Starting phenix.real_space_refine on Sun Aug 24 09:50:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yks_33896/08_2025/7yks_33896.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yks_33896/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/7yks_33896/08_2025/7yks_33896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yks_33896/08_2025/7yks_33896.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yks_33896/08_2025/7yks_33896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yks_33896/08_2025/7yks_33896.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 12 Restraints were copied for chains: B, C, D Time building chain proxies: 4.74, per 1000 atoms: 0.25 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: 1.66 Conformation dependent library (CDL) restraints added in 881.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.61 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: 3.39 Time building geometry restraints manager: 2.19 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.710 Find NCS groups from input model: 0.150 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:10.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.560 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.014 0.001 ARG D1123 TYR 0.028 0.003 TYR B 623 PHE 0.033 0.003 PHE A 948 TRP 0.012 0.002 TRP B 867 HIS 0.008 0.002 HIS D 518 Details of bonding type rmsd covalent geometry : bond 0.00790 (19372) covalent geometry : angle 0.99517 (26244) hydrogen bonds : bond 0.32927 ( 912) hydrogen bonds : angle 10.27385 ( 2688) *********************** 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 : 0.439 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: 0.3629 (p) REVERT: B 655 LEU cc_start: 0.2730 (mt) cc_final: 0.2394 (mt) REVERT: C 580 ASN cc_start: 0.2991 (m-40) cc_final: 0.2773 (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: 0.3012 (t60) outliers start: 0 outliers final: 2 residues processed: 257 average time/residue: 0.6054 time to fit residues: 175.3416 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 : 0.664 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0050 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 235 optimal weight: 1.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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 726 HIS 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 842 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 ** C 518 HIS ** 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 C1115 ASN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1144 GLN D 491 ASN D 518 HIS D 726 HIS D 742 GLN D 753 HIS D 991 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1136 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.203811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.165451 restraints weight = 21086.008| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.01 r_work: 0.3668 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1929 moved from start: 0.3012 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= 0.133 Angle : 0.643 8.306 26244 Z= 0.334 Chirality : 0.042 0.155 3088 Planarity : 0.006 0.054 3256 Dihedral : 5.290 40.109 2573 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.81 % Allowed : 9.03 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.26 (0.14), residues: 2332 helix: -2.68 (0.10), residues: 1632 sheet: -2.80 (0.79), residues: 40 loop : -2.60 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 845 TYR 0.014 0.001 TYR B 617 PHE 0.020 0.002 PHE C1005 TRP 0.017 0.001 TRP B1061 HIS 0.008 0.001 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00276 (19372) covalent geometry : angle 0.64286 (26244) hydrogen bonds : bond 0.04452 ( 912) hydrogen bonds : angle 4.67241 ( 2688) *********************** 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 250 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 0.644 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 691 PHE cc_start: 0.3676 (OUTLIER) cc_final: 0.3340 (t80) REVERT: A 845 ARG cc_start: 0.6973 (ttp80) cc_final: 0.6764 (tmm160) REVERT: A 922 MET cc_start: 0.3069 (tpp) cc_final: 0.2320 (tpp) REVERT: A 993 TYR cc_start: 0.5645 (t80) cc_final: 0.5275 (OUTLIER) REVERT: A 1131 MET cc_start: 0.2307 (OUTLIER) cc_final: 0.0159 (mmm) REVERT: B 912 ARG cc_start: 0.5795 (tmt-80) cc_final: 0.5508 (ppt170) REVERT: B 970 MET cc_start: 0.0594 (tpt) cc_final: -0.0195 (mpm) REVERT: B 1002 MET cc_start: 0.1264 (OUTLIER) cc_final: 0.0731 (ppp) REVERT: B 1146 MET cc_start: 0.1258 (ptt) cc_final: -0.0716 (tmt) REVERT: C 554 MET cc_start: 0.1624 (mtt) cc_final: -0.0616 (tpt) REVERT: C 609 VAL cc_start: 0.6317 (t) cc_final: 0.5924 (p) REVERT: C 876 MET cc_start: -0.0398 (mtp) cc_final: -0.1139 (ptt) REVERT: C 979 MET cc_start: 0.1006 (ppp) cc_final: 0.0661 (ppp) REVERT: C 1002 MET cc_start: 0.6026 (tpp) cc_final: 0.5478 (ttt) REVERT: D 621 TYR cc_start: 0.4429 (m-80) cc_final: 0.3679 (m-10) REVERT: D 641 MET cc_start: 0.2667 (mmm) cc_final: 0.1907 (pp-130) REVERT: D 676 CYS cc_start: 0.5109 (m) cc_final: 0.4801 (t) REVERT: D 726 HIS cc_start: 0.2884 (m90) cc_final: 0.1844 (m170) REVERT: D 935 MET cc_start: 0.4846 (tmm) cc_final: 0.4527 (ttp) REVERT: D 1061 TRP cc_start: 0.3502 (t-100) cc_final: 0.2956 (t60) outliers start: 38 outliers final: 10 residues processed: 228 average time/residue: 0.5670 time to fit residues: 146.8554 Evaluate side-chains 191 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 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 956 ILE Chi-restraints excluded: chain A residue 978 MET 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 1002 MET Chi-restraints excluded: chain C residue 561 ILE 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 34 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 107 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 146 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 HIS ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS B 842 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1144 GLN C 482 HIS ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 GLN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 HIS ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1144 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.214536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.174433 restraints weight = 21489.233| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.11 r_work: 0.3770 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2848 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 19372 Z= 0.163 Angle : 0.641 10.637 26244 Z= 0.330 Chirality : 0.041 0.173 3088 Planarity : 0.005 0.059 3256 Dihedral : 4.696 41.772 2571 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.19 % Allowed : 10.60 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.51 (0.16), residues: 2332 helix: -1.21 (0.12), residues: 1612 sheet: -2.62 (0.82), residues: 40 loop : -2.38 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 821 TYR 0.024 0.001 TYR D 687 PHE 0.028 0.002 PHE D 689 TRP 0.012 0.001 TRP B1061 HIS 0.007 0.001 HIS D 962 Details of bonding type rmsd covalent geometry : bond 0.00317 (19372) covalent geometry : angle 0.64149 (26244) hydrogen bonds : bond 0.04410 ( 912) hydrogen bonds : angle 4.14871 ( 2688) *********************** 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 266 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 220 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 MET cc_start: 0.2528 (pp-130) cc_final: 0.2281 (pp-130) REVERT: A 922 MET cc_start: 0.3984 (OUTLIER) cc_final: 0.3725 (ttm) REVERT: A 993 TYR cc_start: 0.6377 (t80) cc_final: 0.5499 (t80) REVERT: A 1131 MET cc_start: 0.2998 (OUTLIER) cc_final: 0.0404 (mmm) REVERT: C 601 MET cc_start: 0.4148 (tpt) cc_final: 0.3641 (ttm) REVERT: C 630 MET cc_start: 0.1097 (tpp) cc_final: 0.0293 (ttt) REVERT: C 774 MET cc_start: 0.4429 (mmp) cc_final: 0.2958 (mtp) REVERT: C 979 MET cc_start: 0.2213 (OUTLIER) cc_final: 0.1725 (ppp) REVERT: C 1131 MET cc_start: 0.1026 (mmm) cc_final: 0.0185 (ptt) REVERT: D 675 ASN cc_start: 0.3123 (p0) cc_final: 0.2599 (m-40) REVERT: D 676 CYS cc_start: 0.4860 (m) cc_final: 0.4090 (t) REVERT: D 978 MET cc_start: -0.0119 (OUTLIER) cc_final: -0.0520 (pp-130) REVERT: D 1020 MET cc_start: 0.3836 (mmm) cc_final: 0.2388 (ppp) REVERT: D 1061 TRP cc_start: 0.3599 (t-100) cc_final: 0.3102 (t60) REVERT: D 1146 MET cc_start: 0.1407 (ppp) cc_final: 0.0308 (ppp) outliers start: 46 outliers final: 7 residues processed: 236 average time/residue: 0.5545 time to fit residues: 148.9237 Evaluate side-chains 196 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 775 MET 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 C residue 561 ILE Chi-restraints excluded: chain C residue 723 MET Chi-restraints excluded: chain C residue 728 ARG Chi-restraints excluded: chain C residue 979 MET 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 171 optimal weight: 0.0030 chunk 152 optimal weight: 0.9980 chunk 233 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- 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 742 GLN A 991 ASN A1050 HIS A1121 GLN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 HIS B 491 ASN B 518 HIS B 543 HIS B 568 HIS B 721 ASN B1021 ASN B1050 HIS B1135 GLN ** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 HIS ** C 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 ASN C 742 GLN C 753 HIS ** C1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 ASN D 525 HIS D 742 GLN D1050 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.251357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.214257 restraints weight = 23705.632| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 2.21 r_work: 0.4182 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6046 moved from start: 1.