Starting phenix.real_space_refine on Sat Sep 28 09:40:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yks_33896/09_2024/7yks_33896.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yks_33896/09_2024/7yks_33896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yks_33896/09_2024/7yks_33896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yks_33896/09_2024/7yks_33896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yks_33896/09_2024/7yks_33896.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yks_33896/09_2024/7yks_33896.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.145 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 12308 2.51 5 N 3196 2.21 5 O 3344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18984 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4746 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 569} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 12 Restraints were copied for chains: C, B, D Time building chain proxies: 10.48, per 1000 atoms: 0.55 Number of scatterers: 18984 At special positions: 0 Unit cell: (112.11, 112.11, 145.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 3344 8.00 N 3196 7.00 C 12308 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.35 Conformation dependent library (CDL) restraints added in 2.5 seconds 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4568 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 8 sheets defined 70.1% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 479 through 487 removed outlier: 3.859A pdb=" N ARG A 486 " --> pdb=" O HIS A 482 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR A 487 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 497 Processing helix chain 'A' and resid 515 through 523 removed outlier: 3.624A pdb=" N SER A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 535 removed outlier: 3.887A pdb=" N LEU A 531 " --> pdb=" O ARG A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 removed outlier: 3.504A pdb=" N ALA A 552 " --> pdb=" O PRO A 548 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 568 removed outlier: 3.684A pdb=" N ILE A 561 " --> pdb=" O TYR A 557 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 589 removed outlier: 3.773A pdb=" N GLU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 599 removed outlier: 3.825A pdb=" N VAL A 597 " --> pdb=" O HIS A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 621 Processing helix chain 'A' and resid 623 through 632 removed outlier: 3.788A pdb=" N ALA A 629 " --> pdb=" O GLU A 625 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 632 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 642 Processing helix chain 'A' and resid 650 through 659 removed outlier: 4.044A pdb=" N ILE A 656 " --> pdb=" O THR A 652 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 669 removed outlier: 3.960A pdb=" N PHE A 663 " --> pdb=" O MET A 659 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 665 " --> pdb=" O LYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 726 removed outlier: 3.530A pdb=" N THR A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 733 Processing helix chain 'A' and resid 734 through 746 removed outlier: 3.683A pdb=" N LYS A 739 " --> pdb=" O PRO A 735 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 746 " --> pdb=" O GLN A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 777 removed outlier: 4.253A pdb=" N ASN A 756 " --> pdb=" O PHE A 752 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 763 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 769 " --> pdb=" O VAL A 765 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 842 removed outlier: 3.661A pdb=" N ILE A 835 " --> pdb=" O CYS A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 853 removed outlier: 3.732A pdb=" N TYR A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 876 Processing helix chain 'A' and resid 877 through 881 Processing helix chain 'A' and resid 888 through 905 removed outlier: 3.536A pdb=" N TYR A 892 " --> pdb=" O ASN A 888 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 893 " --> pdb=" O THR A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.741A pdb=" N ARG A 912 " --> pdb=" O PHE A 909 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE A 913 " --> pdb=" O LEU A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 913' Processing helix chain 'A' and resid 917 through 934 removed outlier: 3.588A pdb=" N VAL A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN A 928 " --> pdb=" O LEU A 924 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 932 " --> pdb=" O GLN A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 953 removed outlier: 3.751A pdb=" N SER A 953 " --> pdb=" O TYR A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 removed outlier: 3.996A pdb=" N SER A 964 " --> pdb=" O ASN A 961 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 965 " --> pdb=" O HIS A 962 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER A 966 " --> pdb=" O LEU A 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 961 through 966' Processing helix chain 'A' and resid 967 through 978 removed outlier: 3.587A pdb=" N LEU