Starting phenix.real_space_refine on Sun Aug 24 03:55:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h8c_34542/08_2025/8h8c_34542.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h8c_34542/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8h8c_34542/08_2025/8h8c_34542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h8c_34542/08_2025/8h8c_34542.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h8c_34542/08_2025/8h8c_34542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h8c_34542/08_2025/8h8c_34542.map" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.02, per 1000 atoms: 0.18 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: 1.59 Conformation dependent library (CDL) restraints added in 529.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.68 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: 3.01 Time building geometry restraints manager: 1.98 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: 0.02 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: 0.920 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.320 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.810 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.001 0.000 ARG A 266 TYR 0.008 0.000 TYR A 409 PHE 0.004 0.000 PHE B 823 TRP 0.004 0.000 TRP B 417 HIS 0.002 0.000 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00161 (17342) covalent geometry : angle 0.46959 (23462) hydrogen bonds : bond 0.15264 ( 332) hydrogen bonds : angle 6.42212 ( 897) *********************** 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 : 0.548 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: 0.1386 time to fit residues: 80.8752 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 : 0.517 ------------------------------------------------------------------------------- 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 98 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 328 GLN B 373 HIS B 510 GLN B 551 GLN B 585 GLN ** B 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN B 692 HIS B 724 GLN B 733 ASN B 738 HIS B 755 GLN B 772 GLN B 869 ASN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 HIS B1071 ASN B1089 ASN B1121 ASN C1213 ASN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 GLN A 251 ASN A 303 ASN A 373 HIS A 421 HIS A 510 GLN A 550 GLN A 574 ASN A 585 GLN A 658 GLN A 692 HIS A 725 HIS A 738 HIS A 740 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 772 GLN A 786 GLN A 799 ASN A 855 GLN A 940 GLN A1026 ASN D1148 GLN D1160 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.177483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.149153 restraints weight = 22448.116| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.59 r_work: 0.3520 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 17342 Z= 0.281 Angle : 0.791 13.811 23462 Z= 0.418 Chirality : 0.049 0.173 2402 Planarity : 0.006 0.053 3092 Dihedral : 5.944 57.564 2373 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.99 % Favored : 84.82 % Rotamer: Outliers : 4.37 % Allowed : 16.94 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.02 (0.15), residues: 2062 helix: -4.23 (0.51), residues: 44 sheet: -0.93 (0.28), residues: 346 loop : -3.35 (0.12), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 830 TYR 0.028 0.002 TYR A1079 PHE 0.019 0.003 PHE B1131 TRP 0.032 0.002 TRP B 177 HIS 0.011 0.002 HIS A 421 Details of bonding type rmsd covalent geometry : bond 0.00673 (17342) covalent geometry : angle 0.79065 (23462) hydrogen bonds : bond 0.05305 ( 332) hydrogen bonds : angle 5.85312 ( 897) *********************** 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 309 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 230 time to evaluate : 0.588 Fit side-chains REVERT: B 159 THR cc_start: 0.6211 (p) cc_final: 0.5760 (t) REVERT: B 249 PHE cc_start: 0.6578 (t80) cc_final: 0.6246 (t80) REVERT: B 263 ASP cc_start: 0.6796 (t70) cc_final: 0.6424 (p0) REVERT: B 290 ARG cc_start: 0.6985 (ttp-170) cc_final: 0.6466 (ttm-80) REVERT: B 355 GLU cc_start: 0.7258 (tp30) cc_final: 0.6913 (tp30) REVERT: B 409 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.7460 (p90) REVERT: B 460 GLN cc_start: 0.7672 (mt0) cc_final: 0.7382 (mt0) REVERT: B 831 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8472 (tp) REVERT: B 839 PHE cc_start: 0.6715 (t80) cc_final: 0.6489 (t80) REVERT: B 886 TYR cc_start: 0.8227 (m-80) cc_final: 0.7938 (m-80) REVERT: C 1152 ASP cc_start: 0.7753 (t0) cc_final: 0.7531 (t0) REVERT: A 153 ASP cc_start: 0.0823 (OUTLIER) cc_final: -0.1514 (t70) REVERT: A 215 THR cc_start: 0.7954 (OUTLIER) cc_final: 0.7738 (p) REVERT: A 290 ARG cc_start: 0.6597 (ttt180) cc_final: 0.6014 (tpt-90) REVERT: A 353 ARG cc_start: 0.7605 (mmt90) cc_final: 0.7042 (mmt90) REVERT: A 408 SER cc_start: 0.7403 (p) cc_final: 0.7114 (m) REVERT: A 516 ASP cc_start: 0.8415 (p0) cc_final: 0.8212 (p0) REVERT: A 586 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8589 (mm) REVERT: A 611 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7723 (mt-10) REVERT: A 727 LYS cc_start: 0.7481 (ttmt) cc_final: 0.7145 (tmtt) REVERT: A 1024 LEU cc_start: 0.6679 (mt) cc_final: 0.6031 (tp) REVERT: A 1068 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7296 (tm-30) REVERT: A 1105 ASP cc_start: 0.6813 (p0) cc_final: 0.6587 (p0) REVERT: A 1107 ILE cc_start: 0.6957 (mt) cc_final: 0.6597 (mt) REVERT: D 1148 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7621 (mm-40) REVERT: D 1180 LYS cc_start: 0.7096 (pttt) cc_final: 0.6765 (ptpt) REVERT: D 1212 ILE cc_start: 0.5468 (OUTLIER) cc_final: 0.5060 (pt) outliers start: 79 outliers final: 51 residues processed: 298 average time/residue: 0.1239 time to fit residues: 55.6385 Evaluate side-chains 248 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 191 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 326 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 458 THR 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 831 LEU Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 834 THR 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 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 215 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 573 VAL 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 685 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 844 LEU 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 930 VAL Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1084 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 53 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 8 optimal weight: 0.4980 chunk 69 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 HIS B 639 GLN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1117 GLN A 201 GLN A 288 GLN A 506 ASN A 692 HIS ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 ASN ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.182222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.154596 restraints weight = 22529.242| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.70 r_work: 0.3573 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17342 Z= 0.114 Angle : 0.554 13.437 23462 Z= 0.295 Chirality : 0.042 0.151 2402 Planarity : 0.003 0.053 3092 Dihedral : 4.829 45.988 2367 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 3.43 % Allowed : 19.16 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.62 (0.15), residues: 2062 helix: -3.78 (0.57), residues: 44 sheet: -0.41 (0.31), residues: 308 loop : -3.07 (0.12), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 280 TYR 0.016 0.001 TYR B 612 PHE 0.016 0.001 PHE A 202 TRP 0.013 0.001 TRP A 513 HIS 0.007 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00253 (17342) covalent geometry : angle 0.55404 (23462) hydrogen bonds : bond 0.03333 ( 332) hydrogen bonds : angle 5.47456 ( 897) *********************** 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 272 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 210 time to evaluate : 0.573 Fit side-chains REVERT: B 249 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.6294 (t80) REVERT: B 263 ASP cc_start: 0.6738 (t70) cc_final: 0.6381 (p0) REVERT: B 290 ARG cc_start: 0.6886 (ttp-170) cc_final: 0.6432 (ttm-80) REVERT: B 355 GLU cc_start: 0.7314 (tp30) cc_final: 0.6951 (tp30) REVERT: B 409 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.7147 (p90) REVERT: B 411 ASP cc_start: 0.7412 (m-30) cc_final: 0.6917 (t0) REVERT: B 460 GLN cc_start: 0.7789 (mt0) cc_final: 0.7462 (mt0) REVERT: B 666 ARG cc_start: 0.8110 (ptm160) cc_final: 0.7689 (ptm160) REVERT: B 831 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8291 (tp) REVERT: B 839 PHE cc_start: 0.6486 (t80) cc_final: 0.6276 (t80) REVERT: B 886 TYR cc_start: 0.8143 (m-80) cc_final: 0.7940 (m-80) REVERT: A 240 GLN cc_start: 0.5717 (OUTLIER) cc_final: 0.5394 (tt0) REVERT: A 290 ARG cc_start: 0.6471 (ttt180) cc_final: 0.5885 (tpt-90) REVERT: A 353 ARG cc_start: 0.7489 (mmt90) cc_final: 0.6946 (mmt90) REVERT: A 401 HIS cc_start: 0.7831 (OUTLIER) cc_final: 0.7436 (t-90) REVERT: A 414 ASP cc_start: 0.7025 (m-30) cc_final: 0.6753 (m-30) REVERT: A 445 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6343 (tt) REVERT: A 516 ASP cc_start: 0.8369 (p0) cc_final: 0.8030 (p0) REVERT: A 586 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8445 (mm) REVERT: A 611 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7598 (mt-10) REVERT: A 727 LYS cc_start: 0.7573 (ttmt) cc_final: 0.7333 (tmtt) REVERT: A 1068 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7335 (tm-30) REVERT: D 1148 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7623 (mm-40) REVERT: D 1173 ASP cc_start: 0.7833 (m-30) cc_final: 0.7327 (m-30) REVERT: D 1180 LYS cc_start: 0.6895 (pttt) cc_final: 0.6417 (ptpt) REVERT: D 1212 ILE cc_start: 0.5304 (OUTLIER) cc_final: 0.4915 (pt) outliers start: 62 outliers final: 42 residues processed: 263 average time/residue: 0.1349 time to fit residues: 52.9118 Evaluate side-chains 244 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 259 LEU 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 445 LEU Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 500 LEU 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 831 LEU 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 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 240 GLN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 401 HIS 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 495 SER 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 665 VAL Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 804 THR 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 981 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 1179 VAL 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 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 132 optimal weight: 0.9980 chunk 118 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 198 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 138 optimal weight: 0.7980 chunk 90 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 