (pttt) cc_final: 0.6915 (ptpt) outliers start: 79 outliers final: 62 residues processed: 251 average time/residue: 0.3006 time to fit residues: 111.4796 Evaluate side-chains 258 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 185 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 903 THR Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1066 VAL Chi-restraints excluded: chain B residue 1076 GLN Chi-restraints excluded: chain B residue 1089 ASN Chi-restraints excluded: chain C residue 1196 LEU Chi-restraints excluded: chain C residue 1206 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 868 GLN Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1084 THR Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain D residue 1167 GLU Chi-restraints excluded: chain D residue 1175 VAL Chi-restraints excluded: chain D residue 1177 SER Chi-restraints excluded: chain D residue 1179 VAL Chi-restraints excluded: chain D residue 1207 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 201 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 205 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 113 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 288 GLN A 444 HIS ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.176649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.148406 restraints weight = 22190.305| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.53 r_work: 0.3520 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17342 Z= 0.153 Angle : 0.617 13.800 23462 Z= 0.330 Chirality : 0.044 0.167 2402 Planarity : 0.004 0.056 3092 Dihedral : 4.810 37.491 2354 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.97 % Favored : 86.03 % Rotamer: Outliers : 4.26 % Allowed : 21.76 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.16), residues: 2062 helix: -2.90 (0.65), residues: 46 sheet: -0.93 (0.28), residues: 380 loop : -2.88 (0.13), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 177 HIS 0.008 0.001 HIS A 444 PHE 0.017 0.001 PHE A1101 TYR 0.021 0.001 TYR A1079 ARG 0.005 0.000 ARG B1042 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 332) hydrogen bonds : angle 5.39955 ( 897) covalent geometry : bond 0.00356 (17342) covalent geometry : angle 0.61725 (23462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7811.49 seconds wall clock time: 136 minutes 6.75 seconds (8166.75 seconds total)