A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 989 Processing helix chain 'A' and resid 989 through 995 Processing helix chain 'A' and resid 1000 through 1015 removed outlier: 3.544A pdb=" N LEU A1006 " --> pdb=" O MET A1002 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A1014 " --> pdb=" O VAL A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1037 removed outlier: 3.512A pdb=" N GLY A1029 " --> pdb=" O GLY A1025 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A1036 " --> pdb=" O GLU A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1055 removed outlier: 4.064A pdb=" N LEU A1043 " --> pdb=" O GLN A1039 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS A1050 " --> pdb=" O GLN A1046 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A1055 " --> pdb=" O THR A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1066 removed outlier: 3.855A pdb=" N LEU A1062 " --> pdb=" O PRO A1058 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A1063 " --> pdb=" O HIS A1059 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG A1064 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A1065 " --> pdb=" O TRP A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1115 Processing helix chain 'A' and resid 1117 through 1146 removed outlier: 3.634A pdb=" N LEU A1138 " --> pdb=" O GLN A1134 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A1143 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A1144 " --> pdb=" O ARG A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 487 removed outlier: 3.860A pdb=" N ARG B 486 " --> pdb=" O HIS B 482 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 487 " --> pdb=" O PHE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 497 Processing helix chain 'B' and resid 515 through 523 removed outlier: 3.624A pdb=" N SER B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 535 removed outlier: 3.887A pdb=" N LEU B 531 " --> pdb=" O ARG B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 556 removed outlier: 3.503A pdb=" N ALA B 552 " --> pdb=" O PRO B 548 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 568 removed outlier: 3.684A pdb=" N ILE B 561 " --> pdb=" O TYR B 557 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 563 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 566 " --> pdb=" O GLU B 562 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 589 removed outlier: 3.773A pdb=" N GLU B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 599 removed outlier: 3.825A pdb=" N VAL B 597 " --> pdb=" O HIS B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 621 Processing helix chain 'B' and resid 623 through 632 removed outlier: 3.788A pdb=" N ALA B 629 " --> pdb=" O GLU B 625 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 632 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 642 Processing helix chain 'B' and resid 650 through 659 removed outlier: 4.044A pdb=" N ILE B 656 " --> pdb=" O THR B 652 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 669 removed outlier: 3.959A pdb=" N PHE B 663 " --> pdb=" O MET B 659 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 665 " --> pdb=" O LYS B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 726 removed outlier: 3.528A pdb=" N THR B 725 " --> pdb=" O ASN B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 733 Processing helix chain 'B' and resid 734 through 746 removed outlier: 3.682A pdb=" N LYS B 739 " --> pdb=" O PRO B 735 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN B 746 " --> pdb=" O GLN B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 777 removed outlier: 4.253A pdb=" N ASN B 756 " --> pdb=" O PHE B 752 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 763 " --> pdb=" O ILE B 759 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 765 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 769 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN B 776 " --> pdb=" O SER B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 842 removed outlier: 3.662A pdb=" N ILE B 835 " --> pdb=" O CYS B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 853 removed outlier: 3.732A pdb=" N TYR B 851 " --> pdb=" O LEU B 847 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 852 " --> pdb=" O ILE B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 876 Processing helix chain 'B' and resid 877 through 881 Processing helix chain 'B' and resid 888 through 905 removed outlier: 3.535A pdb=" N TYR B 892 " --> pdb=" O ASN B 888 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 893 " --> pdb=" O THR B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 913 removed outlier: 3.741A pdb=" N ARG B 912 " --> pdb=" O PHE B 909 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE B 913 " --> pdb=" O LEU B 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 909 through 913' Processing helix chain 'B' and resid 917 through 934 removed outlier: 3.588A pdb=" N VAL B 921 " --> pdb=" O GLY B 917 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN B 928 " --> pdb=" O LEU B 924 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS B 932 " --> pdb=" O GLN B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 953 removed outlier: 3.751A pdb=" N SER B 953 " --> pdb=" O