Starting phenix.real_space_refine on Mon May 19 19:28:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yks_33896/05_2025/7yks_33896.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yks_33896/05_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_33896/05_2025/7yks_33896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yks_33896/05_2025/7yks_33896.map" model { file = "/net/cci-nas-00/data/ceres_data/7yks_33896/05_2025/7yks_33896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yks_33896/05_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.28, per 1000 atoms: 0.54 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: 4.23 Conformation dependent library (CDL) restraints added in 2.2 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: 1.98 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: 5.31 Time building geometry restraints manager: 5.01 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: 0.14 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 39.360 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.410 ------------------------------------------------------------------------------- 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 : 1.910 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: 1.2391 time to fit residues: 360.6784 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 : 1.807 ------------------------------------------------------------------------------- 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 = 0.206462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.166591 restraints weight = 21137.153| |-----------------------------------------------------------------------------| 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: 0.2247 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 8.499 26244 Z= 0.352 Chirality : 0.043 0.153 3088 Planarity : 0.006 0.056 3256 Dihedral : 5.339 40.794 2573 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.26 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: -2.73 (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 0.002 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 4.80484 ( 2688) covalent geometry : bond 0.00324 (19372) covalent geometry : angle 0.68079 (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 : 1.826 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: 0.2427 (ttm) REVERT: A 691 PHE cc_start: 0.3935 (OUTLIER) cc_final: 0.3513 (t80) REVERT: A 845 ARG cc_start: 0.7013 (ttp80) cc_final: 0.6726 (tmm160) REVERT: A 922 MET cc_start: 0.3639 (OUTLIER) cc_final: 0.3221 (tpp) REVERT: A 993 TYR cc_start: 0.6047 (t80) cc_final: 0.5335 (t80) REVERT: A 1131 MET cc_start: 0.2494 (OUTLIER) cc_final: 0.0218 (mmm) REVERT: B 912 ARG cc_start: 0.5974 (tmt-80) cc_final: 0.5711 (ppt170) REVERT: B 1002 MET cc_start: 0.1722 (OUTLIER) cc_final: 0.1048 (ppp) REVERT: C 554 MET cc_start: 0.1870 (mtt) cc_final: -0.0173 (tpt) REVERT: C 876 MET cc_start: 0.0061 (mtp) cc_final: -0.0567 (ptt) REVERT: C 979 MET cc_start: 0.1624 (ppp) cc_final: 0.1222 (ppp) REVERT: C 1002 MET cc_start: 0.6028 (tpp) cc_final: 0.5462 (ttt) REVERT: D 598 LEU cc_start: 0.0503 (OUTLIER) cc_final: -0.0195 (mt) REVERT: D 641 MET cc_start: 0.3078 (mmm) cc_final: 0.2119 (pp-130) REVERT: D 676 CYS cc_start: 0.5109 (m) cc_final: 0.4791 (t) REVERT: D 935 MET cc_start: 0.5095 (tmm) cc_final: 0.4781 (ttp) REVERT: D 992 THR cc_start: 0.4038 (OUTLIER) cc_final: 0.3808 (t) REVERT: D 1061 TRP cc_start: 0.3413 (t-100) cc_final: 0.2949 (t60) outliers start: 37 outliers final: 10 residues processed: 235 average time/residue: 1.1916 time to fit residues: 318.0198 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 : 1.843 ------------------------------------------------------------------------------- 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: 10.0000 chunk 52 optimal weight: 0.6980 chunk 192 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 200 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 175 optimal weight: 0.8980 chunk 53 optimal weight: 20.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 593 HIS B 891 HIS B1050 HIS ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS ** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 HIS ** C 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.238349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.202891 restraints weight = 22437.743| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 2.15 r_work: 0.4084 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3953 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5020 moved from start: 0.8809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.203 19372 Z= 0.272 Angle : 0.941 16.276 26244 Z= 0.480 Chirality : 0.050 0.322 3088 Planarity : 0.007 0.086 3256 Dihedral : 