Starting phenix.real_space_refine on Mon Jun 16 17:36:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yks_33896/06_2025/7yks_33896.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yks_33896/06_2025/7yks_33896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yks_33896/06_2025/7yks_33896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yks_33896/06_2025/7yks_33896.map" model { file = "/net/cci-nas-00/data/ceres_data/7yks_33896/06_2025/7yks_33896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yks_33896/06_2025/7yks_33896.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.145 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 136 5.16 5 C 12308 2.51 5 N 3196 2.21 5 O 3344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18984 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4746 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 569} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 12 Restraints were copied for chains: C, B, D Time building chain proxies: 11.11, per 1000 atoms: 0.59 Number of scatterers: 18984 At special positions: 0 Unit cell: (112.11, 112.11, 145.44, 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 136 16.00 O 3344 8.00 N 3196 7.00 C 12308 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: 4.74 Conformation dependent library (CDL) restraints added in 2.6 seconds 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4568 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 8 sheets defined 70.1% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 479 through 487 removed outlier: 3.859A pdb=" N ARG A 486 " --> pdb=" O HIS A 482 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR A 487 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 497 Processing helix chain 'A' and resid 515 through 523 removed outlier: 3.624A pdb=" N SER A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 535 removed outlier: 3.887A pdb=" N LEU A 531 " --> pdb=" O ARG A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 removed outlier: 3.504A pdb=" N ALA A 552 " --> pdb=" O PRO A 548 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 568 removed outlier: 3.684A pdb=" N ILE A 561 " --> pdb=" O TYR A 557 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 589 removed outlier: 3.773A pdb=" N GLU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 599 removed outlier: 3.825A pdb=" N VAL A 597 " --> pdb=" O HIS A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 621 Processing helix chain 'A' and resid 623 through 632 removed outlier: 3.788A pdb=" N ALA A 629 " --> pdb=" O GLU A 625 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 632 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 642 Processing helix chain 'A' and resid 650 through 659 removed outlier: 4.044A pdb=" N ILE A 656 " --> pdb=" O THR A 652 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 669 removed outlier: 3.960A pdb=" N PHE A 663 " --> pdb=" O MET A 659 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 665 " --> pdb=" O LYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 726 removed outlier: 3.530A pdb=" N THR A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 733 Processing helix chain 'A' and resid 734 through 746 removed outlier: 3.683A pdb=" N LYS A 739 " --> pdb=" O PRO A 735 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 746 " --> pdb=" O GLN A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 777 removed outlier: 4.253A pdb=" N ASN A 756 " --> pdb=" O PHE A 752 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 763 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 769 " --> pdb=" O VAL A 765 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 842 removed outlier: 3.661A pdb=" N ILE A 835 " --> pdb=" O CYS A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 853 removed outlier: 3.732A pdb=" N TYR A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 876 Processing helix chain 'A' and resid 877 through 881 Processing helix chain 'A' and resid 888 through 905 removed outlier: 3.536A pdb=" N TYR A 892 " --> pdb=" O ASN A 888 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 893 " --> pdb=" O THR A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.741A pdb=" N ARG A 912 " --> pdb=" O PHE A 909 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE A 913 " --> pdb=" O LEU A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 913' Processing helix chain 'A' and resid 917 through 934 removed outlier: 3.588A pdb=" N VAL A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN A 928 " --> pdb=" O LEU A 924 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 932 " --> pdb=" O GLN A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 953 removed outlier: 3.751A pdb=" N SER A 953 " --> pdb=" O TYR A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 removed outlier: 3.996A pdb=" N SER A 964 " --> pdb=" O ASN A 961 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 965 " --> pdb=" O HIS A 962 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER A 966 " --> pdb=" O LEU A 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 961 through 966' Processing helix chain 'A' and resid 967 through 978 removed outlier: 3.587A pdb=" N LEU A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 989 Processing helix chain 'A' and resid 989 through 995 Processing helix chain 'A' and resid 1000 through 1015 removed outlier: 3.544A pdb=" N LEU A1006 " --> pdb=" O MET A1002 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A1014 " --> pdb=" O VAL A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1037 removed outlier: 3.512A pdb=" N GLY A1029 " --> pdb=" O GLY A1025 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A1036 " --> pdb=" O GLU A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1055 removed outlier: 4.064A pdb=" N LEU A1043 " --> pdb=" O GLN A1039 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS A1050 " --> pdb=" O GLN A1046 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A1055 " --> pdb=" O THR A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1066 removed outlier: 3.855A pdb=" N LEU A1062 " --> pdb=" O PRO A1058 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A1063 " --> pdb=" O HIS A1059 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG A1064 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A1065 " --> pdb=" O TRP A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1115 Processing helix chain 'A' and resid 1117 through 1146 removed outlier: 3.634A pdb=" N LEU A1138 " --> pdb=" O GLN A1134 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A1143 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A1144 " --> pdb=" O ARG A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 487 removed outlier: 3.860A pdb=" N ARG B 486 " --> pdb=" O HIS B 482 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 487 " --> pdb=" O PHE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 497 Processing helix chain 'B' and resid 515 through 523 removed outlier: 3.624A pdb=" N SER B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 535 removed outlier: 3.887A pdb=" N LEU B 531 " --> pdb=" O ARG B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 556 removed outlier: 3.503A pdb=" N ALA B 552 " --> pdb=" O PRO B 548 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 568 removed outlier: 3.684A pdb=" N ILE B 561 " --> pdb=" O TYR B 557 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 563 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 566 " --> pdb=" O GLU B 562 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 589 removed outlier: 3.773A pdb=" N GLU B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 599 removed outlier: 3.825A pdb=" N VAL B 597 " --> pdb=" O HIS B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 621 Processing helix chain 'B' and resid 623 through 632 removed outlier: 3.788A pdb=" N ALA B 629 " --> pdb=" O GLU B 625 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 632 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 642 Processing helix chain 'B' and resid 650 through 659 removed outlier: 4.044A pdb=" N ILE B 656 " --> pdb=" O THR B 652 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 669 removed outlier: 3.959A pdb=" N PHE B 663 " --> pdb=" O MET B 659 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 665 " --> pdb=" O LYS