TYR B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 966 removed outlier: 3.996A pdb=" N SER B 964 " --> pdb=" O ASN B 961 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 965 " --> pdb=" O HIS B 962 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER B 966 " --> pdb=" O LEU B 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 961 through 966' Processing helix chain 'B' and resid 967 through 978 removed outlier: 3.587A pdb=" N LEU B 973 " --> pdb=" O PRO B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 989 Processing helix chain 'B' and resid 989 through 995 Processing helix chain 'B' and resid 1000 through 1015 removed outlier: 3.543A pdb=" N LEU B1006 " --> pdb=" O MET B1002 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B1014 " --> pdb=" O VAL B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1037 removed outlier: 3.512A pdb=" N GLY B1029 " --> pdb=" O GLY B1025 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B1036 " --> pdb=" O GLU B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1037 through 1055 removed outlier: 4.064A pdb=" N LEU B1043 " --> pdb=" O GLN B1039 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS B1050 " --> pdb=" O GLN B1046 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1066 removed outlier: 3.854A pdb=" N LEU B1062 " --> pdb=" O PRO B1058 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B1063 " --> pdb=" O HIS B1059 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG B1064 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL B1065 " --> pdb=" O TRP B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1110 through 1115 Processing helix chain 'B' and resid 1117 through 1146 removed outlier: 3.632A pdb=" N LEU B1138 " --> pdb=" O GLN B1134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B1143 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B1144 " --> pdb=" O ARG B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 487 removed outlier: 3.859A pdb=" N ARG C 486 " --> pdb=" O HIS C 482 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR C 487 " --> pdb=" O PHE C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 497 Processing helix chain 'C' and resid 515 through 523 removed outlier: 3.624A pdb=" N SER C 521 " --> pdb=" O LEU C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 535 removed outlier: 3.887A pdb=" N LEU C 531 " --> pdb=" O ARG C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 556 removed outlier: 3.504A pdb=" N ALA C 552 " --> pdb=" O PRO C 548 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.684A pdb=" N ILE C 561 " --> pdb=" O TYR C 557 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 563 " --> pdb=" O GLU C 559 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 566 " --> pdb=" O GLU C 562 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 567 " --> pdb=" O LEU C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 589 removed outlier: 3.773A pdb=" N GLU C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 599 removed outlier: 3.825A pdb=" N VAL C 597 " --> pdb=" O HIS C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 621 Processing helix chain 'C' and resid 623 through 632 removed outlier: 3.788A pdb=" N ALA C 629 " --> pdb=" O GLU C 625 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR C 632 " --> pdb=" O LEU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 642 Processing helix chain 'C' and resid 650 through 659 removed outlier: 4.044A pdb=" N ILE C 656 " --> pdb=" O THR C 652 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C 657 " --> pdb=" O LEU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 669 removed outlier: 3.960A pdb=" N PHE C 663 " --> pdb=" O MET C 659 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA C 665 " --> pdb=" O LYS C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 726 removed outlier: 3.529A pdb=" N THR C 725 " --> pdb=" O ASN C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 733 Processing helix chain 'C' and resid 734 through 746 removed outlier: 3.683A pdb=" N LYS C 739 " --> pdb=" O PRO C 735 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN C 746 " --> pdb=" O GLN C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 777 removed outlier: 4.253A pdb=" N ASN C 756 " --> pdb=" O PHE C 752 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 763 " --> pdb=" O ILE C 759 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL C 765 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 769 " --> pdb=" O VAL C 765 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN C 776 " --> pdb=" O SER C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 842 removed outlier: 3.662A pdb=" N ILE C 835 " --> pdb=" O CYS C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 853 removed outlier: 3.731A pdb=" N TYR C 851 " --> pdb=" O LEU C 847 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN C 852 " --> pdb=" O ILE C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 876 Processing helix chain 'C' and resid 877 through 881 Processing helix chain 'C' and resid 888 through 905 removed outlier: 3.535A pdb=" N TYR C 892 " --> pdb=" O ASN C 888 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 893 " --> pdb=" O THR C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 913 removed outlier: 3.742A pdb=" N ARG C 912 " --> pdb=" O PHE C 909 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE C 913 " --> pdb=" O LEU C 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 909 through 913' Processing helix chain 'C' and resid 917 through 934 removed outlier: 3.588A pdb=" N VAL C 921 " --> pdb=" O GLY C 917 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN C 928 " --> pdb=" O LEU C 924 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS C 932 " --> pdb=" O GLN C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 953 removed outlier: 3.750A pdb=" N SER C 953 " --> pdb=" O TYR C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 966 removed outlier: 3.996A pdb=" N SER C 964 " --> pdb=" O ASN C 961 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE C 965 " --> pdb=" O HIS C 962 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER C 966 " --> pdb=" O LEU C 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 961 through 966' Processing helix chain 'C' and resid 967 through 978 removed outlier: 3.587A pdb=" N LEU C 973 " --> pdb=" O PRO C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 989 Processing helix chain 'C' and resid 989 through 995 Processing helix chain 'C' and resid 1000 through 1015 removed outlier: 3.543A pdb=" N LEU C1006 " --> pdb=" O MET C1002 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C1014 " --> pdb=" O VAL C1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1037 removed outlier: 3.512A pdb=" N GLY C1029 " --> pdb=" O GLY C1025 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C1036 " --> pdb=" O GLU C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1037 through 1055 removed outlier: 4.064A pdb=" N LEU C1043 " --> pdb=" O GLN C1039 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS C1050 " --> pdb=" O GLN C1046 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C1055 " --> pdb=" O THR C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1058 through 1066 removed outlier: 3.855A pdb=" N LEU C1062 " --> pdb=" O PRO C1058 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN C1063 " --> pdb=" O HIS C1059 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG C1064 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C1065 " --> pdb=" O TRP C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1110 through 1115 Processing helix chain 'C' and resid 1117 through 1146 removed outlier: 3.634A pdb=" N LEU C1138 " --> pdb=" O GLN C1134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C1143 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN C1144 " --> pdb=" O ARG C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 487 removed outlier: 3.860A pdb=" N ARG D 486 " --> pdb=" O HIS D 482 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR D 487 " --> pdb=" O PHE D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 497 Processing helix chain 'D' and resid 515 through 523 removed outlier: 3.624A pdb=" N SER D 521 " --> pdb=" O LEU D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 535 removed outlier: 3.887A pdb=" N LEU D 531 " --> pdb=" O ARG D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 556 removed outlier: 3.504A pdb=" N ALA D 552 " --> pdb=" O PRO D 548 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 568 removed outlier: 3.684A pdb=" N ILE D 561 " --> pdb=" O TYR D 557 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU D 563 " --> pdb=" O GLU D 559 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER D 566 " --> pdb=" O GLU D 562 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 567 " --> pdb=" O LEU D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 589 removed outlier: 3.773A pdb=" N GLU D 589 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 599 removed outlier: 3.824A pdb=" N VAL D 597 " --> pdb=" O HIS D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 621 Processing helix chain 'D' and resid 623 through 632 removed outlier: 3.789A pdb=" N ALA D 629 " --> pdb=" O GLU D 625 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET D 630 " --> pdb=" O ALA D 626 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR D 632 " --> pdb=" O LEU D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 650 through 659 removed outlier: 4.043A pdb=" N ILE D 656 " --> pdb=" O THR D 652 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA D 657 " --> pdb=" O LEU D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 659 through 669 removed outlier: 3.959A pdb=" N PHE D 663 " --> pdb=" O MET D 659 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA D 665 " --> pdb=" O LYS D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 726 removed outlier: 3.530A pdb=" N THR D 725 " --> pdb=" O ASN D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 733 Processing helix chain 'D' and resid 734 through 746 removed outlier: 3.682A pdb=" N LYS D 739 " --> pdb=" O PRO D 735 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN D 746 " --> pdb=" O GLN D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 777 removed outlier: 4.252A pdb=" N ASN D 756 " --> pdb=" O PHE D 752 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE D 763 " --> pdb=" O ILE D 759 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D 765 " --> pdb=" O SER D 761 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE D 769 " --> pdb=" O VAL D 765 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 842 removed outlier: 3.662A pdb=" N ILE D 835 " --> pdb=" O CYS D 831 " (cutoff:3.500A) Processing helix chain 'D' and resid 847 through 853 removed outlier: 3.731A pdb=" N TYR D 851 " --> pdb=" O LEU D 847 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN D 852 " --> pdb=" O ILE D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 876 Processing helix chain 'D' and resid 877 through 881 Processing helix chain 'D' and resid 888 through 905 removed outlier: 3.536A pdb=" N TYR D 892 " --> pdb=" O ASN D 888 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER D 893 " --> pdb=" O THR D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 909 through 913 removed outlier: 3.741A pdb=" N ARG D 912 " --> pdb=" O PHE D 909 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE D 913 " --> pdb=" O LEU D 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 909 through 913' Processing helix chain 'D' and resid 917 through 934 removed outlier: 3.588A pdb=" N VAL D 921 " --> pdb=" O GLY D 917 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN D 928 " --> pdb=" O LEU D 924 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS D 932 " --> pdb=" O GLN D 928 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 953 removed outlier: 3.751A pdb=" N SER D 953 " --> pdb=" O TYR D 949 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 966 removed outlier: 3.996A pdb=" N SER D 964 " --> pdb=" O ASN D 961 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE D 965 " --> pdb=" O HIS D 962 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER D 966 " --> pdb=" O LEU D 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 961 through 966' Processing helix chain 'D' and resid 967 through 978 removed outlier: 3.588A pdb=" N LEU D 973 " --> pdb=" O PRO D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 989 Processing helix chain 'D' and resid 989 through 995 Processing helix chain 'D' and resid 1000 through 1015 removed outlier: 3.543A pdb=" N LEU D1006 " --> pdb=" O MET D1002 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D1014 " --> pdb=" O VAL D1010 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1037 removed outlier: 3.512A pdb=" N GLY D1029 " --> pdb=" O GLY D1025 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D1036 " --> pdb=" O GLU D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1037 through 1055 removed outlier: 4.065A pdb=" N LEU D1043 " --> pdb=" O GLN D1039 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS D1050 " --> pdb=" O GLN D1046 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG D1055 " --> pdb=" O THR D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1066 removed outlier: 3.854A pdb=" N LEU D1062 " --> pdb=" O PRO D1058 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN D1063 " --> pdb=" O HIS D1059 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG D1064 " --> pdb=" O VAL D1060 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL D1065 " --> pdb=" O TRP D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1110 through 1115 Processing helix chain 'D' and resid 1117 through 1146 removed outlier: 3.634A pdb=" N LEU D1138 " --> pdb=" O GLN D1134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D1143 " --> pdb=" O VAL D1139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN D1144 " --> pdb=" O ARG D1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 671 through 673 Processing sheet with id=AA2, first strand: chain 'A' and resid 820 through 821 removed outlier: 4.732A pdb=" N GLU A 820 " --> pdb=" O ILE A 887 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 671 through 673 Processing sheet with id=AA4, first strand: chain 'B' and resid 820 through 821 removed outlier: 4.732A pdb=" N GLU B 820 " --> pdb=" O ILE B 887 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 671 through 673 Processing sheet with id=AA6, first strand: chain 'C' and resid 820 through 821 removed outlier: 4.732A pdb=" N GLU C 820 " --> pdb=" O ILE C 887 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 671 through 673 Processing sheet with id=AA8, first strand: chain 'D' and resid 820 through 821 removed outlier: 4.732A pdb=" N GLU D 820 " --> pdb=" O ILE D 887 " (cutoff:3.500A) 912 hydrogen bonds defined for protein. 2688 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.53 Time building geometry restraints manager: 5.19 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: 0.00 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 40.860 Find NCS groups from input model: 0.550 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: 0.010 Load rotamer database and sin/cos tables:11.