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 19372 Z= 0.293 Angle : 1.098 23.665 26244 Z= 0.554 Chirality : 0.057 0.356 3088 Planarity : 0.007 0.074 3256 Dihedral : 6.630 46.184 2571 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 4.33 % Allowed : 11.03 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.15), residues: 2332 helix: -1.72 (0.12), residues: 1638 sheet: -2.80 (0.80), residues: 40 loop : -2.39 (0.21), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 905 TYR 0.041 0.003 TYR B 617 PHE 0.057 0.003 PHE D 689 TRP 0.044 0.003 TRP B1061 HIS 0.018 0.003 HIS D 525 Details of bonding type rmsd covalent geometry : bond 0.00632 (19372) covalent geometry : angle 1.09847 (26244) hydrogen bonds : bond 0.06689 ( 912) hydrogen bonds : angle 5.60706 ( 2688) *********************** 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 461 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 370 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 ILE cc_start: 0.5445 (OUTLIER) cc_final: 0.5245 (mt) REVERT: A 617 TYR cc_start: 0.5261 (t80) cc_final: 0.4117 (t80) REVERT: A 630 MET cc_start: 0.6747 (mpt) cc_final: 0.6477 (mpt) REVERT: A 841 LEU cc_start: 0.6923 (tt) cc_final: 0.6704 (tm) REVERT: A 956 ILE cc_start: 0.5947 (OUTLIER) cc_final: 0.5055 (mt) REVERT: A 1009 SER cc_start: 0.8724 (t) cc_final: 0.8506 (p) REVERT: A 1032 GLU cc_start: 0.7944 (tt0) cc_final: 0.7704 (tp30) REVERT: A 1131 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6918 (tpp) REVERT: B 510 ASP cc_start: 0.4764 (p0) cc_final: 0.4444 (m-30) REVERT: B 551 LEU cc_start: 0.5795 (mt) cc_final: 0.5136 (mt) REVERT: B 562 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7356 (tt0) REVERT: B 1045 MET cc_start: 0.4911 (OUTLIER) cc_final: 0.4707 (ptp) REVERT: C 630 MET cc_start: 0.3063 (tpp) cc_final: 0.2531 (ttt) REVERT: C 905 ARG cc_start: 0.7945 (ttt-90) cc_final: 0.7735 (tpt170) REVERT: C 925 GLU cc_start: 0.7388 (tt0) cc_final: 0.7184 (mt-10) REVERT: D 746 ASN cc_start: 0.6833 (m-40) cc_final: 0.6585 (m-40) REVERT: D 844 MET cc_start: 0.5333 (OUTLIER) cc_final: 0.5128 (tpp) REVERT: D 1032 GLU cc_start: 0.7403 (pt0) cc_final: 0.7176 (mp0) outliers start: 91 outliers final: 12 residues processed: 417 average time/residue: 0.5809 time to fit residues: 273.6953 Evaluate side-chains 249 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 232 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 877 VAL Chi-restraints excluded: chain B residue 967 ASN Chi-restraints excluded: chain B residue 1045 MET Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 884 ASP Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1062 LEU 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 27 optimal weight: 0.9990 chunk 230 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 chunk 137 optimal weight: 0.7980 chunk 216 optimal weight: 0.9980 chunk 178 optimal weight: 0.0980 chunk 108 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS A 540 HIS A 590 ASN A 648 HIS A 742 GLN A 777 ASN A1046 GLN A1136 HIS B 522 GLN ** B 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN B 753 HIS B1136 HIS B1144 GLN C 608 ASN C 967 ASN C1039 GLN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 HIS D 742 GLN D 753 HIS D1037 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.232551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.193994 restraints weight = 23068.669| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 2.03 r_work: 0.3968 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3846 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 1.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19372 Z= 0.140 Angle : 0.670 11.662 26244 Z= 0.339 Chirality : 0.042 0.221 3088 Planarity : 0.005 0.062 3256 Dihedral : 5.050 45.966 2571 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.14 % Allowed : 16.30 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.17), residues: 2332 helix: -0.71 (0.13), residues: 1626 sheet: -2.64 (0.74), residues: 40 loop : -2.35 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 546 TYR 0.037 0.002 TYR B 684 PHE 0.025 0.001 PHE D 752 TRP 0.010 0.001 TRP B1061 HIS 0.016 0.001 HIS B 648 Details of bonding type rmsd covalent geometry : bond 0.00310 (19372) covalent geometry : angle 0.66991 (26244) hydrogen bonds : bond 0.04057 ( 912) hydrogen bonds : angle 4.31020 ( 2688) *********************** 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 356 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 290 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 615 ILE cc_start: 0.6406 (OUTLIER) cc_final: 0.6197 (mp) REVERT: A 617 TYR cc_start: 0.5537 (t80) cc_final: 0.4491 (t80) REVERT: A 821 ARG cc_start: 0.6055 (OUTLIER) cc_final: 0.5753 (ppt170) REVERT: A 841 LEU cc_start: 0.7175 (tt) cc_final: 0.6937 (tm) REVERT: A 956 ILE cc_start: 0.6261 (OUTLIER) cc_final: 0.5388 (mt) REVERT: A 983 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8401 (mt) REVERT: A 1009 SER cc_start: 0.8619 (t) cc_final: 0.8414 (m) REVERT: A 1032 GLU cc_start: 0.8201 (tt0) cc_final: 0.7868 (tp30) REVERT: A 1046 GLN cc_start: 0.7454 (mt0) cc_final: 0.7230 (mt0) REVERT: B 562 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7550 (tt0) REVERT: B 1020 MET cc_start: 0.8515 (mmm) cc_final: 0.8224 (mmp) REVERT: C 630 MET cc_start: 0.3311 (tpp) cc_final: 0.3071 (ttt) REVERT: C 1032 GLU cc_start: 0.7718 (mp0) cc_final: 0.7448 (mp0) REVERT: C 1131 MET cc_start: 0.6363 (tpp) cc_final: 0.6110 (tpt) REVERT: D 601 MET cc_start: 0.5560 (tmm) cc_final: 0.5075 (tmm) REVERT: D 742 GLN cc_start: 0.6541 (OUTLIER) cc_final: 0.6282 (pp30) REVERT: D 746 ASN cc_start: 0.6907 (m-40) cc_final: 0.6682 (m-40) REVERT: D 847 LEU cc_start: 0.5148 (OUTLIER) cc_final: 0.4510 (pp) REVERT: D 913 PHE cc_start: 0.8489 (m-10) cc_final: 0.8216 (m-10) REVERT: D 959 GLN cc_start: 0.6886 (mt0) cc_final: 0.6533 (mm-40) REVERT: D 982 GLU cc_start: 0.6532 (mt-10) cc_final: 0.6273 (pt0) REVERT: D 1032 GLU cc_start: 0.7673 (pt0) cc_final: 0.7123 (mp0) REVERT: D 1036 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.6752 (ptp90) REVERT: D 1068 MET cc_start: 0.4730 (OUTLIER) cc_final: 0.4296 (ttt) REVERT: D 1146 MET cc_start: 0.6201 (ppp) cc_final: 0.5878 (pp-130) outliers start: 66 outliers final: 11 residues processed: 329 average time/residue: 0.5825 time to fit residues: 216.6568 Evaluate side-chains 254 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain A residue 877 VAL 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 739 LYS Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 742 GLN Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 1036 ARG Chi-restraints excluded: chain D residue 1068 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 92 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 226 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 211 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1144 GLN C 550 GLN C 570 HIS C 991 ASN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.204455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.161930 restraints weight = 21809.142| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.44 r_work: 0.3558 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 1.6405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 19372 Z= 0.201 Angle : 0.784 12.476 26244 Z= 0.398 Chirality : 0.045 0.222 3088 Planarity : 0.005 0.053 3256 Dihedral : 4.785 20.598 2568 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.33 % Allowed : 17.21 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.17), residues: 2332 helix: -0.42 (0.13), residues: 1631 sheet: -2.60 (0.73), residues: 40 loop : -2.20 (0.21), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 636 TYR 0.035 0.002 TYR A 621 PHE 0.020 0.002 PHE D 923 TRP 0.030 0.002 TRP B1061 HIS 0.015 0.002 HIS C 753 Details of bonding type rmsd covalent geometry : bond 0.00432 (19372) covalent geometry : angle 0.78447 (26244) hydrogen bonds : bond 0.04971 ( 912) hydrogen bonds : angle 4.39655 ( 2688) *********************** 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 436 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 366 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 686 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6870 (tptt) REVERT: A 721 ASN cc_start: 0.8387 (t0) cc_final: 0.8179 (m-40) REVERT: A 821 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.6276 (ppt170) REVERT: A 956 ILE cc_start: 0.6943 (OUTLIER) cc_final: 0.6243 (mt) REVERT: A 986 VAL cc_start: 0.9064 (m) cc_final: 0.8854 (t) REVERT: A 1032 GLU cc_start: 0.8343 (tt0) cc_final: 0.8009 (tp30) REVERT: A 1146 MET cc_start: 0.6374 (tmt) cc_final: 0.5913 (tmt) REVERT: B 580 ASN cc_start: 0.7130 (m-40) cc_final: 0.6298 (m-40) REVERT: B 664 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8074 (tt0) REVERT: B 686 LYS cc_start: 0.6613 (mtpp) cc_final: 0.6413 (mmtt) REVERT: C 730 GLU cc_start: 0.7568 (tp30) cc_final: 0.7163 (pm20) REVERT: C 1009 SER cc_start: 0.8720 (t) cc_final: 