B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 726 removed outlier: 3.528A pdb=" N THR B 725 " --> pdb=" O ASN B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 733 Processing helix chain 'B' and resid 734 through 746 removed outlier: 3.682A pdb=" N LYS B 739 " --> pdb=" O PRO B 735 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN B 746 " --> pdb=" O GLN B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 777 removed outlier: 4.253A pdb=" N ASN B 756 " --> pdb=" O PHE B 752 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 763 " --> pdb=" O ILE B 759 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 765 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 769 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN B 776 " --> pdb=" O SER B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 842 removed outlier: 3.662A pdb=" N ILE B 835 " --> pdb=" O CYS B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 853 removed outlier: 3.732A pdb=" N TYR B 851 " --> pdb=" O LEU B 847 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 852 " --> pdb=" O ILE B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 876 Processing helix chain 'B' and resid 877 through 881 Processing helix chain 'B' and resid 888 through 905 removed outlier: 3.535A pdb=" N TYR B 892 " --> pdb=" O ASN B 888 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 893 " --> pdb=" O THR B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 913 removed outlier: 3.741A pdb=" N ARG B 912 " --> pdb=" O PHE B 909 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE B 913 " --> pdb=" O LEU B 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 909 through 913' Processing helix chain 'B' and resid 917 through 934 removed outlier: 3.588A pdb=" N VAL B 921 " --> pdb=" O GLY B 917 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN B 928 " --> pdb=" O LEU B 924 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS B 932 " --> pdb=" O GLN B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 953 removed outlier: 3.751A pdb=" N SER B 953 " --> pdb=" O TYR B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 966 removed outlier: 3.996A pdb=" N SER B 964 " --> pdb=" O ASN B 961 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 965 " --> pdb=" O HIS B 962 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER B 966 " --> pdb=" O LEU B 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 961 through 966' Processing helix chain 'B' and resid 967 through 978 removed outlier: 3.587A pdb=" N LEU B 973 " --> pdb=" O PRO B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 989 Processing helix chain 'B' and resid 989 through 995 Processing helix chain 'B' and resid 1000 through 1015 removed outlier: 3.543A pdb=" N LEU B1006 " --> pdb=" O MET B1002 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B1014 " --> pdb=" O VAL B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1037 removed outlier: 3.512A pdb=" N GLY B1029 " --> pdb=" O GLY B1025 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B1036 " --> pdb=" O GLU B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1037 through 1055 removed outlier: 4.064A pdb=" N LEU B1043 " --> pdb=" O GLN B1039 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS B1050 " --> pdb=" O GLN B1046 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1066 removed outlier: 3.854A pdb=" N LEU B1062 " --> pdb=" O PRO B1058 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B1063 " --> pdb=" O HIS B1059 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG B1064 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL B1065 " --> pdb=" O TRP B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1110 through 1115 Processing helix chain 'B' and resid 1117 through 1146 removed outlier: 3.632A pdb=" N LEU B1138 " --> pdb=" O GLN B1134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B1143 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B1144 " --> pdb=" O ARG B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 487 removed outlier: 3.859A pdb=" N ARG C 486 " --> pdb=" O HIS C 482 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR C 487 " --> pdb=" O PHE C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 497 Processing helix chain 'C' and resid 515 through 523 removed outlier: 3.624A pdb=" N SER C 521 " --> pdb=" O LEU C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 535 removed outlier: 3.887A pdb=" N LEU C 531 " --> pdb=" O ARG C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 556 removed outlier: 3.504A pdb=" N ALA C 552 " --> pdb=" O PRO C 548 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.684A pdb=" N ILE C 561 " --> pdb=" O TYR C 557 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 563 " --> pdb=" O GLU C 559 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 566 " --> pdb=" O GLU C 562 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 567 " --> pdb=" O LEU C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 589 removed outlier: 3.773A pdb=" N GLU C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 599 removed outlier: 3.825A pdb=" N VAL C 597 " --> pdb=" O HIS C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 621 Processing helix chain 'C' and resid 623 through 632 removed outlier: 3.788A pdb=" N ALA C 629 " --> pdb=" O GLU C 625 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR C 632 " --> pdb=" O LEU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 642 Processing helix chain 'C' and resid 650 through 659 removed outlier: 4.044A pdb=" N ILE C 656 " --> pdb=" O THR C 652 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C 657 " --> pdb=" O LEU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 669 removed outlier: 3.960A pdb=" N PHE C 663 " --> pdb=" O MET C 659 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA C 665 " --> pdb=" O LYS C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 726 removed outlier: 3.529A pdb=" N THR C 725 " --> pdb=" O ASN C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 733 Processing helix chain 'C' and resid 734 through 746 removed outlier: 3.683A pdb=" N LYS C 739 " --> pdb=" O PRO C 735 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN C 746 " --> pdb=" O GLN C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 777 removed outlier: 4.253A pdb=" N ASN C 756 " --> pdb=" O PHE C 752 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 763 " --> pdb=" O ILE C 759 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL C 765 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 769 " --> pdb=" O VAL C 765 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN C 776 " --> pdb=" O SER C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 842 removed outlier: 3.662A pdb=" N ILE C 835 " --> pdb=" O CYS C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 853 removed outlier: 3.731A pdb=" N TYR C 851 " --> pdb=" O LEU C 847 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN C 852 " --> pdb=" O ILE C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 876 Processing helix chain 'C' and resid 877 through 881 Processing helix chain 'C' and resid 888 through 905 removed outlier: 3.535A pdb=" N TYR C 892 " --> pdb=" O ASN C 888 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 893 " --> pdb=" O THR C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 913 removed outlier: 3.742A pdb=" N ARG C 912 " --> pdb=" O PHE C 909 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE C 913 " --> pdb=" O LEU C 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 909 through 913' Processing helix chain 'C' and resid 917 through 934 removed outlier: 3.588A pdb=" N VAL C 921 " --> pdb=" O GLY C 917 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN C 928 " --> pdb=" O LEU C 924 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS C 932 " --> pdb=" O GLN C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 953 removed outlier: 3.750A pdb=" N SER C 953 " --> pdb=" O TYR C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 966 removed outlier: 3.996A pdb=" N SER C 964 " --> pdb=" O ASN C 961 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE C 965 " --> pdb=" O HIS C 962 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER C 966 " --> pdb=" O LEU C 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 961 through 966' Processing helix chain 'C' and