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS B 885 GLN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN A 474 HIS ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.184729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.156475 restraints weight = 22460.334| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.44 r_work: 0.3628 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17342 Z= 0.091 Angle : 0.508 13.922 23462 Z= 0.270 Chirality : 0.041 0.158 2402 Planarity : 0.003 0.053 3092 Dihedral : 4.265 45.119 2362 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 4.04 % Allowed : 19.82 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.38 (0.16), residues: 2062 helix: -3.32 (0.62), residues: 44 sheet: -0.45 (0.30), residues: 338 loop : -2.89 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 280 TYR 0.008 0.001 TYR B 409 PHE 0.017 0.001 PHE A 202 TRP 0.014 0.001 TRP B 177 HIS 0.012 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00192 (17342) covalent geometry : angle 0.50797 (23462) hydrogen bonds : bond 0.02763 ( 332) hydrogen bonds : angle 5.22324 ( 897) *********************** 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 285 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 212 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: B 181 TYR cc_start: 0.8194 (t80) cc_final: 0.7787 (t80) REVERT: B 249 PHE cc_start: 0.6585 (OUTLIER) cc_final: 0.6238 (t80) REVERT: B 275 LEU cc_start: 0.3985 (OUTLIER) cc_final: 0.3590 (tp) REVERT: B 280 ARG cc_start: 0.7071 (mmm-85) cc_final: 0.6868 (mmm-85) REVERT: B 290 ARG cc_start: 0.6733 (ttp-170) cc_final: 0.6340 (ttm-80) REVERT: B 355 GLU cc_start: 0.7215 (tp30) cc_final: 0.6868 (tp30) REVERT: B 411 ASP cc_start: 0.7380 (m-30) cc_final: 0.6939 (t0) REVERT: B 460 GLN cc_start: 0.7784 (mt0) cc_final: 0.7510 (mt0) REVERT: B 470 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8248 (tp) REVERT: B 658 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7857 (mm110) REVERT: A 153 ASP cc_start: 0.0630 (OUTLIER) cc_final: 0.0360 (p0) REVERT: A 240 GLN cc_start: 0.5642 (OUTLIER) cc_final: 0.5402 (tt0) REVERT: A 290 ARG cc_start: 0.6496 (ttt180) cc_final: 0.5884 (tpt-90) REVERT: A 353 ARG cc_start: 0.7388 (mmt90) cc_final: 0.6871 (mmt-90) REVERT: A 414 ASP cc_start: 0.7075 (m-30) cc_final: 0.6802 (m-30) REVERT: A 445 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6086 (tt) REVERT: A 516 ASP cc_start: 0.8338 (p0) cc_final: 0.8021 (p0) REVERT: A 586 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8338 (mm) REVERT: A 611 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7538 (mt-10) REVERT: A 790 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7610 (tp40) REVERT: A 855 GLN cc_start: 0.6936 (pt0) cc_final: 0.6716 (pt0) REVERT: A 897 GLU cc_start: 0.7500 (tp30) cc_final: 0.7190 (tt0) REVERT: A 1068 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7249 (tm-30) REVERT: D 1173 ASP cc_start: 0.7769 (m-30) cc_final: 0.7242 (m-30) REVERT: D 1180 LYS cc_start: 0.6811 (pttt) cc_final: 0.6334 (ptpt) REVERT: D 1212 ILE cc_start: 0.5077 (OUTLIER) cc_final: 0.4714 (pt) outliers start: 73 outliers final: 45 residues processed: 272 average time/residue: 0.1252 time to fit residues: 51.2361 Evaluate side-chains 256 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 249 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 275 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 452 VAL Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 495 SER 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 665 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 834 THR 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 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 240 GLN 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 495 SER 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 573 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 692 HIS Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 41 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 167 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 574 ASN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 885 GLN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 HIS A 401 HIS A 474 HIS A 640 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.173438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.145450 restraints weight = 22364.470| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.60 r_work: 0.3457 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 17342 Z= 0.280 Angle : 0.737 13.869 23462 Z= 0.394 Chirality : 0.048 0.222 2402 Planarity : 0.005 0.056 3092 Dihedral : 5.643 41.151 2360 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.71 % Favored : 84.29 % Rotamer: Outliers : 4.82 % Allowed : 20.