0.8482 (m) REVERT: C 1020 MET cc_start: 0.8864 (mmm) cc_final: 0.8597 (mmp) REVERT: C 1035 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7604 (ttp-170) REVERT: C 1120 ARG cc_start: 0.6493 (ttm170) cc_final: 0.6199 (ttp-170) REVERT: D 844 MET cc_start: 0.6448 (OUTLIER) cc_final: 0.6186 (tpp) REVERT: D 1009 SER cc_start: 0.8753 (t) cc_final: 0.8474 (m) REVERT: D 1020 MET cc_start: 0.8890 (mmm) cc_final: 0.8560 (mmp) REVERT: D 1032 GLU cc_start: 0.7770 (pt0) cc_final: 0.7466 (mp0) REVERT: D 1133 GLU cc_start: 0.7826 (tt0) cc_final: 0.7390 (tt0) outliers start: 70 outliers final: 12 residues processed: 405 average time/residue: 0.6232 time to fit residues: 283.4791 Evaluate side-chains 294 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 277 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain A residue 852 GLN Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain C residue 570 HIS Chi-restraints excluded: chain C residue 713 SER 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 1035 ARG Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 844 MET 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 223 optimal weight: 0.8980 chunk 42 optimal weight: 0.0980 chunk 131 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 chunk 182 optimal weight: 0.2980 chunk 119 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 HIS ** A 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN B 648 HIS B 967 ASN B1144 GLN C 550 GLN C 590 ASN C 608 ASN C 991 ASN C1046 GLN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1144 GLN ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 ASN D 753 HIS ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.198146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.157721 restraints weight = 21974.306| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.56 r_work: 0.3484 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 1.7167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19372 Z= 0.124 Angle : 0.632 12.098 26244 Z= 0.319 Chirality : 0.042 0.239 3088 Planarity : 0.004 0.045 3256 Dihedral : 4.243 17.694 2568 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.14 % Allowed : 22.34 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.17), residues: 2332 helix: 0.12 (0.13), residues: 1604 sheet: -2.27 (0.76), residues: 40 loop : -2.28 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 489 TYR 0.024 0.001 TYR C 838 PHE 0.022 0.001 PHE D 752 TRP 0.017 0.001 TRP B1061 HIS 0.017 0.001 HIS C 734 Details of bonding type rmsd covalent geometry : bond 0.00272 (19372) covalent geometry : angle 0.63156 (26244) hydrogen bonds : bond 0.03683 ( 912) hydrogen bonds : angle 3.98720 ( 2688) *********************** 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 346 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 301 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 956 ILE cc_start: 0.7007 (OUTLIER) cc_final: 0.6303 (mt) REVERT: A 1032 GLU cc_start: 0.8190 (tt0) cc_final: 0.7869 (tp30) REVERT: A 1146 MET cc_start: 0.6922 (tmt) cc_final: 0.6575 (tmt) REVERT: B 587 THR cc_start: 0.7328 (m) cc_final: 0.7070 (m) REVERT: B 593 HIS cc_start: 0.8044 (t70) cc_final: 0.7409 (m90) REVERT: B 664 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8163 (tt0) REVERT: B 725 THR cc_start: 0.8976 (p) cc_final: 0.8742 (p) REVERT: B 839 ILE cc_start: 0.7470 (mm) cc_final: 0.7140 (mp) REVERT: B 844 MET cc_start: 0.6243 (ppp) cc_final: 0.5952 (ppp) REVERT: B 1035 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7524 (mtt90) REVERT: B 1045 MET cc_start: 0.7020 (ptp) cc_final: 0.6581 (ttp) REVERT: C 514 MET cc_start: 0.5989 (tpp) cc_final: 0.5714 (tpp) REVERT: C 1009 SER cc_start: 0.8699 (t) cc_final: 0.8394 (m) REVERT: C 1020 MET cc_start: 0.8793 (mmm) cc_final: 0.8535 (mmp) REVERT: D 560 THR cc_start: 0.5546 (t) cc_final: 0.4889 (m) REVERT: D 562 GLU cc_start: 0.6363 (mt-10) cc_final: 0.6113 (mt-10) REVERT: D 772 SER cc_start: 0.8090 (m) cc_final: 0.7531 (t) REVERT: D 1009 SER cc_start: 0.8701 (t) cc_final: 0.8423 (m) REVERT: D 1032 GLU cc_start: 0.7522 (pt0) cc_final: 0.7247 (mp0) REVERT: D 1133 GLU cc_start: 0.7843 (tt0) cc_final: 0.7390 (tt0) outliers start: 45 outliers final: 11 residues processed: 332 average time/residue: 0.6281 time to fit residues: 233.9095 Evaluate side-chains 274 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 261 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 852 GLN Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 1035 ARG Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 887 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 186 optimal weight: 0.2980 chunk 209 optimal weight: 8.9990 chunk 196 optimal weight: 0.9990 chunk 