resid 967 through 978 removed outlier: 3.587A pdb=" N LEU C 973 " --> pdb=" O PRO C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 989 Processing helix chain 'C' and resid 989 through 995 Processing helix chain 'C' and resid 1000 through 1015 removed outlier: 3.543A pdb=" N LEU C1006 " --> pdb=" O MET C1002 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C1014 " --> pdb=" O VAL C1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1037 removed outlier: 3.512A pdb=" N GLY C1029 " --> pdb=" O GLY C1025 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C1036 " --> pdb=" O GLU C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1037 through 1055 removed outlier: 4.064A pdb=" N LEU C1043 " --> pdb=" O GLN C1039 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS C1050 " --> pdb=" O GLN C1046 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C1055 " --> pdb=" O THR C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1058 through 1066 removed outlier: 3.855A pdb=" N LEU C1062 " --> pdb=" O PRO C1058 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN C1063 " --> pdb=" O HIS C1059 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG C1064 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C1065 " --> pdb=" O TRP C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1110 through 1115 Processing helix chain 'C' and resid 1117 through 1146 removed outlier: 3.634A pdb=" N LEU C1138 " --> pdb=" O GLN C1134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C1143 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN C1144 " --> pdb=" O ARG C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 487 removed outlier: 3.860A pdb=" N ARG D 486 " --> pdb=" O HIS D 482 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR D 487 " --> pdb=" O PHE D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 497 Processing helix chain 'D' and resid 515 through 523 removed outlier: 3.624A pdb=" N SER D 521 " --> pdb=" O LEU D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 535 removed outlier: 3.887A pdb=" N LEU D 531 " --> pdb=" O ARG D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 556 removed outlier: 3.504A pdb=" N ALA D 552 " --> pdb=" O PRO D 548 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 568 removed outlier: 3.684A pdb=" N ILE D 561 " --> pdb=" O TYR D 557 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU D 563 " --> pdb=" O GLU D 559 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER D 566 " --> pdb=" O GLU D 562 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 567 " --> pdb=" O LEU D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 589 removed outlier: 3.773A pdb=" N GLU D 589 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 599 removed outlier: 3.824A pdb=" N VAL D 597 " --> pdb=" O HIS D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 621 Processing helix chain 'D' and resid 623 through 632 removed outlier: 3.789A pdb=" N ALA D 629 " --> pdb=" O GLU D 625 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET D 630 " --> pdb=" O ALA D 626 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR D 632 " --> pdb=" O LEU D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 650 through 659 removed outlier: 4.043A pdb=" N ILE D 656 " --> pdb=" O THR D 652 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA D 657 " --> pdb=" O LEU D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 659 through 669 removed outlier: 3.959A pdb=" N PHE D 663 " --> pdb=" O MET D 659 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA D 665 " --> pdb=" O LYS D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 726 removed outlier: 3.530A pdb=" N THR D 725 " --> pdb=" O ASN D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 733 Processing helix chain 'D' and resid 734 through 746 removed outlier: 3.682A pdb=" N LYS D 739 " --> pdb=" O PRO D 735 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN D 746 " --> pdb=" O GLN D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 777 removed outlier: 4.252A pdb=" N ASN D 756 " --> pdb=" O PHE D 752 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE D 763 " --> pdb=" O ILE D 759 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D 765 " --> pdb=" O SER D 761 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE D 769 " --> pdb=" O VAL D 765 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 842 removed outlier: 3.662A pdb=" N ILE D 835 " --> pdb=" O CYS D 831 " (cutoff:3.500A) Processing helix chain 'D' and resid 847 through 853 removed outlier: 3.731A pdb=" N TYR D 851 " --> pdb=" O LEU D 847 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN D 852 " --> pdb=" O ILE D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 876 Processing helix chain 'D' and resid 877 through 881 Processing helix chain 'D' and resid 888 through 905 removed outlier: 3.536A pdb=" N TYR D 892 " --> pdb=" O ASN D 888 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER D 893 " --> pdb=" O THR D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 909 through 913 removed outlier: 3.741A pdb=" N ARG D 912 " --> pdb=" O PHE D 909 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE D 913 " --> pdb=" O LEU D 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 909 through 913' Processing helix chain 'D' and resid 917 through 934 removed outlier: 3.588A pdb=" N VAL D 921 " --> pdb=" O GLY D 917 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN D 928 " --> pdb=" O LEU D 924 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS D 932 " --> pdb=" O GLN D 928 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 953 removed outlier: 3.751A pdb=" N SER D 953 " --> pdb=" O TYR D 949 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 966 removed outlier: 3.996A pdb=" N SER D 964 " --> pdb=" O ASN D 961 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE D 965 " --> pdb=" O HIS D 962 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER D 966 " --> pdb=" O LEU D 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 961 through 966' Processing helix chain 'D' and resid 967 through 978 removed outlier: 3.588A pdb=" N LEU D 973 " --> pdb=" O PRO D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 989 Processing helix chain 'D' and resid 989 through 995 Processing helix chain 'D' and resid 1000 through 1015 removed outlier: 3.543A pdb=" N LEU D1006 " --> pdb=" O MET D1002 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D1014 " --> pdb=" O VAL D1010 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1037 removed outlier: 3.512A pdb=" N GLY D1029 " --> pdb=" O GLY D1025 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D1036 " --> pdb=" O GLU D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1037 through 1055 removed outlier: 4.065A pdb=" N LEU D1043 " --> pdb=" O GLN D1039 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS D1050 " --> pdb=" O GLN D1046 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG D1055 " --> pdb=" O THR D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1066 removed outlier: 3.854A pdb=" N LEU D1062 " --> pdb=" O PRO D1058 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN D1063 " --> pdb=" O HIS D1059 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG D1064 " --> pdb=" O VAL D1060 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL D1065 " --> pdb=" O TRP D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1110 through 1115 Processing helix chain 'D' and resid 1117 through 1146 removed outlier: 3.634A pdb=" N LEU D1138 " --> pdb=" O GLN D1134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D1143 " --> pdb=" O VAL D1139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN D1144 " --> pdb=" O ARG D1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 671 through 673 Processing sheet with id=AA2, first strand: chain 'A' and resid 820 through 821 removed outlier: 4.732A pdb=" N GLU A 820 " --> pdb=" O ILE A 887 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 671 through 673 Processing sheet with id=AA4, first strand: chain 'B' and resid 820 through 821 removed outlier: 4.732A pdb=" N GLU B 820 " --> pdb=" O ILE B 887 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 671 through 673 Processing sheet with id=AA6, first strand: chain 'C' and resid 820 through 821 removed outlier: 4.732A pdb=" N GLU C 820 " --> pdb=" O ILE C 887 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 671 through 673 Processing sheet with id=AA8, first strand: chain 'D' and resid 820 through 821 removed outlier: 4.732A pdb=" N GLU D 820 " --> pdb=" O ILE D 887 " (cutoff:3.500A) 912 hydrogen bonds defined for protein. 