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.79 (0.15), residues: 2062 helix: -3.50 (0.59), residues: 46 sheet: -1.31 (0.28), residues: 362 loop : -3.07 (0.12), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1074 TYR 0.023 0.002 TYR D1214 PHE 0.022 0.002 PHE A 202 TRP 0.016 0.002 TRP B 177 HIS 0.007 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00675 (17342) covalent geometry : angle 0.73701 (23462) hydrogen bonds : bond 0.04965 ( 332) hydrogen bonds : angle 5.82896 ( 897) *********************** 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 287 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 200 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: B 181 TYR cc_start: 0.8443 (t80) cc_final: 0.8085 (t80) REVERT: B 249 PHE cc_start: 0.6705 (OUTLIER) cc_final: 0.6171 (t80) REVERT: B 263 ASP cc_start: 0.6822 (t70) cc_final: 0.6525 (p0) REVERT: B 290 ARG cc_start: 0.7018 (ttp-170) cc_final: 0.6417 (ttm-80) REVERT: B 320 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6369 (mm-30) REVERT: B 353 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.7524 (mmm-85) REVERT: B 388 ARG cc_start: 0.7227 (tpt170) cc_final: 0.6883 (tpt-90) REVERT: B 411 ASP cc_start: 0.7580 (m-30) cc_final: 0.7310 (m-30) REVERT: B 689 ASP cc_start: 0.7705 (p0) cc_final: 0.7399 (p0) REVERT: B 795 LYS cc_start: 0.7560 (mmtp) cc_final: 0.7098 (mmtm) REVERT: B 923 ARG cc_start: 0.7223 (ptt180) cc_final: 0.7018 (ptt180) REVERT: B 1076 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7438 (tp40) REVERT: A 290 ARG cc_start: 0.6947 (ttt180) cc_final: 0.6149 (tpt90) REVERT: A 291 TYR cc_start: 0.7348 (m-80) cc_final: 0.6913 (m-80) REVERT: A 353 ARG cc_start: 0.7545 (mmt90) cc_final: 0.6881 (mmt90) REVERT: A 414 ASP cc_start: 0.7695 (m-30) cc_final: 0.7467 (m-30) REVERT: A 445 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6892 (tt) REVERT: A 586 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8539 (mm) REVERT: A 611 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7545 (mt-10) REVERT: A 654 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7588 (mt-10) REVERT: A 719 ASP cc_start: 0.6984 (t0) cc_final: 0.6639 (t0) REVERT: A 727 LYS cc_start: 0.7559 (tmtt) cc_final: 0.6959 (tttt) REVERT: A 790 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: A 897 GLU cc_start: 0.7820 (tp30) cc_final: 0.7539 (tt0) REVERT: A 942 LYS cc_start: 0.7902 (mttp) cc_final: 0.7139 (tttp) REVERT: A 1068 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7438 (tm-30) REVERT: D 1180 LYS cc_start: 0.7268 (pttt) cc_final: 0.6962 (ptpt) REVERT: D 1212 ILE cc_start: 0.6339 (OUTLIER) cc_final: 0.5877 (pt) outliers start: 87 outliers final: 60 residues processed: 271 average time/residue: 0.1359 time to fit residues: 55.0247 Evaluate side-chains 248 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 181 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 347 ASP 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 495 SER 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 574 ASN 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 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 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 1206 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 157 LEU 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 495 SER Chi-restraints excluded: chain A residue 520 CYS 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 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 985 THR Chi-restraints excluded: chain A residue 989 ILE 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 1086 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 37 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 574 ASN B 885 GLN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN A 288 GLN ** A 755 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 = 0.3991 r_free = 0.3991 target = 0.177017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.148857 restraints weight = 22266.727| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.59 r_work: 0.3509 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17342 Z= 0.153 Angle : 0.599 13.819 23462 Z= 0.321 Chirality : 0.044 0.191 2402 Planarity : 0.004 0.058 3092 Dihedral : 5.011 37.496 2360 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.61 % Favored : 87.39 % Rotamer: Outliers : 4.87 % Allowed : 20.65 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.63 (0.16), residues: 2062 helix: -3.28 (0.63), residues: 46 sheet: -1.08 (0.28), residues: 380 loop : -3.00 (0.13), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 280 TYR 0.020 0.001 TYR A1079 PHE 0.027 0.001 PHE B1080 TRP 0.018 0.001 TRP B 177 HIS 0.005 0.001 HIS B 766 Details of bonding type rmsd covalent geometry : bond 0.00355 (17342) covalent geometry : angle 0.59893 (23462) hydrogen bonds : bond 0.03663 ( 332) hydrogen bonds : angle 5.59253 ( 897) *********************** 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 283 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 195 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: B 181 TYR cc_start: 0.8376 (t80) cc_final: 0.8050 (t80) REVERT: B 242 TYR cc_start: 0.5976 (OUTLIER) cc_final: 0.5169 (t80) REVERT: B 249 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.6384 (t80) REVERT: B 263 ASP cc_start: 0.6839 (t70) cc_final: 0.6614 (p0) REVERT: B 290 ARG cc_start: 0.6928 (ttp-170) cc_final: 0.6341 (ttm-80) REVERT: B 353 ARG cc_start: 0.7824 (mmm-85) cc_final: 0.7578 (mmm-85) REVERT: B 460 GLN cc_start: 0.7791 (mt0) cc_final: 0.7479 (mt0) REVERT: B 470 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8340 (tp) REVERT: B 689 ASP cc_start: 0.7718 (p0) cc_final: 0.7478 (p0) REVERT: B 795 LYS cc_start: 0.7511 (mmtp) cc_final: 0.7131 (mmtm) REVERT: B 859 ARG cc_start: 0.7404 (ttp80) cc_final: 0.7196 (mtp-110) REVERT: B 923 ARG cc_start: 0.7217 (ptt180) cc_final: 0.6962 (ptt180) REVERT: B 1076 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7139 (tp40) REVERT: B 1107 ILE cc_start: 0.8108 (mt) cc_final: 0.7887 (mt) REVERT: A 290 ARG cc_start: 0.6988 (ttt180) cc_final: 0.6134 (tpt90) REVERT: A 291 TYR cc_start: 0.7266 (m-80) cc_final: 0.6895 (m-80) REVERT: A 320 GLU cc_start: 0.5959 (OUTLIER) cc_final: 