173 optimal weight: 0.0670 chunk 29 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 112 optimal weight: 30.0000 chunk 235 optimal weight: 0.7980 chunk 192 optimal weight: 0.4980 chunk 124 optimal weight: 10.0000 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 HIS A 962 HIS ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN B 648 HIS B1144 GLN C 608 ASN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1144 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.195649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.145690 restraints weight = 21881.978| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.23 r_work: 0.3489 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 1.7661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19372 Z= 0.110 Angle : 0.622 16.055 26244 Z= 0.310 Chirality : 0.041 0.194 3088 Planarity : 0.004 0.042 3256 Dihedral : 4.053 16.705 2568 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.43 % Allowed : 24.19 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.18), residues: 2332 helix: 0.39 (0.14), residues: 1612 sheet: -2.24 (0.78), residues: 40 loop : -2.21 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1042 TYR 0.024 0.001 TYR A 620 PHE 0.019 0.001 PHE D 752 TRP 0.016 0.001 TRP B1061 HIS 0.016 0.001 HIS C 734 Details of bonding type rmsd covalent geometry : bond 0.00241 (19372) covalent geometry : angle 0.62180 (26244) hydrogen bonds : bond 0.03531 ( 912) hydrogen bonds : angle 3.85592 ( 2688) *********************** 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 325 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 295 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 913 PHE cc_start: 0.8851 (m-80) cc_final: 0.8645 (m-10) REVERT: A 956 ILE cc_start: 0.7056 (OUTLIER) cc_final: 0.6399 (mt) REVERT: A 959 GLN cc_start: 0.4674 (pm20) cc_final: 0.4038 (pt0) REVERT: A 1032 GLU cc_start: 0.8304 (tt0) cc_final: 0.7755 (tp30) REVERT: A 1127 ASP cc_start: 0.7847 (t0) cc_final: 0.7136 (m-30) REVERT: B 554 MET cc_start: 0.8827 (ptm) cc_final: 0.8577 (mtm) REVERT: B 559 GLU cc_start: 0.8327 (tp30) cc_final: 0.8047 (mt-10) REVERT: B 564 LEU cc_start: 0.7705 (mm) cc_final: 0.7451 (mm) REVERT: B 587 THR cc_start: 0.7513 (m) cc_final: 0.7276 (m) REVERT: B 593 HIS cc_start: 0.8054 (t70) cc_final: 0.7357 (m90) REVERT: B 664 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8153 (tt0) REVERT: B 730 GLU cc_start: 0.7987 (mm-30) cc_final: 0.6977 (pt0) REVERT: B 839 ILE cc_start: 0.7265 (mm) cc_final: 0.6955 (mp) REVERT: B 979 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8791 (ttt) REVERT: B 1035 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7487 (mtt90) REVERT: B 1045 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6806 (ttp) REVERT: B 1126 ARG cc_start: 0.7360 (ttp80) cc_final: 0.7074 (tmt170) REVERT: B 1146 MET cc_start: 0.6827 (ttt) cc_final: 0.6327 (ttt) REVERT: C 514 MET cc_start: 0.5863 (tpp) cc_final: 0.5384 (mmm) REVERT: C 641 MET cc_start: 0.6553 (OUTLIER) cc_final: 0.6158 (mpp) REVERT: C 1009 SER cc_start: 0.8644 (t) cc_final: 0.8337 (m) REVERT: C 1020 MET cc_start: 0.8819 (mmm) cc_final: 0.8587 (mmp) REVERT: D 560 THR cc_start: 0.5858 (t) cc_final: 0.5045 (m) REVERT: D 562 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6359 (mt-10) REVERT: D 909 PHE cc_start: 0.8535 (m-80) cc_final: 0.8286 (m-80) REVERT: D 913 PHE cc_start: 0.8757 (m-10) cc_final: 0.8522 (m-10) REVERT: D 1032 GLU cc_start: 0.7666 (pt0) cc_final: 0.7138 (mp0) REVERT: D 1133 GLU cc_start: 0.7984 (tt0) cc_final: 0.7580 (tt0) outliers start: 30 outliers final: 12 residues processed: 315 average time/residue: 0.5872 time to fit residues: 209.3616 Evaluate side-chains 277 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 260 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 979 MET Chi-restraints excluded: chain B residue 1035 ARG Chi-restraints excluded: chain B residue 1045 MET Chi-restraints excluded: chain C residue 519 ILE 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 580 ASN 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 26 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 113 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 134 optimal weight: 0.3980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 HIS A 863 ASN A1046 GLN B 568 HIS B 608 ASN B 648 HIS B1144 GLN C 590 ASN C 608 ASN D 491 ASN D 842 ASN ** 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 = 0.3915 r_free = 0.3915 target = 0.171813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129739 restraints weight = 21518.070| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.02 r_work: 0.3024 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 