2688 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: 5.90 Time building geometry restraints manager: 5.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5565 1.33 - 1.45: 2783 1.45 - 1.57: 10776 1.57 - 1.69: 0 1.69 - 1.81: 248 Bond restraints: 19372 Sorted by residual: bond pdb=" CA GLU B 982 " pdb=" CB GLU B 982 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.33e-02 5.65e+03 1.30e+01 bond pdb=" CA GLU C 982 " pdb=" CB GLU C 982 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.33e-02 5.65e+03 1.30e+01 bond pdb=" CA GLU A 982 " pdb=" CB GLU A 982 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.33e-02 5.65e+03 1.28e+01 bond pdb=" CA GLU D 982 " pdb=" CB GLU D 982 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.33e-02 5.65e+03 1.28e+01 bond pdb=" CB ARG B1140 " pdb=" CG ARG B1140 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.46e+00 ... (remaining 19367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 25249 2.23 - 4.47: 799 4.47 - 6.70: 140 6.70 - 8.93: 52 8.93 - 11.16: 4 Bond angle restraints: 26244 Sorted by residual: angle pdb=" N PRO D1074 " pdb=" CA PRO D1074 " pdb=" CB PRO D1074 " ideal model delta sigma weight residual 103.00 110.44 -7.44 1.10e+00 8.26e-01 4.57e+01 angle pdb=" N PRO B1074 " pdb=" CA PRO B1074 " pdb=" CB PRO B1074 " ideal model delta sigma weight residual 103.00 110.40 -7.40 1.10e+00 8.26e-01 4.53e+01 angle pdb=" N PRO C1074 " pdb=" CA PRO C1074 " pdb=" CB PRO C1074 " ideal model delta sigma weight residual 103.00 110.39 -7.39 1.10e+00 8.26e-01 4.52e+01 angle pdb=" N PRO A1074 " pdb=" CA PRO A1074 " pdb=" CB PRO A1074 " ideal model delta sigma weight residual 103.00 110.38 -7.38 1.10e+00 8.26e-01 4.51e+01 angle pdb=" C LEU C 610 " pdb=" N ASP C 611 " pdb=" CA ASP C 611 " ideal model delta sigma weight residual 122.46 130.04 -7.58 1.41e+00 5.03e-01 2.89e+01 ... (remaining 26239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.81: 10992 14.81 - 29.62: 543 29.62 - 44.43: 177 44.43 - 59.23: 4 59.23 - 74.04: 8 Dihedral angle restraints: 11724 sinusoidal: 4700 harmonic: 7024 Sorted by residual: dihedral pdb=" CA PHE A 937 " pdb=" C PHE A 937 " pdb=" N SER A 938 " pdb=" CA SER A 938 " ideal model delta harmonic sigma weight residual 180.00 152.48 27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA PHE B 937 " pdb=" C PHE B 937 " pdb=" N SER B 938 " pdb=" CA SER B 938 " ideal model delta harmonic sigma weight residual 180.00 152.48 27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA PHE D 937 " pdb=" C PHE D 937 " pdb=" N SER D 938 " pdb=" CA SER D 938 " ideal model delta harmonic sigma weight residual 180.00 152.53 27.47 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 11721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1938 0.050 - 0.100: 885 0.100 - 0.150: 202 0.150 - 0.200: 35 0.200 - 0.250: 28 Chirality restraints: 3088 Sorted by residual: chirality pdb=" CA PRO D1074 " pdb=" N PRO D1074 " pdb=" C PRO D1074 " pdb=" CB PRO D1074 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA PRO A1074 " pdb=" N PRO A1074 " pdb=" C PRO A1074 " pdb=" CB PRO A1074 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA PRO C1074 " pdb=" N PRO C1074 " pdb=" C PRO C1074 " pdb=" CB PRO C1074 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 3085 not shown) Planarity restraints: 3256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 547 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO B 548 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 548 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 548 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 547 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.69e+00 pdb=" N PRO C 548 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 548 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 548 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 547 " 0.043 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO A 548 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 548 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 548 " 0.036 5.00e-02 4.00e+02 ... (remaining 3253 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5518 2.81 - 3.33: 16374 3.33 - 3.86: 29532 3.86 - 4.38: 36420 4.38 - 4.90: 61899 Nonbonded interactions: 149743 Sorted by model distance: nonbonded pdb=" OH TYR B 748 " pdb=" OE2 GLU B1054 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR A 748 " pdb=" OE2 GLU A1054 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR C 748 " pdb=" OE2 GLU C1054 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR D 748 " pdb=" OE2 GLU D1054 " model vdw 2.292 3.040 nonbonded pdb=" O GLN A 523 " pdb=" NH2 ARG B1140 " model vdw 2.325 3.120 ... (remaining 149738 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 44.020 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1101 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 : 0.008 0.093 19372 Z= 0.322 Angle : 0.995 11.164 26244 Z= 0.515 Chirality : 0.061 0.250 3088 Planarity : 0.007 0.065 3256 Dihedral : 10.268 74.042 7156 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.69 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.58 (0.10), residues: 2332 helix: -4.65 (0.05), residues: 1568 sheet: -2.11 (0.81), residues: 40 loop : -3.17 (0.18), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 867 HIS 0.008 0.002 HIS D 518 PHE 0.033 0.003 PHE A 948 TYR 0.028 0.003 TYR B 623 ARG 0.014 0.001 ARG D1123 Details of bonding type rmsd hydrogen bonds : bond 0.32927 ( 912) hydrogen bonds : angle 10.27385 ( 2688) covalent geometry : bond 0.00790 (19372) covalent geometry : angle 0.99517 (26244) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 855 LEU cc_start: 0.6134 (mm) cc_final: 0.5904 (tm) REVERT: B 606 VAL cc_start: 0.3908 (m) cc_final: 0.3625 (p) REVERT: B 655 LEU cc_start: 0.2730 (mt) cc_final: 0.2430 (mt) REVERT: C 580 ASN cc_start: 0.2991 (m-40) cc_final: 0.2787 (t0) REVERT: D 726 HIS cc_start: 0.3912 (m-70) cc_final: 0.1837 (m170) REVERT: D 1061 TRP cc_start: 0.3381 (t-100) cc_final: 0.3011 (t60) outliers start: 0 outliers final: 2 residues processed: 257 average time/residue: 1.3472 time to fit residues: 390.9523 Evaluate side-chains 192 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain D residue 675 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 9.9990 chunk 178 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 120 optimal weight: 0.2980 chunk 95 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 112 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 214 optimal weight: 0.0970 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN A 518 HIS ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 GLN A 753 HIS A 882 GLN A 962 HIS A 991 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 HIS B 491 ASN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 HIS B 738 GLN B 746 ASN B 888 ASN B 962 HIS B 991 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 HIS C 570 HIS C 608 ASN C 726 HIS C 742 GLN C 753 HIS C 991 ASN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1144 GLN D 491 ASN ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 GLN D 753 HIS D 991 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1144 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.206458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.166588 restraints weight = 21137.269| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.95 r_work: 0.3701 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2246 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19372 Z= 0.156 Angle : 0.681 8.497 26244 Z= 0.352 Chirality : 0.043 0.153 3088 Planarity : 0.006 0.056 3256 Dihedral : 5.339 40.792 2573 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.76 % Allowed : 8.98 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.32 (0.14), residues: 2332 helix: -2.72 (0.10), residues: 1628 sheet: -2.80 (0.79), residues: 40 loop : -2.64 (0.21), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B1061 HIS 0.008 0.001 HIS A 568 PHE 0.024 0.002 PHE C1005 TYR 0.013 0.001 TYR B 617 ARG 0.006 0.001 ARG C 728 