0.5684 (mt-10) REVERT: A 353 ARG cc_start: 0.7478 (mmt90) cc_final: 0.6800 (mmt90) REVERT: A 445 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6773 (tt) REVERT: A 586 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8431 (mm) REVERT: A 611 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7482 (mt-10) REVERT: A 654 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: A 719 ASP cc_start: 0.7000 (t0) cc_final: 0.6692 (t0) REVERT: A 727 LYS cc_start: 0.7457 (tmtt) cc_final: 0.6891 (tttt) REVERT: A 790 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7918 (tm-30) REVERT: A 897 GLU cc_start: 0.7783 (tp30) cc_final: 0.7555 (tt0) REVERT: A 942 LYS cc_start: 0.7835 (mttp) cc_final: 0.7087 (tttp) REVERT: A 1068 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7399 (tm-30) REVERT: D 1180 LYS cc_start: 0.7052 (pttt) cc_final: 0.6718 (ptpt) outliers start: 88 outliers final: 64 residues processed: 262 average time/residue: 0.1303 time to fit residues: 50.4678 Evaluate side-chains 254 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 181 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 458 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 500 LEU 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 574 ASN Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 844 LEU 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 963 VAL Chi-restraints excluded: chain B residue 1017 THR 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 158 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 332 THR 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 495 SER Chi-restraints excluded: chain A residue 520 CYS 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 654 GLU Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 692 HIS 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 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 916 ASP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 195 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 111 optimal weight: 0.0670 chunk 145 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 GLN B 885 GLN ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN ** A 755 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 = 0.4027 r_free = 0.4027 target = 0.180429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.152616 restraints weight = 21962.104| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.47 r_work: 0.3556 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17342 Z= 0.106 Angle : 0.547 13.956 23462 Z= 0.292 Chirality : 0.042 0.174 2402 Planarity : 0.004 0.057 3092 Dihedral : 4.549 34.776 2358 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.00 % Favored : 87.00 % Rotamer: Outliers : 4.10 % Allowed : 21.65 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.37 (0.16), residues: 2062 helix: -2.99 (0.67), residues: 46 sheet: -0.57 (0.28), residues: 388 loop : -2.92 (0.13), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 280 TYR 0.014 0.001 TYR B 409 PHE 0.022 0.001 PHE B1080 TRP 0.016 0.001 TRP B 177 HIS 0.003 0.001 HIS B 766 Details of bonding type rmsd covalent geometry : bond 0.00231 (17342) covalent geometry : angle 0.54705 (23462) hydrogen bonds : bond 0.03000 ( 332) hydrogen bonds : angle 5.27167 ( 897) *********************** 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 273 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 199 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: B 159 THR cc_start: 0.6441 (p) cc_final: 0.6040 (t) REVERT: B 181 TYR cc_start: 0.8397 (t80) cc_final: 0.8009 (t80) REVERT: B 242 TYR cc_start: 0.6026 (OUTLIER) cc_final: 0.5299 (t80) REVERT: B 249 PHE cc_start: 0.6928 (OUTLIER) cc_final: 0.6458 (t80) REVERT: B 263 ASP cc_start: 0.6974 (t70) cc_final: 0.6717 (p0) REVERT: B 290 ARG cc_start: 0.6935 (ttp-170) cc_final: 0.6296 (ttm-80) REVERT: B 353 ARG cc_start: 0.8026 (mmm-85) cc_final: 0.7800 (mmm-85) REVERT: B 411 ASP cc_start: 0.7470 (m-30) cc_final: 0.7127 (t0) REVERT: B 460 GLN cc_start: 0.7973 (mt0) cc_final: 0.7684 (mt0) REVERT: B 470 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8320 (tp) REVERT: B 689 ASP cc_start: 0.7829 (p0) cc_final: 0.7569 (p0) REVERT: B 795 LYS cc_start: 0.7610 (mmtp) cc_final: 0.7239 (mmtm) REVERT: B 923 ARG cc_start: 0.7347 (ptt180) cc_final: 0.7105 (ptt180) REVERT: A 240 GLN cc_start: 0.6055 (OUTLIER) cc_final: 0.5338 (tt0) REVERT: A 290 ARG cc_start: 0.7015 (ttt180) cc_final: 0.6144 (tpt90) REVERT: A 291 TYR cc_start: 0.7088 (m-80) cc_final: 0.6835 (m-80) REVERT: A 353 ARG cc_start: 0.7618 (mmt90) cc_final: 0.6868 (mmt-90) REVERT: A 445 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6765 (tt) REVERT: A 586 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8455 (mm) REVERT: A 611 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7651 (mt-10) REVERT: A 654 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7689 (mm-30) REVERT: A 719 ASP cc_start: 0.7092 (t0) cc_final: 0.6804 (t0) REVERT: A 727 LYS cc_start: 0.7494 (tmtt) cc_final: 0.6959 (tttt) REVERT: A 790 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: A 835 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.7855 (pm20) REVERT: A 868 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8532 (mt0) REVERT: A 897 GLU cc_start: 0.7805 (tp30) cc_final: 0.7524 (tt0) REVERT: A 942 LYS cc_start: 0.7863 (mttp) cc_final: 0.7097 (tttp) REVERT: A 1068 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7405 (tm-30) REVERT: D 1180 LYS cc_start: 0.6963 (pttt) cc_final: 0.6613 (ptpt) outliers start: 74 outliers final: 56 residues processed: 256 average time/residue: 0.1373 time to fit residues: 53.1000 Evaluate side-chains 251 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 185 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 409 TYR 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 500 LEU 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 833 VAL Chi-restraints excluded: chain B residue 844 LEU 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 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 1206 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 332 THR 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 495 SER 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 654 GLU Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 692 HIS 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 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 922 ASP 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 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 1207 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 56 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN A 444 HIS ** A 755 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 = 0.4012 r_free = 0.4012 target = 0.179752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.151856 restraints weight = 22033.864| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.26 r_work: 0.3564 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17342 Z= 0.110 Angle : 0.547 13.835 23462 Z= 0.292 Chirality : 0.042 0.171 2402 Planarity : 0.003 0.056 3092 Dihedral : 4.470 35.825 2358 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 4.10 % Allowed : 21.87 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.27 (0.16), residues: 2062 helix: -2.87 (0.69), residues: 46 sheet: -0.55 (0.28), residues: 392 loop : -2.84 (0.13), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 280 TYR 0.013 0.001 TYR B 409 PHE 0.018 0.001 PHE A 202 TRP 0.016 0.001 TRP B 177 HIS 0.010 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00246 (17342) covalent geometry : angle 0.54666 (23462) hydrogen bonds : bond 0.02980 ( 332) hydrogen bonds : angle 5.15514 ( 897) *********************** 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 273 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 199 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: B 159 THR cc_start: 0.6474 (p) cc_final: 0.6024 (t) REVERT: B 181 TYR cc_start: 0.8374 (t80) cc_final: 0.7994 (t80) REVERT: B 242 TYR cc_start: 0.6073 (OUTLIER) cc_final: 0.5223 (t80) REVERT: B 249 PHE cc_start: 0.6941 (OUTLIER) cc_final: 0.6481 (t80) REVERT: B 263 ASP cc_start: 0.7098 (t70) cc_final: 0.6864 (p0) REVERT: B 275 LEU cc_start: 0.3994 (OUTLIER) cc_final: 0.3778 (tt) REVERT: B 290 ARG cc_start: 0.6939 (ttp-170) cc_final: 0.6325 (ttm-80) REVERT: B 353 ARG cc_start: 0.8002 (mmm-85) cc_final: 0.7773 (mmm-85) REVERT: B 411 ASP cc_start: 0.7414 (m-30) cc_final: 0.7133 (t0) REVERT: B 424 GLN cc_start: 0.7795 (mm-40) cc_final: 0.7543 (mm-40) REVERT: B 460 GLN cc_start: 0.7932 (mt0) cc_final: 0.7695 (mt0) REVERT: B 470 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8302 (tp) REVERT: B 795 LYS cc_start: 0.7686 (mmtp) cc_final: 0.7278 (mmtm) REVERT: A 240 GLN cc_start: 0.6136 (OUTLIER) cc_final: 0.5321 (tt0) REVERT: A 288 GLN cc_start: 0.5597 (mp-120) cc_final: 0.5015 (mp10) REVERT: A 290 ARG cc_start: 0.7069 (ttt180) cc_final: 0.6198 (tpt90) REVERT: A 320 GLU cc_start: 0.6026 (OUTLIER) cc_final: 0.5749 (mt-10) REVERT: A 353 ARG cc_start: 0.7701 (mmt90) cc_final: 0.6951 (mmt-90) REVERT: A 445 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6784 (tt) REVERT: A 586 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8456 (mm) REVERT: A 611 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7650 (mt-10) REVERT: A 627 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8276 (mp0) REVERT: A 719 ASP cc_start: 0.7043 (t0) cc_final: 0.6790 (t0) REVERT: A 790 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: A 835 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: A 868 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8470 (mt0) REVERT: A 897 GLU cc_start: 0.7822 (tp30) cc_final: 0.7616 (tt0) REVERT: A 1068 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7398 (tm-30) REVERT: D 1180 LYS cc_start: 0.6968 (pttt) cc_final: 0.6553 (ptpt) outliers start: 74 outliers final: 59 residues processed: 256 average time/residue: 0.1456 time to fit residues: 56.0668 Evaluate side-chains 259 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 189 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 275 LEU 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 445 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 500 LEU 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 833 VAL Chi-restraints excluded: chain B residue 844 LEU 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 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 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 158 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 332 THR 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 495 SER 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 665 VAL Chi-restraints excluded: chain A residue 692 HIS 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 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 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 1207 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 