5.643 45.718 2571 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.18 % Allowed : 11.26 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.98 (0.16), residues: 2332 helix: -1.58 (0.12), residues: 1576 sheet: -2.95 (0.61), residues: 60 loop : -2.43 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 745 HIS 0.010 0.002 HIS D 525 PHE 0.034 0.003 PHE A 965 TYR 0.027 0.003 TYR A 989 ARG 0.012 0.001 ARG D 821 Details of bonding type rmsd hydrogen bonds : bond 0.07070 ( 912) hydrogen bonds : angle 4.96058 ( 2688) covalent geometry : bond 0.00614 (19372) covalent geometry : angle 0.94138 (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 343 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 276 time to evaluate : 1.993 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: A 617 TYR cc_start: 0.4927 (t80) cc_final: 0.4706 (t80) REVERT: A 829 LEU cc_start: 0.6525 (tp) cc_final: 0.6319 (mt) REVERT: A 845 ARG cc_start: 0.7531 (ttp80) cc_final: 0.7219 (ttp80) REVERT: A 905 ARG cc_start: 0.7695 (tmt-80) cc_final: 0.7494 (tmt-80) REVERT: A 1131 MET cc_start: 0.5621 (OUTLIER) cc_final: 0.5242 (tpt) REVERT: B 514 MET cc_start: 0.6588 (OUTLIER) cc_final: 0.6209 (tmt) REVERT: B 743 MET cc_start: 0.5061 (mmp) cc_final: 0.4529 (mtp) REVERT: B 1015 MET cc_start: 0.9127 (tpp) cc_final: 0.8772 (tpt) REVERT: B 1031 ILE cc_start: 0.7587 (mt) cc_final: 0.7312 (tt) REVERT: C 500 GLU cc_start: 0.3222 (tp30) cc_final: 0.2293 (tm-30) REVERT: C 630 MET cc_start: 0.1730 (tpp) cc_final: 0.1366 (ttt) REVERT: C 774 MET cc_start: 0.5811 (mmp) cc_final: 0.5412 (mtm) REVERT: C 844 MET cc_start: 0.4055 (tmm) cc_final: 0.3787 (ttm) REVERT: C 982 GLU cc_start: 0.7067 (pm20) cc_final: 0.6258 (mt-10) REVERT: C 1131 MET cc_start: 0.2739 (tpt) cc_final: 0.2131 (tpt) REVERT: D 881 PHE cc_start: 0.4739 (OUTLIER) cc_final: 0.4515 (m-80) REVERT: D 978 MET cc_start: 0.5455 (OUTLIER) cc_final: 0.5158 (ppp) REVERT: D 1002 MET cc_start: 0.5590 (ppp) cc_final: 0.5242 (tpp) REVERT: D 1030 ASP cc_start: 0.7614 (m-30) cc_final: 0.7403 (m-30) outliers start: 67 outliers final: 7 residues processed: 312 average time/residue: 1.1498 time to fit residues: 409.3076 Evaluate side-chains 214 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 566 SER 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 C residue 1048 VAL Chi-restraints excluded: chain D residue 881 PHE 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: 0.8980 chunk 53 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 777 ASN A 911 GLN A1050 HIS ** A1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1144 GLN B 543 HIS B 753 HIS B 888 ASN ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 ASN B1136 HIS ** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 608 ASN ** C 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1039 GLN C1063 GLN ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 HIS D 991 ASN ** D1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1136 HIS ** D1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.227754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.187595 restraints weight = 22591.836| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.67 r_work: 0.3878 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 1.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 19372 Z= 0.212 Angle : 0.838 14.016 26244 Z= 0.423 Chirality : 0.048 0.233 3088 Planarity : 0.007 0.128 3256 Dihedral : 5.332 45.897 2571 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.18 % Allowed : 13.55 % Favored : 83.27 % 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: -2.49 (0.16), residues: 2332 helix: -1.23 (0.12), residues: 1644 sheet: -2.49 (0.65), residues: 60 loop : -2.28 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C1061 HIS 0.017 0.002 HIS B 753 PHE 0.037 0.003 PHE D 752 TYR 0.017 0.002 TYR C 760 ARG 0.023 0.001 ARG B 527 Details of bonding type rmsd hydrogen bonds : bond 0.04688 ( 912) hydrogen bonds : angle 4.76691 ( 2688) covalent geometry : bond 0.00462 (19372) covalent geometry : angle 0.83803 (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 397 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 330 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 ILE cc_start: 0.5874 (OUTLIER) cc_final: 0.5605 (mt) REVERT: A 617 TYR cc_start: 0.5698 (t80) cc_final: 0.4626 (t80) REVERT: A 845 ARG cc_start: 0.7513 (ttp80) cc_final: 0.7173 (tmt90) REVERT: A 956 ILE cc_start: 0.6128 (OUTLIER) cc_final: 0.5129 (mt) REVERT: A 1030 ASP cc_start: 0.8342 (m-30) cc_final: 0.8140 (m-30) REVERT: A 1046 GLN cc_start: 0.7183 (tt0) cc_final: 0.6978 (mt0) REVERT: B 514 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.5824 (tmt) REVERT: B 743 MET cc_start: 0.5633 (mmp) cc_final: 0.5413 (ttp) REVERT: B 905 ARG