2.0267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 19372 Z= 0.221 Angle : 0.878 16.391 26244 Z= 0.439 Chirality : 0.050 0.255 3088 Planarity : 0.006 0.087 3256 Dihedral : 5.233 46.471 2568 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.28 % Allowed : 24.10 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.17), residues: 2332 helix: -0.27 (0.13), residues: 1636 sheet: -2.22 (0.81), residues: 40 loop : -2.66 (0.21), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 546 TYR 0.031 0.003 TYR A 617 PHE 0.021 0.002 PHE A 691 TRP 0.019 0.002 TRP D 867 HIS 0.026 0.002 HIS B 648 Details of bonding type rmsd covalent geometry : bond 0.00515 (19372) covalent geometry : angle 0.87785 (26244) hydrogen bonds : bond 0.06570 ( 912) hydrogen bonds : angle 4.50467 ( 2688) *********************** 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 459 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 411 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 559 GLU cc_start: 0.7287 (tm-30) cc_final: 0.7024 (tp30) REVERT: A 956 ILE cc_start: 0.7242 (OUTLIER) cc_final: 0.6793 (mt) REVERT: A 959 GLN cc_start: 0.5935 (pm20) cc_final: 0.5421 (mt0) REVERT: A 1032 GLU cc_start: 0.8226 (tt0) cc_final: 0.7785 (tp30) REVERT: A 1122 ARG cc_start: 0.7777 (ttp-110) cc_final: 0.7561 (ttp80) REVERT: A 1149 LYS cc_start: 0.8371 (tppp) cc_final: 0.7752 (mmtm) REVERT: B 563 LEU cc_start: 0.8448 (tp) cc_final: 0.8237 (tt) REVERT: B 593 HIS cc_start: 0.8329 (t70) cc_final: 0.7832 (m90) REVERT: B 615 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6811 (mm) REVERT: B 730 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7864 (pt0) REVERT: B 747 SER cc_start: 0.8969 (m) cc_final: 0.8544 (p) REVERT: B 758 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7723 (tp) REVERT: B 1035 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7660 (mtt90) REVERT: B 1045 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7661 (ttp) REVERT: C 492 THR cc_start: 0.6373 (m) cc_final: 0.6069 (p) REVERT: C 601 MET cc_start: 0.6377 (tmm) cc_final: 0.5188 (mtt) REVERT: C 1009 SER cc_start: 0.8776 (t) cc_final: 0.8544 (m) REVERT: D 478 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: D 517 LEU cc_start: 0.7165 (mp) cc_final: 0.6942 (tp) REVERT: D 559 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8104 (tt0) REVERT: D 562 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7058 (mt-10) REVERT: D 572 LEU cc_start: 0.5936 (mp) cc_final: 0.5716 (mt) REVERT: D 628 LEU cc_start: 0.8447 (tp) cc_final: 0.8246 (mt) REVERT: D 659 MET cc_start: 0.8860 (ptp) cc_final: 0.8526 (mpp) REVERT: D 668 ASP cc_start: 0.8073 (m-30) cc_final: 0.7671 (m-30) REVERT: D 730 GLU cc_start: 0.8117 (pm20) cc_final: 0.7905 (pm20) REVERT: D 1020 MET cc_start: 0.9059 (mmm) cc_final: 0.8834 (mmp) REVERT: D 1032 GLU cc_start: 0.7926 (pt0) cc_final: 0.7377 (mm-30) REVERT: D 1130 ARG cc_start: 0.7804 (mtm180) cc_final: 0.7254 (mtp180) REVERT: D 1133 GLU cc_start: 0.8177 (tt0) cc_final: 0.7726 (mt-10) outliers start: 48 outliers final: 13 residues processed: 440 average time/residue: 0.6058 time to fit residues: 299.2788 Evaluate side-chains 323 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 304 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1035 ARG Chi-restraints excluded: chain B residue 1045 MET Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain D residue 478 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 202 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 HIS B 534 ASN B1144 GLN C 823 ASN C 888 ASN C1046 GLN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 534 ASN D 693 GLN D 753 HIS D 777 ASN D 967 ASN D 991 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.165064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.117472 restraints weight = 21675.030| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.26 r_work: 0.3091 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 2.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 19372 Z= 0.174 Angle : 0.724 11.003 26244 Z= 0.364 Chirality : 0.045 0.200 3088 Planarity : 0.004 0.062 3256 Dihedral : 4.566 20.641 2568 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.47 % Allowed : 27.76 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.17), residues: 2332 helix: 0.21 (0.13), residues: 1616 sheet: -1.98 (0.85), residues: 40 loop : -2.41 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 546 TYR 0.031 0.002 TYR D 623 PHE 0.019 0.002 PHE B 504 TRP 0.012 0.001 TRP B1061 HIS 0.016 0.002 HIS C 734 Details of bonding type rmsd covalent geometry : bond 0.00421 (19372) covalent geometry : angle 0.72360 (26244) hydrogen bonds : bond 0.04734 ( 912) hydrogen bonds : angle 4.03701 ( 2688) ********************** 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 374 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 343 time to evaluate : 0.817 Fit side-chains REVERT: A 559 GLU cc_start: 0.7229 (tm-30) cc_final: 0.7017 (tp30) REVERT: A 588 MET cc_start: 0.8702 (mtp) cc_final: 0.8255 (mtp) REVERT: A 607 TYR cc_start: 0.8413 (m-80) cc_final: 0.8069 (m-80) REVERT: A 849 GLN cc_start: 0.6419 (tp40) cc_final: 0.5998 (tp40) REVERT: A 956 ILE cc_start: 0.7351 (OUTLIER) cc_final: 0.6942 (mt) REVERT: A 959 GLN cc_start: 0.6210 (pm20) cc_final: 0.5806 (mt0) REVERT: A 1032 GLU cc_start: 0.8202 (tt0) cc_final: 0.7651 (tp30) REVERT: A 1130 ARG cc_start: 0.7899 (ttp-170) cc_final: 0.7238 (mtm180) REVERT: A 1149 LYS cc_start: 0.8206 (tppp) cc_final: 0.7981 (mmpt) REVERT: B 519 ILE cc_start: 0.7902 (tp) cc_final: 0.7599 (pt) REVERT: B 563 LEU cc_start: 0.8532 (tp) cc_final: 0.8325 (tt) REVERT: B 593 HIS cc_start: 0.8480 (t70) cc_final: 0.7883 (m90) REVERT: B 612 MET cc_start: 0.7496 (tpt) cc_final: 0.6997 (ttt) REVERT: B 671 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7206 (mt) REVERT: B 730 GLU cc_start: 0.8735 (mm-30) cc_final: 0.7978 (pm20) REVERT: B 747 SER cc_start: 0.9026 (m) cc_final: 0.8602 (p) REVERT: B 1035 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7644 (mtt90) REVERT: B 1130 ARG cc_start: 0.7956 (ttp-170) cc_final: 0.7413 (ptm160) REVERT: B 1147 GLU cc_start: 0.8296 (tt0) cc_final: 0.7678 (tp30) REVERT: C 559 GLU cc_start: 0.8204 (tt0) cc_final: 0.7997 (tt0) REVERT: C 562 GLU cc_start: 0.7727 (tt0) cc_final: 0.7254 (mt-10) REVERT: C 601 MET cc_start: 0.7120 (tmm) cc_final: 0.6696 (mtt) REVERT: C 668 ASP cc_start: 0.8111 (m-30) cc_final: 0.7907 (m-30) REVERT: C 1009 SER cc_start: 0.8656 (t) cc_final: 0.8388 (m) REVERT: C 1039 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8457 (tt0) REVERT: D 530 GLN cc_start: 0.7153 (tt0) cc_final: 0.6651 (tp40) REVERT: D 534 ASN cc_start: 0.7514 (m-40) cc_final: 0.6799 (m110) REVERT: D 559 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8168 (tt0) REVERT: D 605 LEU cc_start: 0.8371 (mp) cc_final: 0.8130 (mp) REVERT: D 616 ASP cc_start: 0.7594 (t0) cc_final: 0.7373 (m-30) REVERT: D 628 LEU cc_start: 0.8422 (tp) cc_final: 0.8203 (mt) REVERT: D 659 MET cc_start: 0.9023 (ptp) cc_final: 0.8688 (ptp) REVERT: D 823 ASN cc_start: 0.7482 (m-40) cc_final: 0.6832 (m-40) REVERT: D 841 LEU cc_start: 0.7732 (tp) cc_final: 0.7529 (mm) REVERT: D 847 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6449 (tm) REVERT: D 1032 GLU cc_start: 0.7911 (pt0) cc_final: 0.7341 (mp0) REVERT: D 1130 ARG cc_start: 0.7896 (mtm180) cc_final: 0.7284 (mtp180) REVERT: D 1133 GLU cc_start: 0.8167 (tt0) cc_final: 0.7589 (mt-10) outliers start: 31 outliers final: 6 residues processed: 362 average time/residue: 0.5701 time to fit residues: 233.7248 Evaluate side-chains 304 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 293 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 1035 ARG Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1039 GLN Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 233 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 181 optimal weight: 0.1980 chunk 121 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN ** A 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 HIS ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 ASN C 608 ASN C 742 GLN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 HIS D 584 HIS D 967 ASN ** 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 = 0.3847 r_free = 0.3847 target = 0.166203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.126626 restraints weight = 21495.660| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.98 r_work: 0.3019 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 2.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19372 Z= 0.138 Angle : 0.677 11.431 26244 Z= 0.338 Chirality : 0.043 0.225 3088 Planarity : 0.004 0.056 3256 Dihedral : 4.287 19.449 2568 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.19 % Allowed : 29.13 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.18), residues: 2332 helix: 0.46 (0.13), residues: 1612 sheet: -2.01 (0.85), residues: 40 loop : -2.25 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 546 TYR 0.028 0.002 TYR A 620 PHE 0.011 0.001 PHE D 483 TRP 0.011 0.001 TRP B1061 HIS 0.023 0.001 HIS B 648 Details of bonding type rmsd covalent geometry : bond 0.00327 (19372) covalent geometry : angle 0.67667 (26244) hydrogen bonds : bond 0.04289 ( 912) hydrogen bonds : angle 3.93375 ( 2688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7152.64 seconds wall clock time: 122 minutes 53.91 seconds (7373.91 seconds total)