Details of bonding type rmsd hydrogen bonds : bond 0.04639 ( 912) hydrogen bonds : angle 4.80469 ( 2688) covalent geometry : bond 0.00324 (19372) covalent geometry : angle 0.68070 (26244) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 588 MET cc_start: 0.3167 (OUTLIER) cc_final: 0.2429 (ttm) REVERT: A 691 PHE cc_start: 0.3935 (OUTLIER) cc_final: 0.3514 (t80) REVERT: A 845 ARG cc_start: 0.7015 (ttp80) cc_final: 0.6729 (tmm160) REVERT: A 922 MET cc_start: 0.3637 (OUTLIER) cc_final: 0.3219 (tpp) REVERT: A 993 TYR cc_start: 0.6046 (t80) cc_final: 0.5335 (t80) REVERT: A 1131 MET cc_start: 0.2495 (OUTLIER) cc_final: 0.0219 (mmm) REVERT: B 912 ARG cc_start: 0.5972 (tmt-80) cc_final: 0.5710 (ppt170) REVERT: B 1002 MET cc_start: 0.1721 (OUTLIER) cc_final: 0.1049 (ppp) REVERT: C 554 MET cc_start: 0.1868 (mtt) cc_final: -0.0174 (tpt) REVERT: C 876 MET cc_start: 0.0061 (mtp) cc_final: -0.0567 (ptt) REVERT: C 979 MET cc_start: 0.1621 (ppp) cc_final: 0.1219 (ppp) REVERT: C 1002 MET cc_start: 0.6031 (tpp) cc_final: 0.5464 (ttt) REVERT: D 598 LEU cc_start: 0.0500 (OUTLIER) cc_final: -0.0197 (mt) REVERT: D 641 MET cc_start: 0.3078 (mmm) cc_final: 0.2120 (pp-130) REVERT: D 676 CYS cc_start: 0.5109 (m) cc_final: 0.4796 (t) REVERT: D 935 MET cc_start: 0.5094 (tmm) cc_final: 0.4780 (ttp) REVERT: D 992 THR cc_start: 0.4037 (OUTLIER) cc_final: 0.3808 (t) REVERT: D 1061 TRP cc_start: 0.3415 (t-100) cc_final: 0.2954 (t60) outliers start: 37 outliers final: 10 residues processed: 235 average time/residue: 1.1909 time to fit residues: 317.8638 Evaluate side-chains 197 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 MET Chi-restraints excluded: chain A residue 691 PHE Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 848 ILE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 978 MET Chi-restraints excluded: chain D residue 992 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 117 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 138 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 192 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 200 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 HIS ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 HIS A 911 GLN ** A1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 568 HIS B 891 HIS ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS C 491 ASN C 518 HIS ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 GLN C 753 HIS C1135 GLN ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1136 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.229520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.193575 restraints weight = 21890.046| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 2.00 r_work: 0.4004 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4385 moved from start: 0.7405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.234 19372 Z= 0.236 Angle : 0.819 12.793 26244 Z= 0.421 Chirality : 0.047 0.285 3088 Planarity : 0.006 0.068 3256 Dihedral : 5.224 43.755 2571 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.66 % Allowed : 11.17 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.16), residues: 2332 helix: -1.36 (0.12), residues: 1580 sheet: -3.03 (0.59), residues: 60 loop : -2.36 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 745 HIS 0.012 0.002 HIS B 518 PHE 0.042 0.002 PHE A 965 TYR 0.022 0.002 TYR D 623 ARG 0.011 0.001 ARG A 489 Details of bonding type rmsd hydrogen bonds : bond 0.05961 ( 912) hydrogen bonds : angle 4.61034 ( 2688) covalent geometry : bond 0.00517 (19372) covalent geometry : angle 0.81877 (26244) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 246 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 829 LEU cc_start: 0.6181 (tp) cc_final: 0.5954 (mt) REVERT: A 845 ARG cc_start: 0.7443 (ttp80) cc_final: 0.7230 (ttp80) REVERT: A 905 ARG cc_start: 0.6766 (tmt-80) cc_final: 0.6537 (tpt170) REVERT: A 983 LEU cc_start: 0.6087 (tt) cc_final: 0.5864 (tt) REVERT: A 1131 MET cc_start: 0.4715 (OUTLIER) cc_final: 0.1089 (mmm) REVERT: B 514 MET cc_start: 0.6296 (OUTLIER) cc_final: 0.5973 (tmt) REVERT: B 743 MET cc_start: 0.4953 (mmp) cc_final: 0.4227 (mtm) REVERT: B 1012 MET cc_start: 0.5869 (OUTLIER) cc_final: 0.5456 (mtt) REVERT: B 1014 LEU cc_start: 0.7487 (pp) cc_final: 0.7178 (pp) REVERT: B 1015 MET cc_start: 0.8952 (tpp) cc_final: 0.8619 (tpt) REVERT: C 630 MET cc_start: 0.1484 (tpp) cc_final: 0.1038 (ttt) REVERT: C 728 ARG cc_start: 0.4273 (OUTLIER) cc_final: 0.4055 (tpp-160) REVERT: C 774 MET cc_start: 0.5208 (mmp) cc_final: 0.4696 (mtm) REVERT: C 844 MET cc_start: 0.3994 (tmm) cc_final: 0.3745 (ttm) REVERT: D 560 THR cc_start: 0.2576 (t) cc_final: 0.1972 (m) REVERT: D 630 MET cc_start: 0.2383 (mpm) cc_final: 0.2110 (mtm) REVERT: D 675 ASN cc_start: 0.3241 (p0) cc_final: 0.2838 (m-40) REVERT: D 978 MET cc_start: 0.3739 (OUTLIER) cc_final: 0.3065 (pp-130) REVERT: D 1002 MET cc_start: 0.4654 (ppp) cc_final: 0.3969 (tpp) outliers start: 56 outliers final: 6 residues processed: 273 average time/residue: 1.1146 time to fit residues: 347.5512 Evaluate side-chains 207 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 196 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 1012 MET Chi-restraints excluded: chain C residue 728 ARG Chi-restraints excluded: chain D residue 978 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS A 491 ASN A 777 ASN A1050 HIS ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1144 GLN B 491 ASN B 522 GLN B 543 HIS ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1039 GLN ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 911 GLN D 962 HIS ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1144 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.232441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.193056 restraints weight = 22598.270| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.40 r_work: 0.3968 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3831 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5822 moved from start: 1.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 19372 Z= 0.198 Angle : 0.808 14.712 26244 Z= 0.403 Chirality : 0.046 0.207 3088 Planarity : 0.006 0.067 3256 Dihedral : 5.151 42.592 2571 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.33 % Allowed : 12.55 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.16), residues: 2332 helix: -0.97 (0.13), residues: 1616 sheet: -2.55 (0.64), residues: 60 loop : -2.20 (0.21), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C1061 HIS 0.014 0.002 HIS B 753 PHE 0.036 0.002 PHE D 752 TYR 0.019 0.002 TYR D 851 ARG 0.007 0.001 ARG B 636 Details of bonding type rmsd hydrogen bonds : bond 0.04332 ( 912) hydrogen bonds : angle 4.65768 ( 2688) covalent geometry : bond 0.00441 (19372) covalent geometry : angle 0.80849 (26244) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 304 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 ILE cc_start: 0.5214 (OUTLIER) cc_final: 0.4935 (mt) REVERT: A 617 TYR cc_start: 0.4999 (t80) cc_final: 0.4637 (t80) REVERT: A 717 LEU cc_start: 0.5845 (OUTLIER) cc_final: 0.5292 (mp) REVERT: A 841 LEU cc_start: 0.6930 (tt) cc_final: 0.6728 (tm) REVERT: A 845 ARG cc_start: 0.7347 (ttp80) cc_final: 0.7073 (tmt90) REVERT: A 892 TYR cc_start: 0.8528 (m-80) cc_final: 0.8304 (m-80) REVERT: B 510 ASP cc_start: 0.4318 (p0) cc_final: 0.4093 (m-30) REVERT: B 514 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.5491 (tmt) REVERT: B 522 GLN cc_start: 0.6872 (pt0) cc_final: 0.6544 (pp30) REVERT: B 562 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7382 (tt0) REVERT: B 612 MET cc_start: 0.6261 (OUTLIER) cc_final: 0.5548 (tmt) REVERT: B 743 MET cc_start: 0.5594 (mmp) cc_final: 0.4907 (ttp) REVERT: B 890 ILE cc_start: 0.7135 (tt) cc_final: 0.6933 (tt) REVERT: B 1002 MET cc_start: 0.6052 (OUTLIER) cc_final: 0.5692 (ppp) REVERT: B 1033 SER cc_start: 0.7694 (t) cc_final: 0.7404 (p) REVERT: B 1146 MET cc_start: 0.2916 (mpt) cc_final: 0.0910 (ttt) REVERT: C 500 GLU cc_start: 0.3407 (tp30) cc_final: 0.2967 (mm-30) REVERT: C 630 MET cc_start: 0.2598 (tpp) cc_final: 0.2280 (ttt) REVERT: C 743 MET cc_start: 0.5824 (tmm) cc_final: 0.5623 (tmt) REVERT: C 914 ASP cc_start: 0.6609 (m-30) cc_final: 0.6373 (m-30) REVERT: C 982 GLU cc_start: 0.7816 (pm20) cc_final: 0.7464 (mt-10) REVERT: C 1000 VAL cc_start: 0.7168 (OUTLIER) cc_final: 0.6871 (m) REVERT: C 1015 MET cc_start: 0.8298 (tpt) cc_final: 0.7958 (tpt) REVERT: C 1068 MET cc_start: 0.3226 (OUTLIER) cc_final: 0.2836 (ppp) REVERT: D 560 THR cc_start: 0.3138 (t) cc_final: 0.2345 (m) REVERT: D 641 MET cc_start: 0.6214 (mmp) cc_final: 0.5968 (mmm) REVERT: D 844 MET cc_start: 0.4953 (OUTLIER) cc_final: 0.4142 (tpt) REVERT: D 984 ASP cc_start: 0.5977 (t0) cc_final: 0.5676 (t0) REVERT: D 1032 GLU cc_start: 0.7051 (pt0) cc_final: 0.6620 (mp0) outliers start: 70 outliers final: 16 residues processed: 338 average time/residue: 1.2305 time to fit residues: 475.7370 Evaluate side-chains 246 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1068 MET Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 615 ILE Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 844 MET Chi-restraints excluded: chain D residue 931 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 88 optimal weight: 3.9990 chunk 204 optimal weight: 0.3980 chunk 69 optimal weight: 0.5980 chunk 53 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 131 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN A 540 HIS A 726 HIS A 753 HIS ** A 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN A1063 GLN A1121 GLN ** B 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 HIS B 753 HIS ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1136 HIS C 608 ASN ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1039 GLN ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 911 GLN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.226823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.188498 restraints weight = 22950.012| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 1.97 r_work: 0.3869 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 1.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 19372 Z= 0.132 Angle : 0.635 10.537 26244 Z= 0.322 Chirality : 0.041 0.187 3088 Planarity : 0.004 0.054 3256 Dihedral : 4.364 23.330 2568 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.19 % Allowed : 16.21 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.17), residues: 2332 helix: -0.38 (0.13), residues: 1648 sheet: -2.20 (0.66), residues: 60 loop : -2.35 (0.21), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 745 HIS 0.016 0.001 HIS B 648 PHE 0.023 0.001 PHE A 909 TYR 0.022 0.001 TYR C 870 ARG 0.008 0.000 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 912) hydrogen bonds : angle 4.05918 ( 2688) covalent geometry : bond 0.00300 (19372) covalent geometry : angle 0.63542 (26244) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 253 time to evaluate : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 MET cc_start: 0.3846 (ptp) cc_final: 0.3585 (ptp) REVERT: A 615 ILE cc_start: 0.6095 (OUTLIER) cc_final: 0.5861 (mt) REVERT: A 617 TYR cc_start: 0.5125 (t80) cc_final: 0.4868 (t80) REVERT: A 630 MET cc_start: 0.6957 (mpt) cc_final: 0.5109 (mmt) REVERT: A 841 LEU cc_start: 0.7172 (tt) cc_final: 0.6964 (tm) REVERT: A 845 ARG cc_start: 0.7531 (ttp80) cc_final: 0.7270 (tmt90) REVERT: A 908 LEU cc_start: 0.7280 (mp) cc_final: 0.6982 (mt) REVERT: A 931 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8121 (mm) REVERT: A 1020 MET cc_start: 0.8700 (mmm) cc_final: 0.8497 (mmp) REVERT: A 1070 LEU cc_start: 0.5907 (tt) cc_final: 0.5416 (tt) REVERT: B 514 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6521 (tmt) REVERT: B 664 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8092 (tm-30) REVERT: B 778 ILE cc_start: 0.8357 (mm) cc_final: 0.7678 (mm) REVERT: B 1146 MET cc_start: 0.3329 (OUTLIER) cc_final: 0.1770 (ttt) REVERT: C 500 GLU cc_start: 0.3528 (tp30) cc_final: 0.3186 (mm-30) REVERT: C 664 GLU cc_start: 0.4679 (mm-30) cc_final: 0.4200 (mt-10) REVERT: C 982 GLU cc_start: 0.8076 (pm20) cc_final: 0.7811 (mt-10) REVERT: C 1000 VAL cc_start: 0.7183 (p) cc_final: 0.6927 (m) REVERT: D 560 THR cc_start: 0.3474 (t) cc_final: 0.2705 (m) REVERT: D 828 ILE cc_start: 0.6871 (OUTLIER) cc_final: 0.6520 (tt) REVERT: D 984 ASP cc_start: 0.6566 (t0) cc_final: 0.6311 (t0) REVERT: D 1032 GLU cc_start: 0.7286 (pt0) cc_final: 0.6992 (mp0) outliers start: 46 outliers final: 16 residues processed: 282 average time/residue: 1.3201 time to fit residues: 420.7181 Evaluate side-chains 246 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 225 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 852 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain B residue 1146 MET Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 723 MET Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 861 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 186 optimal weight: 0.0000 chunk 188 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 0.1980 chunk 8 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1144 GLN B 648 HIS ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 742 GLN C 842 ASN C 962 HIS C1039 GLN ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 HIS D 991 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1144 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 = 0.4360 r_free = 0.4360 target = 0.221252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.179711 restraints weight = 22529.513| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 1.92 r_work: 0.3777 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 1.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19372 Z= 0.133 Angle : 0.651 12.595 26244 Z= 0.327 Chirality : 0.042 0.261 3088 Planarity : 0.004 0.050 3256 Dihedral : 4.286 21.783 2568 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.76 % Allowed : 17.30 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 2332 helix: 0.06 (0.13), residues: 1660 sheet: -1.70 (0.87), residues: 40 loop : -2.32 (0.21), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C1061 HIS 0.012 0.001 HIS B 648 PHE 0.017 0.001 PHE A 909 TYR 0.027 0.001 TYR C 870 ARG 0.011 0.001 ARG B 546 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 912) hydrogen bonds : angle 4.07707 ( 2688) covalent geometry : bond 0.00288 (19372) covalent geometry : angle 0.65149 (26244) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 288 time to evaluate : 2.110 Fit side-chains revert: symmetry clash REVERT: A 588 MET cc_start: 0.7848 (ttm) cc_final: 0.7558 (ttm) REVERT: A 617 TYR cc_start: 0.5633 (t80) cc_final: 0.4638 (t80) REVERT: A 730 GLU cc_start: 0.7724 (tp30) cc_final: 0.7452 (pm20) REVERT: A 829 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7500 (mm) REVERT: A 841 LEU cc_start: 0.7363 (tt) cc_final: 0.7156 (tm) REVERT: A 908 LEU cc_start: 0.7613 (mp) cc_final: 0.7348 (mt) REVERT: A 956 ILE cc_start: 0.6488 (OUTLIER) cc_final: 0.5714 (mt) REVERT: A 1146 MET cc_start: 0.4277 (OUTLIER) cc_final: 0.1310 (ptt) REVERT: B 487 TYR cc_start: 0.7039 (m-80) cc_final: 0.6833 (m-80) REVERT: B 562 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7546 (tt0) REVERT: B 664 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8012 (tt0) REVERT: B 905 ARG cc_start: 0.8421 (tpt-90) cc_final: 0.8025 (tmt-80) REVERT: B 1002 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.6192 (mmp) REVERT: B 1146 MET cc_start: 0.3305 (OUTLIER) cc_final: 0.2729 (ttt) REVERT: C 659 MET cc_start: 0.1464 (OUTLIER) cc_final: 0.0035 (tmm) REVERT: C 1120 ARG cc_start: 0.5633 (ttm170) cc_final: 0.5383 (ttm110) REVERT: D 560 THR cc_start: 0.3809 (t) cc_final: 0.2915 (m) REVERT: D 601 MET cc_start: 0.5278 (tmm) cc_final: 0.4940 (tmm) REVERT: D 1032 GLU cc_start: 0.7596 (pt0) cc_final: 0.7268 (mp0) REVERT: D 1133 GLU cc_start: 0.7112 (tp30) cc_final: 0.6575 (tt0) REVERT: D 1146 MET cc_start: 0.4822 (pp-130) cc_final: 0.2173 (ptt) outliers start: 58 outliers final: 15 residues processed: 316 average time/residue: 1.4663 time to fit residues: 525.7458 Evaluate side-chains 252 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 852 GLN Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1146 MET Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 659 MET Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 916 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 32 optimal weight: 0.7980 chunk 186 optimal weight: 0.0870 chunk 174 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 15 optimal weight: 0.0000 chunk 101 optimal weight: 3.9990 chunk 196 optimal weight: 0.3980 chunk 182 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN A1063 GLN ** B 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 891 HIS C 525 HIS C1136 HIS ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 GLN D 777 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.217953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.175370 restraints weight = 22197.586| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.96 r_work: 0.3708 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 1.