cc_start: 0.8478 (tpt-90) cc_final: 0.7958 (tpt170) REVERT: B 1002 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6312 (mmp) REVERT: B 1009 SER cc_start: 0.8556 (t) cc_final: 0.8204 (m) REVERT: B 1032 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7644 (tp30) REVERT: B 1033 SER cc_start: 0.8500 (t) cc_final: 0.8204 (p) REVERT: C 500 GLU cc_start: 0.3481 (tp30) cc_final: 0.2981 (mm-30) REVERT: C 664 GLU cc_start: 0.4915 (mm-30) cc_final: 0.4312 (mt-10) REVERT: C 743 MET cc_start: 0.5971 (tmm) cc_final: 0.5729 (tmt) REVERT: C 775 MET cc_start: 0.7909 (mmm) cc_final: 0.7625 (mpp) REVERT: C 1045 MET cc_start: 0.5509 (tpp) cc_final: 0.4942 (tpt) REVERT: D 560 THR cc_start: 0.3514 (t) cc_final: 0.2958 (m) REVERT: D 601 MET cc_start: 0.5499 (tmm) cc_final: 0.5295 (tmm) REVERT: D 999 LYS cc_start: 0.7444 (tptp) cc_final: 0.6692 (ttpt) REVERT: D 1032 GLU cc_start: 0.8052 (pp20) cc_final: 0.7557 (mp0) outliers start: 67 outliers final: 11 residues processed: 362 average time/residue: 1.1973 time to fit residues: 493.6907 Evaluate side-chains 262 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 247 time to evaluate : 1.992 ------------------------------------------------------------------------------- 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 847 LEU Chi-restraints excluded: chain A residue 956 ILE 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 1002 MET Chi-restraints excluded: chain C residue 723 MET Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 1032 GLU 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 844 MET 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: 0.5980 chunk 69 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 173 optimal weight: 0.2980 chunk 189 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 523 GLN A 590 ASN A 648 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 HIS ** B 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 HIS C 742 GLN ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1046 GLN C1136 HIS ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 525 HIS D 777 ASN ** D 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.221418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.180063 restraints weight = 22606.498| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 1.94 r_work: 0.3806 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 1.3714 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= 0.128 Angle : 0.619 11.115 26244 Z= 0.316 Chirality : 0.041 0.157 3088 Planarity : 0.004 0.054 3256 Dihedral : 4.389 20.894 2568 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.09 % Allowed : 17.02 % Favored : 79.90 % 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: -1.66 (0.17), residues: 2332 helix: -0.55 (0.13), residues: 1684 sheet: -1.98 (0.69), residues: 60 loop : -2.29 (0.22), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 745 HIS 0.023 0.001 HIS B 648 PHE 0.020 0.001 PHE D 752 TYR 0.025 0.001 TYR D 623 ARG 0.004 0.000 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 912) hydrogen bonds : angle 4.06279 ( 2688) covalent geometry : bond 0.00277 (19372) covalent geometry : angle 0.61946 (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 337 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 272 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 ILE cc_start: 0.6705 (OUTLIER) cc_final: 0.6444 (mp) REVERT: A 617 TYR cc_start: 0.5824 (t80) cc_final: 0.4887 (t80) REVERT: A 621 TYR cc_start: 0.5833 (OUTLIER) cc_final: 0.5543 (t80) REVERT: A 721 ASN cc_start: 0.8316 (m-40) cc_final: 0.8012 (m-40) REVERT: A 845 ARG cc_start: 0.7457 (ttp80) cc_final: 0.7214 (tmt90) REVERT: A 931 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8161 (tp) REVERT: A 956 ILE cc_start: 0.6308 (OUTLIER) cc_final: 0.5561 (mt) REVERT: B 589 GLU cc_start: 0.6010 (OUTLIER) cc_final: 0.5731 (tp30) REVERT: B 663 PHE cc_start: 0.7963 (t80) cc_final: 0.7677 (t80) REVERT: B 664 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8259 (tp30) REVERT: B 1009 SER cc_start: 0.8697 (t) cc_final: 0.8411 (m) REVERT: B 1032 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8033 (tp30) REVERT: C 1045 MET cc_start: 0.5900 (tpp) cc_final: 0.5690 (tpt) REVERT: D 560 THR cc_start: 0.3926 (t) cc_final: 0.2967 (m) REVERT: D 742 GLN cc_start: 0.6733 (OUTLIER) cc_final: 0.6376 (pp30) REVERT: D 844 MET cc_start: 0.5523 (OUTLIER) cc_final: 0.5267 (tpp) REVERT: D 913 PHE cc_start: 0.8510 (m-10) cc_final: 0.8210 (m-10) REVERT: D 931 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8154 (tp) REVERT: D 999 LYS cc_start: 0.7826 (tptp) cc_final: 0.7158 (ttpt) REVERT: D 1032 GLU cc_start: 0.8494 (pp20) cc_final: 0.7624 (mp0) REVERT: D 1133 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6533 (tt0) outliers start: 65 outliers final: 19 residues processed: 308 average time/residue: 1.2062 time to fit residues: 420.7975 Evaluate side-chains 259 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 589 GLU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 570 HIS Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 876 MET Chi-restraints excluded: chain D residue 659 MET Chi-restraints excluded: chain D residue 742 GLN 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 928 GLN Chi-restraints excluded: chain D residue 931 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 186 optimal weight: 4.9990 chunk 188 optimal weight: 0.5980 chunk 161 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 8 optimal weight: 0.0470 chunk 132 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 HIS A1121 GLN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 882 GLN B 891 HIS ** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.215226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.174047 restraints weight = 22416.683| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.05 r_work: 0.3723 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 1.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19372 Z= 0.131 Angle : 0.612 14.574 26244 Z= 0.312 Chirality : 0.041 0.169 3088 Planarity : 0.004 0.056 3256 Dihedral : 4.212 21.033 2568 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.52 % Allowed : 18.58 % Favored : 78.90 % 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: -1.18 (0.17), residues: 2332 helix: -0.16 (0.13), residues: 1680 sheet: -1.74 (0.85), residues: 40 loop : -2.20 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 745 HIS 0.013 0.001 HIS C 570 PHE 0.020 0.001 PHE D 923 TYR 0.027 0.001 TYR D 623 ARG 0.005 0.000 ARG C 636 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 912) hydrogen bonds : angle 3.95063 ( 2688) covalent geometry : bond 0.00288 (19372) covalent geometry : angle 0.61236 (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 338 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 285 time to evaluate : 2.219 Fit side-chains revert: symmetry clash REVERT: A 617 TYR cc_start: 0.6072 (t80) cc_final: 0.5026 (t80) REVERT: A 621 TYR cc_start: 0.6177 (OUTLIER) cc_final: 0.5707 (t80) REVERT: A 908 LEU cc_start: 0.7913 (mp) cc_final: 0.7708 (mt) REVERT: A 931 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8226 (tp) REVERT: A 956 ILE cc_start: 0.6511 (OUTLIER) cc_final: 0.5754 (mt) REVERT: A 1122 ARG cc_start: 0.6699 (ttp-110) cc_final: 0.6084 (ttp-110) REVERT: B 554 MET cc_start: 0.8263 (ptm) cc_final: 0.7934 (mtm) REVERT: B 559 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7587 (tp30) REVERT: B 905 ARG cc_start: 0.8508 (tpt-90) cc_final: 0.8303 (ttt90) REVERT: B 1009 SER cc_start: 0.8663 (t) cc_final: 0.8391 (m) REVERT: B 1032 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8010 (tp30) REVERT: C 730 GLU cc_start: 0.7179 (tp30) cc_final: 0.6765 (pm20) REVERT: C 1020 MET cc_start: 0.8966 (mmm) cc_final: 0.8728 (mmp) REVERT: C 1068 MET cc_start: 0.5203 (ptm) cc_final: 0.4921 (ttm) REVERT: C 1120 ARG cc_start: 0.6063 (OUTLIER) cc_final: 0.5703 (ttm110) REVERT: D 560 THR cc_start: 0.4445 (t) cc_final: 0.3476 (m) REVERT: D 999 LYS cc_start: 0.7887 (tptp) cc_final: 0.7206 (ttpt) REVERT: D 1032 GLU cc_start: 0.8399 (pp20) cc_final: 0.7535 (mm-30) REVERT: D 1039 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7863 (tm-30) REVERT: D 1133 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6786 (tt0) outliers start: 53 outliers final: 20 residues processed: 315 average time/residue: 1.2133 time to fit residues: 432.8103 Evaluate side-chains 270 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 246 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 820 GLU Chi-restraints excluded: chain A residue 852 GLN Chi-restraints excluded: chain A residue 877 VAL 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 B residue 515 THR Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 729 VAL 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 1120 ARG 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 931 ILE Chi-restraints excluded: chain D residue 1048 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 32 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 0.0050 chunk 101 optimal weight: 0.8980 chunk 196 optimal weight: 0.0670 chunk 182 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN A 777 ASN A 823 ASN A1144 GLN B 482 HIS B 580 ASN B 608 ASN B 648 HIS ** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 GLN ** D 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.208554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.167321 restraints weight = 22037.558| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.97 r_work: 0.3682 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 1.