78 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 GLN B 574 ASN B 639 GLN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 937 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1188 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.173409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.145376 restraints weight = 22283.647| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.50 r_work: 0.3471 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17342 Z= 0.236 Angle : 0.689 13.956 23462 Z= 0.369 Chirality : 0.046 0.182 2402 Planarity : 0.004 0.057 3092 Dihedral : 5.409 40.034 2358 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.71 % Favored : 84.29 % Rotamer: Outliers : 4.82 % Allowed : 21.71 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.56 (0.16), residues: 2062 helix: -3.19 (0.63), residues: 46 sheet: -1.10 (0.28), residues: 384 loop : -2.94 (0.13), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1074 TYR 0.023 0.002 TYR A1018 PHE 0.019 0.002 PHE A 202 TRP 0.024 0.002 TRP B 177 HIS 0.007 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00565 (17342) covalent geometry : angle 0.68911 (23462) hydrogen bonds : bond 0.04455 ( 332) hydrogen bonds : angle 5.57966 ( 897) *********************** 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 277 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 190 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: B 159 THR cc_start: 0.6711 (p) cc_final: 0.6382 (t) REVERT: B 181 TYR cc_start: 0.8523 (t80) cc_final: 0.8220 (t80) REVERT: B 242 TYR cc_start: 0.6218 (OUTLIER) cc_final: 0.5409 (t80) REVERT: B 249 PHE cc_start: 0.7009 (OUTLIER) cc_final: 0.6456 (t80) REVERT: B 263 ASP cc_start: 0.7232 (t70) cc_final: 0.6948 (p0) REVERT: B 290 ARG cc_start: 0.7114 (ttp-170) cc_final: 0.6463 (ttm-80) REVERT: B 320 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6443 (mm-30) REVERT: B 321 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7480 (mp) REVERT: B 353 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7775 (mmm-85) REVERT: B 388 ARG cc_start: 0.7313 (tpt170) cc_final: 0.6968 (tpt-90) REVERT: B 411 ASP cc_start: 0.7629 (m-30) cc_final: 0.7226 (t0) REVERT: B 460 GLN cc_start: 0.7853 (mt0) cc_final: 0.7587 (mt0) REVERT: B 689 ASP cc_start: 0.7743 (p0) cc_final: 0.7389 (p0) REVERT: B 795 LYS cc_start: 0.7521 (mmtp) cc_final: 0.7111 (mmtm) REVERT: B 1076 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7346 (tp40) REVERT: B 1107 ILE cc_start: 0.8464 (mt) cc_final: 0.8245 (mt) REVERT: A 290 ARG cc_start: 0.7236 (ttt180) cc_final: 0.6332 (tpt90) REVERT: A 320 GLU cc_start: 0.6195 (OUTLIER) cc_final: 0.5906 (mt-10) REVERT: A 328 GLN cc_start: 0.7014 (mp10) cc_final: 0.6742 (mp10) REVERT: A 353 ARG cc_start: 0.7784 (mmt90) cc_final: 0.7025 (mmt90) REVERT: A 445 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.6971 (tt) REVERT: A 586 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8567 (mm) REVERT: A 611 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7703 (mt-10) REVERT: A 654 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7622 (mt-10) REVERT: A 719 ASP cc_start: 0.7168 (t0) cc_final: 0.6837 (t0) REVERT: A 727 LYS cc_start: 0.7897 (tmtt) cc_final: 0.7252 (tttt) REVERT: A 790 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: A 835 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.7843 (pm20) REVERT: A 868 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8546 (mt0) REVERT: A 942 LYS cc_start: 0.7953 (mttp) cc_final: 0.7136 (tttp) REVERT: A 1068 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7478 (tm-30) REVERT: A 1079 TYR cc_start: 0.8105 (t80) cc_final: 0.7666 (t80) REVERT: D 1180 LYS cc_start: 0.7240 (pttt) cc_final: 0.6899 (ptpt) outliers start: 87 outliers final: 68 residues processed: 261 average time/residue: 0.1501 time to fit residues: 58.1341 Evaluate side-chains 266 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 187 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 321 LEU 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 500 LEU 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 574 ASN Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 844 LEU 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 963 VAL Chi-restraints excluded: chain B residue 1017 THR 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 C residue 1180 LYS 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 158 VAL 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 273 ILE Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 332 THR 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 495 SER Chi-restraints excluded: chain A residue 520 CYS 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 654 GLU Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 692 HIS 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 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 916 ASP Chi-restraints excluded: chain A residue 922 ASP 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 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 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 55 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 191 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 574 ASN A 288 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4023 r_free = 0.4023 target = 0.180055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.151872 restraints weight = 22098.684| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.58 r_work: 0.3549 