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19372 Z= 0.110 Angle : 0.580 11.368 26244 Z= 0.293 Chirality : 0.040 0.151 3088 Planarity : 0.004 0.052 3256 Dihedral : 3.948 17.781 2568 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.90 % Allowed : 20.58 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 2332 helix: 0.32 (0.13), residues: 1656 sheet: -1.82 (0.84), residues: 40 loop : -2.28 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 745 HIS 0.009 0.001 HIS C 518 PHE 0.013 0.001 PHE A 909 TYR 0.025 0.001 TYR B 490 ARG 0.007 0.000 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 912) hydrogen bonds : angle 3.83534 ( 2688) covalent geometry : bond 0.00236 (19372) covalent geometry : angle 0.58050 (26244) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 268 time to evaluate : 2.150 Fit side-chains revert: symmetry clash REVERT: A 588 MET cc_start: 0.7960 (ttm) cc_final: 0.7470 (ttm) REVERT: A 617 TYR cc_start: 0.6142 (t80) cc_final: 0.4798 (t80) REVERT: A 730 GLU cc_start: 0.7874 (tp30) cc_final: 0.7508 (pm20) REVERT: A 841 LEU cc_start: 0.7301 (tt) cc_final: 0.7074 (tm) REVERT: A 908 LEU cc_start: 0.7616 (mp) cc_final: 0.7404 (mt) REVERT: A 1122 ARG cc_start: 0.6757 (ttp-110) cc_final: 0.6232 (ttp-110) REVERT: B 487 TYR cc_start: 0.7114 (m-80) cc_final: 0.6868 (m-80) REVERT: B 664 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7975 (tt0) REVERT: B 1002 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.6223 (mmp) REVERT: B 1133 GLU cc_start: 0.6594 (mt-10) cc_final: 0.6391 (mt-10) REVERT: C 659 MET cc_start: 0.2619 (OUTLIER) cc_final: 0.1021 (tmm) REVERT: C 730 GLU cc_start: 0.7322 (tp30) cc_final: 0.7022 (pm20) REVERT: C 872 SER cc_start: 0.8745 (p) cc_final: 0.8538 (m) REVERT: C 967 ASN cc_start: 0.7926 (t0) cc_final: 0.7695 (t0) REVERT: C 1020 MET cc_start: 0.9031 (mmm) cc_final: 0.8696 (mmp) REVERT: D 560 THR cc_start: 0.4075 (t) cc_final: 0.3262 (m) REVERT: D 928 GLN cc_start: 0.8535 (tt0) cc_final: 0.8300 (tt0) REVERT: D 983 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7438 (tt) REVERT: D 1032 GLU cc_start: 0.7512 (pt0) cc_final: 0.7247 (mp0) REVERT: D 1133 GLU cc_start: 0.7092 (tp30) cc_final: 0.6719 (tt0) outliers start: 40 outliers final: 14 residues processed: 285 average time/residue: 1.1997 time to fit residues: 388.5488 Evaluate side-chains 255 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 238 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 522 GLN Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 641 MET Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 876 MET Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 159 optimal weight: 0.9980 chunk 151 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 227 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN B1144 GLN C 842 ASN ** C1137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 525 HIS D 742 GLN D 777 ASN D1050 HIS ** D1135 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 = 0.4151 r_free = 0.4151 target = 0.197277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.147723 restraints weight = 21786.604| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.50 r_work: 0.3463 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 1.7343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 19372 Z= 0.169 Angle : 0.792 24.938 26244 Z= 0.396 Chirality : 0.045 0.200 3088 Planarity : 0.005 0.065 3256 Dihedral : 4.665 27.288 2568 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.42 % Allowed : 21.25 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.17), residues: 2332 helix: 0.03 (0.13), residues: 1668 sheet: -1.72 (0.91), residues: 40 loop : -2.60 (0.21), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 903 HIS 0.012 0.002 HIS B1136 PHE 0.022 0.002 PHE B 691 TYR 0.039 0.002 TYR D 838 ARG 0.011 0.001 ARG D1120 Details of bonding type rmsd hydrogen bonds : bond 0.05068 ( 912) hydrogen bonds : angle 4.32789 ( 2688) covalent geometry : bond 0.00384 (19372) covalent geometry : angle 0.79218 (26244) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 367 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.8200 (mm) cc_final: 0.7941 (tm) REVERT: A 730 GLU cc_start: 0.8192 (tp30) cc_final: 0.7780 (pm20) REVERT: A 829 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7938 (mt) REVERT: A 931 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8322 (tp) REVERT: A 956 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6600 (mt) REVERT: A 982 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7798 (mt-10) REVERT: A 1008 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8368 (tp) REVERT: B 516 PRO cc_start: 0.5191 (Cg_endo) cc_final: 0.4821 (Cg_exo) REVERT: B 554 MET cc_start: 0.8652 (ptm) cc_final: 0.8398 (mtm) REVERT: B 593 HIS cc_start: 0.7750 (t-90) cc_final: 0.7110 (m-70) REVERT: B 673 LYS cc_start: 0.7520 (ttmt) cc_final: 0.7245 (tptt) REVERT: B 824 ARG cc_start: 0.7285 (ttp80) cc_final: 0.6989 (ttp80) REVERT: B 839 ILE cc_start: 0.7171 (mm) cc_final: 0.6919 (mp) REVERT: B 845 ARG cc_start: 0.6896 (tpp80) cc_final: 0.6666 (ttm170) REVERT: B 959 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.6682 (tm-30) REVERT: B 1002 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6489 (mmp) REVERT: B 1009 SER cc_start: 0.8601 (t) cc_final: 0.8332 (m) REVERT: B 1045 MET cc_start: 0.7045 (ptp) cc_final: 0.6453 (ttp) REVERT: B 1126 ARG cc_start: 0.7193 (ttp80) cc_final: 0.6727 (tmt170) REVERT: B 1129 SER cc_start: 0.8174 (OUTLIER) cc_final: 0.7756 (p) REVERT: C 522 GLN cc_start: 0.6745 (tt0) cc_final: 0.6540 (tt0) REVERT: C 554 MET cc_start: 0.4533 (mmm) cc_final: 0.3969 (mmm) REVERT: C 661 LYS cc_start: 0.6155 (mmtt) cc_final: 0.5731 (pttp) REVERT: C 673 LYS cc_start: 0.6001 (ttmm) cc_final: 0.5798 (tttm) REVERT: C 730 GLU cc_start: 0.7800 (tp30) cc_final: 0.7295 (pm20) REVERT: D 560 THR cc_start: 0.5419 (t) cc_final: 0.4801 (m) REVERT: D 562 GLU cc_start: 0.6411 (mt-10) cc_final: 0.6206 (mt-10) REVERT: D 928 GLN cc_start: 0.8530 (tt0) cc_final: 0.8296 (tt0) REVERT: D 1020 MET cc_start: 0.8823 (mmm) cc_final: 0.8604 (mmp) REVERT: D 1032 GLU cc_start: 0.7583 (pt0) cc_final: 0.7244 (mm-30) REVERT: D 1126 ARG cc_start: 0.7767 (ttt-90) cc_final: 0.7251 (ttt180) outliers start: 51 outliers final: 14 residues processed: 391 average time/residue: 1.2372 time to fit residues: 544.8226 Evaluate side-chains 307 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 286 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 621 TYR Chi-restraints excluded: chain B residue 959 GLN Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1129 SER Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 876 MET Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 861 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 210 optimal weight: 0.9990 chunk 188 optimal weight: 0.7980 chunk 181 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 93 optimal weight: 0.0980 chunk 144 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 HIS A 753 HIS ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 HIS B 522 GLN ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 HIS C 525 HIS C 608 ASN C 742 GLN ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1144 GLN ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 HIS D 525 HIS D 738 GLN D 742 GLN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.192807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.152028 restraints weight = 21816.837| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.58 r_work: 0.3421 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 1.7977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19372 Z= 0.127 Angle : 0.643 11.315 26244 Z= 0.323 Chirality : 0.042 0.184 3088 Planarity : 0.004 0.051 3256 Dihedral : 4.072 20.077 2568 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.52 % Allowed : 24.33 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.17), residues: 