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19372 Z= 0.118 Angle : 0.610 12.120 26244 Z= 0.306 Chirality : 0.041 0.234 3088 Planarity : 0.004 0.052 3256 Dihedral : 4.068 20.217 2568 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.95 % Allowed : 20.15 % Favored : 76.90 % 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: -1.00 (0.18), residues: 2332 helix: 0.02 (0.13), residues: 1708 sheet: -1.70 (0.84), residues: 40 loop : -2.42 (0.22), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 903 HIS 0.013 0.001 HIS C 518 PHE 0.009 0.001 PHE A 766 TYR 0.029 0.001 TYR D 623 ARG 0.009 0.000 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 912) hydrogen bonds : angle 3.88229 ( 2688) covalent geometry : bond 0.00257 (19372) covalent geometry : angle 0.61020 (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 353 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 291 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 TYR cc_start: 0.6221 (t80) cc_final: 0.5146 (t80) REVERT: A 621 TYR cc_start: 0.6270 (OUTLIER) cc_final: 0.5728 (t80) REVERT: A 908 LEU cc_start: 0.7917 (mp) cc_final: 0.7656 (mt) REVERT: A 931 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8284 (tp) REVERT: A 956 ILE cc_start: 0.6797 (OUTLIER) cc_final: 0.6076 (mt) REVERT: A 1122 ARG cc_start: 0.6981 (ttp-110) cc_final: 0.6303 (ttp-110) REVERT: B 664 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: B 905 ARG cc_start: 0.8462 (tpt-90) cc_final: 0.8114 (ttt90) REVERT: B 914 ASP cc_start: 0.7259 (m-30) cc_final: 0.7050 (p0) REVERT: B 1009 SER cc_start: 0.8631 (t) cc_final: 0.8371 (m) REVERT: B 1032 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7917 (tp30) REVERT: B 1122 ARG cc_start: 0.6988 (ttp80) cc_final: 0.6035 (ttp-170) REVERT: C 730 GLU cc_start: 0.7331 (tp30) cc_final: 0.6869 (pm20) REVERT: C 1032 GLU cc_start: 0.7559 (tp30) cc_final: 0.7055 (mp0) REVERT: D 560 THR cc_start: 0.4971 (t) cc_final: 0.4008 (m) REVERT: D 693 GLN cc_start: 0.7163 (pt0) cc_final: 0.6746 (pt0) REVERT: D 913 PHE cc_start: 0.8706 (m-10) cc_final: 0.8451 (m-10) REVERT: D 931 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8343 (tp) REVERT: D 986 VAL cc_start: 0.9115 (p) cc_final: 0.8766 (t) REVERT: D 999 LYS cc_start: 0.7960 (tptp) cc_final: 0.7444 (ttpt) REVERT: D 1032 GLU cc_start: 0.8282 (pp20) cc_final: 0.7608 (mp0) REVERT: D 1039 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7782 (tm-30) REVERT: D 1045 MET cc_start: 0.7573 (tpp) cc_final: 0.7195 (ttp) REVERT: D 1126 ARG cc_start: 0.7503 (ttt-90) cc_final: 0.7018 (ttt180) REVERT: D 1133 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6761 (tt0) outliers start: 62 outliers final: 23 residues processed: 331 average time/residue: 1.1754 time to fit residues: 442.3907 Evaluate side-chains 291 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 263 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 774 MET 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 956 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 580 ASN Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain B residue 775 MET Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 656 ILE 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 659 MET Chi-restraints excluded: chain D residue 742 GLN Chi-restraints excluded: chain D residue 743 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 Chi-restraints excluded: chain D residue 931 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 159 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 227 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 991 ASN A1121 GLN B 522 GLN B 540 HIS B 648 HIS B1144 GLN ** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1137 HIS C1144 GLN ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 GLN ** D 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.194359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.152963 restraints weight = 21702.446| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.43 r_work: 0.3382 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 1.7524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19372 Z= 0.156 Angle : 0.725 13.000 26244 Z= 0.366 Chirality : 0.046 0.472 3088 Planarity : 0.005 0.055 3256 Dihedral : 4.421 20.963 2568 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.38 % Allowed : 21.44 % Favored : 76.19 % Cbeta Deviations : 0.04 % 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: -1.06 (0.17), residues: 2332 helix: 0.00 (0.13), residues: 1672 sheet: -1.48 (0.88), residues: 40 loop : -2.43 (0.21), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 903 HIS 0.014 0.001 HIS C 518 PHE 0.018 0.002 PHE D 