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17342 Z= 0.109 Angle : 0.568 13.669 23462 Z= 0.305 Chirality : 0.043 0.173 2402 Planarity : 0.004 0.057 3092 Dihedral : 4.602 34.998 2356 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Rotamer: Outliers : 3.71 % Allowed : 22.92 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.27 (0.16), residues: 2062 helix: -2.90 (0.67), residues: 46 sheet: -0.46 (0.29), residues: 372 loop : -2.84 (0.13), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 280 TYR 0.015 0.001 TYR A 291 PHE 0.016 0.001 PHE A 202 TRP 0.017 0.001 TRP B 177 HIS 0.003 0.001 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00236 (17342) covalent geometry : angle 0.56828 (23462) hydrogen bonds : bond 0.02935 ( 332) hydrogen bonds : angle 5.25737 ( 897) ********************** 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 266 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 199 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: B 159 THR cc_start: 0.6392 (p) cc_final: 0.6010 (t) REVERT: B 181 TYR cc_start: 0.8293 (t80) cc_final: 0.7928 (t80) REVERT: B 242 TYR cc_start: 0.6169 (OUTLIER) cc_final: 0.5150 (t80) REVERT: B 249 PHE cc_start: 0.6985 (OUTLIER) cc_final: 0.6503 (t80) REVERT: B 263 ASP cc_start: 0.7133 (t70) cc_final: 0.6868 (p0) REVERT: B 290 ARG cc_start: 0.6821 (ttp-170) cc_final: 0.6242 (ttm-80) REVERT: B 353 ARG cc_start: 0.7835 (mmm-85) cc_final: 0.7595 (mmm-85) REVERT: B 411 ASP cc_start: 0.7319 (m-30) cc_final: 0.6983 (t0) REVERT: B 424 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7546 (mm-40) REVERT: B 460 GLN cc_start: 0.7723 (mt0) cc_final: 0.7466 (mt0) REVERT: B 795 LYS cc_start: 0.7560 (mmtp) cc_final: 0.7237 (mmtm) REVERT: B 894 LYS cc_start: 0.7729 (tttp) cc_final: 0.6595 (mtmm) REVERT: B 1011 TYR cc_start: 0.8885 (m-80) cc_final: 0.8652 (m-80) REVERT: A 290 ARG cc_start: 0.6990 (ttt180) cc_final: 0.6134 (tpt90) REVERT: A 353 ARG cc_start: 0.7443 (mmt90) cc_final: 0.6746 (mmt90) REVERT: A 445 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.6938 (tt) REVERT: A 551 GLN cc_start: 0.7749 (mm110) cc_final: 0.7062 (tp40) REVERT: A 586 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8330 (mm) REVERT: A 611 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7432 (mt-10) REVERT: A 627 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8255 (mp0) REVERT: A 675 TRP cc_start: 0.7987 (m100) cc_final: 0.7751 (m100) REVERT: A 719 ASP cc_start: 0.6899 (t0) cc_final: 0.6650 (t0) REVERT: A 727 LYS cc_start: 0.7833 (tmtt) cc_final: 0.7202 (tttt) REVERT: A 790 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: A 835 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.7728 (pm20) REVERT: A 868 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8380 (mt0) REVERT: A 942 LYS cc_start: 0.7816 (mttp) cc_final: 0.7044 (tttp) REVERT: A 1068 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7348 (tm-30) REVERT: D 1180 LYS cc_start: 0.6818 (pttt) cc_final: 0.6409 (ptpt) outliers start: 67 outliers final: 53 residues processed: 252 average time/residue: 0.1486 time to fit residues: 56.0643 Evaluate side-chains 252 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 192 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 409 TYR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 500 LEU 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 844 LEU 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 963 VAL Chi-restraints excluded: chain B residue 1023 VAL 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 158 VAL 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 332 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 520 CYS 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 692 HIS 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 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 922 ASP 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 D residue 1175 VAL Chi-restraints excluded: chain D residue 1177 SER 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 80 optimal weight: 5.9990 chunk 37 optimal weight: 0.0870 chunk 192 optimal weight: 10.0000 chunk 159 optimal weight: 0.8980 chunk 179 optimal weight: 0.5980 chunk 187 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 156 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 639 GLN B 786 GLN A 474 HIS A 755 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.181796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.153423 restraints weight = 21851.345| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.05 r_work: 0.3619 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17342 Z= 0.097 Angle : 0.548 13.784 23462 Z= 0.292 Chirality : 0.042 0.159 2402 Planarity : 0.003 0.057 3092 Dihedral : 4.156 34.650 2353 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.08 % Favored : 87.92 % Rotamer: Outliers : 3.60 % Allowed : 23.15 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.99 (0.17), residues: 2062 helix: -2.67 (0.70), residues: 46 sheet: -0.29 (0.28), residues: 380 loop : -2.65 (0.13), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 280 TYR 0.012 0.001 TYR A 239 PHE 0.018 0.001 PHE A 202 TRP 0.010 0.001 TRP B 177 HIS 0.003 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00203 (17342) covalent geometry : angle 0.54821 (23462) hydrogen bonds : bond 0.02612 ( 332) hydrogen bonds : angle 5.01891 ( 897) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3741.91 seconds wall clock time: 64 minutes 56.79 seconds (3896.79 seconds total)