2332 helix: 0.41 (0.13), residues: 1648 sheet: -1.73 (0.88), residues: 40 loop : -2.46 (0.21), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 867 HIS 0.007 0.001 HIS D 525 PHE 0.018 0.001 PHE A 483 TYR 0.024 0.002 TYR B 490 ARG 0.008 0.001 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 912) hydrogen bonds : angle 3.92412 ( 2688) covalent geometry : bond 0.00286 (19372) covalent geometry : angle 0.64346 (26244) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 329 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 562 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6891 (mt-10) REVERT: A 730 GLU cc_start: 0.8207 (tp30) cc_final: 0.7743 (pm20) REVERT: A 914 ASP cc_start: 0.6877 (m-30) cc_final: 0.6511 (p0) REVERT: A 956 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6605 (mt) REVERT: A 982 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7840 (mt-10) REVERT: A 1127 ASP cc_start: 0.7536 (t0) cc_final: 0.6882 (m-30) REVERT: B 554 MET cc_start: 0.8656 (ptm) cc_final: 0.8430 (mtm) REVERT: B 559 GLU cc_start: 0.8233 (tp30) cc_final: 0.7967 (mt-10) REVERT: B 587 THR cc_start: 0.7511 (m) cc_final: 0.7290 (m) REVERT: B 593 HIS cc_start: 0.7926 (t-90) cc_final: 0.7394 (m-70) REVERT: B 630 MET cc_start: 0.8219 (mtm) cc_final: 0.7995 (ttp) REVERT: B 824 ARG cc_start: 0.7304 (ttp80) cc_final: 0.6839 (tpp80) REVERT: B 839 ILE cc_start: 0.7259 (mm) cc_final: 0.6991 (mp) REVERT: B 845 ARG cc_start: 0.6799 (tpp80) cc_final: 0.6599 (ttm170) REVERT: B 1009 SER cc_start: 0.8618 (t) cc_final: 0.8356 (m) REVERT: B 1045 MET cc_start: 0.7115 (ptp) cc_final: 0.6665 (OUTLIER) REVERT: B 1122 ARG cc_start: 0.7369 (ttp80) cc_final: 0.6768 (ttp80) REVERT: B 1130 ARG cc_start: 0.7933 (ptm160) cc_final: 0.7291 (ttp-170) REVERT: C 593 HIS cc_start: 0.7177 (t70) cc_final: 0.6668 (m-70) REVERT: C 661 LYS cc_start: 0.6855 (mmtt) cc_final: 0.6266 (pttp) REVERT: C 730 GLU cc_start: 0.7784 (tp30) cc_final: 0.7474 (pm20) REVERT: C 1020 MET cc_start: 0.8862 (mmm) cc_final: 0.8568 (mmp) REVERT: D 478 GLU cc_start: 0.6708 (pt0) cc_final: 0.6194 (pm20) REVERT: D 559 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7258 (tm-30) REVERT: D 612 MET cc_start: 0.6938 (mmm) cc_final: 0.6371 (mmm) REVERT: D 928 GLN cc_start: 0.8580 (tt0) cc_final: 0.8356 (tt0) REVERT: D 1032 GLU cc_start: 0.7507 (pt0) cc_final: 0.7272 (mm-30) REVERT: D 1126 ARG cc_start: 0.7833 (ttt-90) cc_final: 0.7363 (ttt-90) outliers start: 32 outliers final: 13 residues processed: 347 average time/residue: 1.2822 time to fit residues: 504.1248 Evaluate side-chains 301 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 288 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 775 MET Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 876 MET Chi-restraints excluded: chain D residue 580 ASN Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 110 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 199 optimal weight: 0.0770 chunk 228 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 144 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 HIS A 584 HIS A 648 HIS A 693 GLN A 753 HIS ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1144 GLN ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1144 GLN C 580 ASN C 608 ASN C 823 ASN ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1046 GLN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.188866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.148154 restraints weight = 21713.671| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.69 r_work: 0.3372 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 1.8556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19372 Z= 0.121 Angle : 0.637 12.393 26244 Z= 0.317 Chirality : 0.042 0.189 3088 Planarity : 0.004 0.046 3256 Dihedral : 4.029 17.373 2568 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.19 % Allowed : 25.62 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.18), residues: 2332 helix: 0.54 (0.13), residues: 1648 sheet: -1.54 (0.90), residues: 40 loop : -2.39 (0.21), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 867 HIS 0.006 0.001 HIS A 648 PHE 0.018 0.001 PHE A 483 TYR 0.040 0.001 TYR A 620 ARG 0.007 0.000 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 912) hydrogen bonds : angle 3.86761 ( 2688) covalent geometry : bond 0.00269 (19372) covalent geometry : angle 0.63706 (26244) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 329 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 562 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7079 (mt-10) REVERT: A 730 GLU cc_start: 0.8211 (tp30) cc_final: 0.7790 (pm20) REVERT: A 774 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8283 (ttt) REVERT: A 908 LEU cc_start: 0.8009 (mp) cc_final: 0.7773 (mt) REVERT: A 914 ASP cc_start: 0.7002 (m-30) cc_final: 0.6677 (p0) REVERT: A 956 ILE cc_start: 0.7272 (OUTLIER) cc_final: 0.6691 (mt) REVERT: A 982 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7809 (mt-10) REVERT: A 1052 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6651 (pt0) REVERT: A 1068 MET cc_start: 0.5606 (tmm) cc_final: 0.5380 (tpt) REVERT: B 587 THR cc_start: 0.7685 (m) cc_final: 0.7449 (m) REVERT: B 593 HIS cc_start: 0.7962 (t-90) cc_final: 0.7466 (m-70) REVERT: B 686 LYS cc_start: 0.7013 (mtpp) cc_final: 0.5953 (tptt) REVERT: B 766 PHE cc_start: 0.8742 (m-10) cc_final: 0.8520 (m-80) REVERT: B 824 ARG cc_start: 0.7381 (ttp80) cc_final: 0.6965 (tpp80) REVERT: B 839 ILE cc_start: 0.7337 (mm) cc_final: 0.7084 (mp) REVERT: B 845 ARG cc_start: 0.6897 (tpp80) cc_final: 0.6619 (ttm170) REVERT: B 986 VAL cc_start: 0.9170 (m) cc_final: 0.8917 (t) REVERT: B 1009 SER cc_start: 0.8671 (t) cc_final: 0.8449 (m) REVERT: B 1045 MET cc_start: 0.7216 (ptp) cc_final: 0.6830 (ttp) REVERT: B 1072 GLU cc_start: 0.6224 (tt0) cc_final: 0.5630 (tt0) REVERT: B 1129 SER cc_start: 0.8492 (t) cc_final: 0.8188 (m) REVERT: B 1130 ARG cc_start: 0.8083 (ptm160) cc_final: 0.7431 (ttp-170) REVERT: C 487 TYR cc_start: 0.6609 (m-80) cc_final: 0.6278 (m-80) REVERT: C 593 HIS cc_start: 0.7386 (t70) cc_final: 0.7048 (m-70) REVERT: C 730 GLU cc_start: 0.7862 (tp30) cc_final: 0.7592 (pm20) REVERT: C 1020 MET cc_start: 0.8866 (mmm) cc_final: 0.8604 (mmp) REVERT: D 478 GLU cc_start: 0.6840 (pt0) cc_final: 0.6599 (pm20) REVERT: D 928 GLN cc_start: 0.8630 (tt0) cc_final: 0.8399 (tt0) REVERT: D 1126 ARG cc_start: 0.7920 (ttt-90) cc_final: 0.7411 (ttt180) outliers start: 25 outliers final: 13 residues processed: 342 average time/residue: 1.4436 time to fit residues: 560.3393 Evaluate side-chains 319 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 304 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 775 MET Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 47 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 177 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 165 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 HIS ** A 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 HIS A 693 GLN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1144 GLN C 608 ASN ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1046 GLN ** D1135 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 = 0.4036 r_free = 0.4036 target = 0.184603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144182 restraints weight = 21707.566| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.84 r_work: 0.3301 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 1.9017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 19372 Z= 0.128 Angle : 0.659 13.720 26244 Z= 0.327 Chirality : 0.042 0.250 3088 Planarity : 0.004 0.040 3256 Dihedral : 3.948 17.532 2568 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.33 % Allowed : 26.57 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.18), residues: 2332 helix: 0.63 (0.13), residues: 1644 sheet: -1.52 (0.90), residues: 40 loop : -2.36 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 867 HIS 0.006 0.001 HIS A 584 PHE 0.017 0.001 PHE A 483 TYR 0.052 0.002 TYR A 621 ARG 0.008 0.000 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 912) hydrogen bonds : angle 3.89057 ( 2688) covalent geometry : bond 0.00293 (19372) covalent geometry : angle 0.65863 (26244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15416.26 seconds wall clock time: 268 minutes 28.42 seconds (16108.42 seconds total)