752 TYR 0.031 0.002 TYR D 623 ARG 0.010 0.001 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 912) hydrogen bonds : angle 4.23180 ( 2688) covalent geometry : bond 0.00336 (19372) covalent geometry : angle 0.72522 (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 390 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 340 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 540 HIS cc_start: 0.6600 (m-70) cc_final: 0.6372 (m-70) REVERT: A 588 MET cc_start: 0.8288 (ttm) cc_final: 0.7926 (mtp) REVERT: A 589 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7778 (mm-30) REVERT: A 617 TYR cc_start: 0.6775 (t80) cc_final: 0.5459 (t80) REVERT: A 620 TYR cc_start: 0.8565 (t80) cc_final: 0.8363 (t80) REVERT: A 686 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6997 (ptmm) REVERT: A 841 LEU cc_start: 0.7375 (tm) cc_final: 0.7077 (tp) REVERT: A 931 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8354 (tp) REVERT: A 956 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6403 (mt) REVERT: A 982 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7868 (mt-10) REVERT: A 1068 MET cc_start: 0.5486 (tpt) cc_final: 0.4981 (tpp) REVERT: B 562 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7346 (tm-30) REVERT: B 593 HIS cc_start: 0.7940 (t-90) cc_final: 0.7373 (m90) REVERT: B 739 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.7002 (tppt) REVERT: B 824 ARG cc_start: 0.7447 (ttp80) cc_final: 0.7089 (ttp80) REVERT: B 839 ILE cc_start: 0.7495 (mm) cc_final: 0.7199 (mp) REVERT: B 845 ARG cc_start: 0.6871 (tpp80) cc_final: 0.6610 (ttm170) REVERT: B 1045 MET cc_start: 0.7283 (ptp) cc_final: 0.6640 (ttp) REVERT: C 514 MET cc_start: 0.2782 (tpt) cc_final: -0.0178 (ptm) REVERT: C 628 LEU cc_start: 0.7734 (tp) cc_final: 0.7528 (tm) REVERT: C 730 GLU cc_start: 0.7777 (tp30) cc_final: 0.7378 (pm20) REVERT: C 743 MET cc_start: 0.6594 (tmt) cc_final: 0.6386 (tmm) REVERT: C 1020 MET cc_start: 0.8959 (mmm) cc_final: 0.8669 (mmp) REVERT: D 559 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7038 (tm-30) REVERT: D 693 GLN cc_start: 0.7517 (pt0) cc_final: 0.7263 (pt0) REVERT: D 999 LYS cc_start: 0.7981 (tptp) cc_final: 0.7510 (ttpt) REVERT: D 1032 GLU cc_start: 0.8069 (pp20) cc_final: 0.7752 (mp0) REVERT: D 1126 ARG cc_start: 0.7824 (ttt-90) cc_final: 0.7245 (ttt180) REVERT: D 1130 ARG cc_start: 0.7833 (ttt-90) cc_final: 0.7539 (mtm180) outliers start: 50 outliers final: 15 residues processed: 370 average time/residue: 1.3134 time to fit residues: 546.4567 Evaluate side-chains 304 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 283 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 774 MET 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 B residue 515 THR Chi-restraints excluded: chain B residue 562 GLU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain C residue 641 MET Chi-restraints excluded: chain C residue 729 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 210 optimal weight: 5.9990 chunk 188 optimal weight: 0.0770 chunk 181 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 HIS A1046 GLN B 540 HIS B 568 HIS B1144 GLN ** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN ** D 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4092 r_free = 0.4092 target = 0.190927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.139977 restraints weight = 21810.696| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.26 r_work: 0.3364 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 1.8210 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= 0.126 Angle : 0.632 11.680 26244 Z= 0.319 Chirality : 0.042 0.221 3088 Planarity : 0.004 0.053 3256 Dihedral : 4.056 18.016 2568 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.66 % Allowed : 24.52 % Favored : 73.81 % 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: -0.75 (0.17), residues: 2332 helix: 0.23 (0.13), residues: 1684 sheet: -1.50 (0.88), residues: 40 loop : -2.35 (0.21), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 867 HIS 0.005 0.001 HIS B 584 PHE 0.013 0.001 PHE D 752 TYR 0.026 0.002 TYR D 623 ARG 0.008 0.000 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 912) hydrogen bonds : angle 3.98057 ( 2688) covalent geometry : bond 0.00279 (19372) covalent geometry : angle 0.63221 (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 371 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 336 time to evaluate : 2.149 Fit side-chains revert: symmetry clash REVERT: A 540 HIS cc_start: 0.7275 (m-70) cc_final: 0.7039 (m-70) REVERT: A 562 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7385 (mt-10) REVERT: A 621 TYR cc_start: 0.7524 (m-10) cc_final: 0.7313 (m-10) REVERT: A 686 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6857 (ptmm) REVERT: A 841 LEU cc_start: 0.7175 (tm) cc_final: 0.6910 (tp) REVERT: A 908 LEU cc_start: 0.8042 (mp) cc_final: 0.7725 (mt) REVERT: A 931 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8342 (tp) REVERT: A 956 ILE cc_start: 0.7173 (OUTLIER) cc_final: 0.6563 (mt) REVERT: A 982 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7828 (mt-10) REVERT: A 1068 MET cc_start: 0.5634 (tpt) cc_final: 0.5309 (tpp) REVERT: B 562 GLU cc_start: 0.8215 (tt0) cc_final: 0.7330 (tm-30) REVERT: B 564 LEU cc_start: 0.7614 (mm) cc_final: 0.7370 (mm) REVERT: B 593 HIS cc_start: 0.8226 (t-90) cc_final: 0.7633 (m90) REVERT: B 686 LYS cc_start: 0.6770 (mtpp) cc_final: 0.6000 (tptt) REVERT: B 730 GLU cc_start: 0.8224 (tp30) cc_final: 0.7058 (pt0) REVERT: B 824 ARG cc_start: 0.7322 (ttp80) cc_final: 0.7021 (ttp80) REVERT: B 839 ILE cc_start: 0.7304 (mm) cc_final: 0.7059 (mp) REVERT: B 845 ARG cc_start: 0.6748 (tpp80) cc_final: 0.6535 (ttm170) REVERT: B 1045 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.7070 (ttp) REVERT: B 1122 ARG cc_start: 0.7491 (ttp80) cc_final: 0.6873 (ptm160) REVERT: C 487 TYR cc_start: 0.6411 (m-80) cc_final: 0.5963 (m-80) REVERT: C 514 MET cc_start: 0.2562 (tpt) cc_final: -0.0805 (ptm) REVERT: C 593 HIS cc_start: 0.7482 (t70) cc_final: 0.7026 (m-70) REVERT: C 601 MET cc_start: 0.5716 (tmm) cc_final: 0.4117 (mtt) REVERT: C 628 LEU cc_start: 0.7719 (tp) cc_final: 0.7453 (tm) REVERT: C 664 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7038 (tt0) REVERT: C 730 GLU cc_start: 0.7926 (tp30) cc_final: 0.7261 (pm20) REVERT: C 1020 MET cc_start: 0.9027 (mmm) cc_final: 0.8716 (mmp) REVERT: C 1032 GLU cc_start: 0.7958 (tp30) cc_final: 0.7052 (mp0) REVERT: C 1035 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7416 (ttp-170) REVERT: C 1120 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6889 (ttm110) REVERT: D 478 GLU cc_start: 0.6805 (pt0) cc_final: 0.6356 (pm20) REVERT: D 554 MET cc_start: 0.7528 (ptm) cc_final: 0.7290 (mtm) REVERT: D 612 MET cc_start: 0.6897 (mmm) cc_final: 0.6376 (mmm) REVERT: D 628 LEU cc_start: 0.8107 (mt) cc_final: 0.7828 (mm) REVERT: D 693 GLN cc_start: 0.7712 (pt0) cc_final: 0.7499 (pt0) REVERT: D 844 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.5915 (mpp) REVERT: D 913 PHE cc_start: 0.8768 (m-10) cc_final: 0.8513 (m-10) REVERT: D 999 LYS cc_start: 0.7912 (tptp) cc_final: 0.7393 (ttpt) REVERT: D 1032 GLU cc_start: 0.8123 (pp20) cc_final: 0.7541 (mp0) REVERT: D 1126 ARG cc_start: 0.7914 (ttt-90) cc_final: 0.7369 (ttt180) REVERT: D 1130 ARG cc_start: 0.7900 (ttt-90) cc_final: 0.7442 (mtm180) outliers start: 35 outliers final: 15 residues processed: 355 average time/residue: 1.2536 time to fit residues: 503.8490 Evaluate side-chains 318 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 296 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 887 ILE 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 B residue 515 THR Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 775 MET Chi-restraints excluded: chain B residue 1045 MET Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 996 ASP Chi-restraints excluded: chain C residue 1035 ARG Chi-restraints excluded: chain C residue 1120 ARG Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 844 MET Chi-restraints excluded: chain D residue 861 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 110 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 199 optimal weight: 0.0270 chunk 228 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 HIS A1046 GLN A1121 GLN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1144 GLN C 491 ASN ** C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4051 r_free = 0.4051 target = 0.186436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.138294 restraints weight = 21621.687| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.28 r_work: 0.3381 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 1.8816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19372 Z= 0.121 Angle : 0.639 11.647 26244 Z= 0.320 Chirality : 0.042 0.224 3088 Planarity : 0.004 0.051 3256 Dihedral : 4.039 18.904 2568 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.19 % Allowed : 26.14 % Favored : 72.67 % 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: -0.55 (0.18), residues: 2332 helix: 0.40 (0.13), residues: 1680 sheet: -1.11 (0.92), residues: 40 loop : -2.33 (0.21), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 867 HIS 0.006 0.001 HIS D 525 PHE 0.013 0.001 PHE D 752 TYR 0.031 0.001 TYR D 623 ARG 0.008 0.000 ARG B1122 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 912) hydrogen bonds : angle 3.97632 ( 2688) covalent geometry : bond 0.00271 (19372) covalent geometry : angle 0.63912 (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 368 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 343 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 508 GLU cc_start: 0.7053 (tt0) cc_final: 0.6619 (tm-30) REVERT: A 562 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7425 (mt-10) REVERT: A 841 LEU cc_start: 0.7113 (tm) cc_final: 0.6841 (tp) REVERT: A 908 LEU cc_start: 0.8101 (mp) cc_final: 0.7785 (mt) REVERT: A 931 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8347 (tp) REVERT: A 956 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6687 (mt) REVERT: A 982 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7786 (mt-10) REVERT: A 1052 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6738 (pt0) REVERT: A 1122 ARG cc_start: 0.7814 (ttp80) cc_final: 0.7167 (ttm170) REVERT: B 562 GLU cc_start: 0.8140 (tt0) cc_final: 0.7228 (tm-30) REVERT: B 593 HIS cc_start: 0.8259 (t-90) cc_final: 0.7715 (m90) REVERT: B 686 LYS cc_start: 0.7201 (mtpp) cc_final: 0.6076 (tptt) REVERT: B 730 GLU cc_start: 0.8409 (tp30) cc_final: 0.7446 (pm20) REVERT: B 824 ARG cc_start: 0.7484 (ttp80) cc_final: 0.7091 (ttp80) REVERT: B 839 ILE cc_start: 0.7296 (mm) cc_final: 0.7070 (mp) REVERT: B 845 ARG cc_start: 0.6870 (tpp80) cc_final: 0.6634 (ttm170) REVERT: B 882 GLN cc_start: 0.7618 (mp10) cc_final: 0.7406 (mp10) REVERT: B 1045 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7202 (ttp) REVERT: B 1122 ARG cc_start: 0.7633 (ttp80) cc_final: 0.7063 (ttp80) REVERT: C 514 MET cc_start: 0.2455 (tpt) cc_final: -0.0575 (ptm) REVERT: C 576 ASP cc_start: 0.3182 (p0) cc_final: 0.2885 (p0) REVERT: C 580 ASN cc_start: 0.5539 (m-40) cc_final: 0.4716 (m110) REVERT: C 593 HIS cc_start: 0.7484 (t70) cc_final: 0.7144 (m-70) REVERT: C 601 MET cc_start: 0.5948 (tmm) cc_final: 0.4491 (mtt) REVERT: C 730 GLU cc_start: 0.7968 (tp30) cc_final: 0.7382 (pm20) REVERT: C 1009 SER cc_start: 0.8777 (t) cc_final: 0.8509 (m) REVERT: C 1032 GLU cc_start: 0.8012 (tp30) cc_final: 0.7042 (mp0) REVERT: C 1045 MET cc_start: 0.7698 (tpp) cc_final: 0.7189 (tpp) REVERT: D 478 GLU cc_start: 0.7097 (pt0) cc_final: 0.6785 (pm20) REVERT: D 560 THR cc_start: 0.6465 (t) cc_final: 0.5766 (m) REVERT: D 628 LEU cc_start: 0.8323 (mt) cc_final: 0.8097 (mm) REVERT: D 693 GLN cc_start: 0.7544 (pt0) cc_final: 0.7326 (pt0) REVERT: D 844 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6192 (mpp) REVERT: D 999 LYS cc_start: 0.7947 (tptp) cc_final: 0.7462 (ttpt) REVERT: D 1032 GLU cc_start: 0.8063 (pp20) cc_final: 0.7604 (mp0) REVERT: D 1126 ARG cc_start: 0.7931 (ttt-90) cc_final: 0.7428 (ttt180) REVERT: D 1130 ARG cc_start: 0.7939 (ttt-90) cc_final: 0.7572 (ttp80) outliers start: 25 outliers final: 12 residues processed: 358 average time/residue: 1.2503 time to fit residues: 505.5156 Evaluate side-chains 321 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 305 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 928 GLN 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 B residue 515 THR Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 775 MET Chi-restraints excluded: chain B residue 1045 MET Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 844 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 47 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 162 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 165 optimal weight: 0.3980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 HIS ** A 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 HIS A 991 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN ** C 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 823 ASN ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.180081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130614 restraints weight = 21631.101| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.37 r_work: 0.3169 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 1.9609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19372 Z= 0.132 Angle : 0.651 15.756 26244 Z= 0.325 Chirality : 0.042 0.218 3088 Planarity : 0.004 0.045 3256 Dihedral : 4.027 19.006 2568 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.52 % Allowed : 26.71 % Favored : 71.77 % 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: -0.48 (0.17), residues: 2332 helix: 0.45 (0.13), residues: 1672 sheet: -1.07 (0.93), residues: 40 loop : -2.29 (0.21), residues: 620 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 0.012 0.001 PHE D 752 TYR 0.028 0.001 TYR D 838 ARG 0.021 0.001 ARG C 546 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 912) hydrogen bonds : angle 3.94407 ( 2688) covalent geometry : bond 0.00301 (19372) covalent geometry : angle 0.65082 (26244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15251.18 seconds wall clock time: 262 minutes 34.07 seconds (15754.07 seconds total)