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.880 ------------------------------------------------------------------------------- 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= 0.504 Angle : 0.995 11.164 26244 Z= 0.515 Chirality : 0.061 0.250 3088 Planarity : 0.007 0.065 3256 Dihedral : 10.268 74.042 7156 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.69 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.58 (0.10), residues: 2332 helix: -4.65 (0.05), residues: 1568 sheet: -2.11 (0.81), residues: 40 loop : -3.17 (0.18), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 867 HIS 0.008 0.002 HIS D 518 PHE 0.033 0.003 PHE A 948 TYR 0.028 0.003 TYR B 623 ARG 0.014 0.001 ARG D1123 *********************** 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 fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 855 LEU cc_start: 0.6134 (mm) cc_final: 0.5904 (tm) REVERT: B 606 VAL cc_start: 0.3908 (m) cc_final: 0.3625 (p) REVERT: B 655 LEU cc_start: 0.2730 (mt) cc_final: 0.2430 (mt) REVERT: C 580 ASN cc_start: 0.2991 (m-40) cc_final: 0.2787 (t0) REVERT: D 726 HIS cc_start: 0.3912 (m-70) cc_final: 0.1837 (m170) REVERT: D 1061 TRP cc_start: 0.3381 (t-100) cc_final: 0.3011 (t60) outliers start: 0 outliers final: 2 residues processed: 257 average time/residue: 1.2346 time to fit residues: 359.4964 Evaluate side-chains 192 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain D residue 675 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 9.9990 chunk 178 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 120 optimal weight: 0.2980 chunk 95 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 112 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 214 optimal weight: 0.0970 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN A 518 HIS ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 GLN A 753 HIS A 882 GLN A 962 HIS A 991 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 HIS B 491 ASN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 HIS B 738 GLN B 746 ASN B 888 ASN B 962 HIS B 991 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 HIS C 570 HIS C 608 ASN C 726 HIS C 742 GLN C 753 HIS C 991 ASN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1144 GLN D 491 ASN ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 GLN D 753 HIS D 991 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1144 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2132 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19372 Z= 0.206 Angle : 0.681 8.499 26244 Z= 0.352 Chirality : 0.043 0.153 3088 Planarity : 0.006 0.056 3256 Dihedral : 5.339 40.794 2573 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.76 % Allowed : 8.98 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.32 (0.14), residues: 2332 helix: -2.73 (0.10), residues: 1628 sheet: -2.80 (0.79), residues: 40 loop : -2.64 (0.21), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B1061 HIS 0.008 0.001 HIS A 568 PHE 0.024 0.002 PHE C1005 TYR 0.013 0.002 TYR B 617 ARG 0.006 0.001 ARG C 728 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4664 Ramachandran restraints generated. 2332 Oldfield, 0 Emsley, 2332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 220 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 588 MET cc_start: 0.3576 (OUTLIER) cc_final: 0.3061 (ttm) REVERT: A 691 PHE cc_start: 0.3860 (OUTLIER) cc_final: 0.3405 (t80) REVERT: A 922 MET cc_start: 0.4112 (OUTLIER) cc_final: 0.3438 (tpp) REVERT: A 993 TYR cc_start: 0.6093 (t80) cc_final: 0.5227 (t80) REVERT: A 1131 MET cc_start: 0.2573 (OUTLIER) cc_final: 0.0325 (mmm) REVERT: B 1002 MET cc_start: 0.2395 (OUTLIER) cc_final: 0.1447 (ppp) REVERT: B 1012 MET cc_start: 0.2841 (OUTLIER) cc_final: 0.2325 (tpp) REVERT: C 554 MET cc_start: 0.1347 (mtt) cc_final: -0.0546 (tpt) REVERT: C 876 MET cc_start: 0.0221 (mtp) cc_final: -0.0414 (ptt) REVERT: C 979 MET cc_start: 0.2193 (ppp) cc_final: 0.1846 (ppp) REVERT: D 598 LEU cc_start: 0.0167 (OUTLIER) cc_final: -0.0456 (mt) REVERT: D 641 MET cc_start: 0.2676 (mmm) cc_final: 0.2092 (pp-130) REVERT: D 992 THR cc_start: 0.4020 (OUTLIER) cc_final: 0.3680 (t) outliers start: 37 outliers final: 10 residues processed: 235 average time/residue: 1.2358 time to fit residues: 329.7778 Evaluate side-chains 195 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 MET Chi-restraints excluded: chain A residue 691 PHE Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 1002 MET Chi-restraints excluded: chain B residue 1012 MET Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 848 ILE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 978 MET Chi-restraints excluded: chain D residue 992 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 178 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 214 optimal weight: 1.9990 chunk 231 optimal weight: 0.6980 chunk 191 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 172 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 HIS ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 HIS ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 568 HIS ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 GLN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS C 491 ASN C 518 HIS ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 GLN C 753 HIS C1135 GLN D 518 HIS ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1136 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4192 moved from start: 0.7439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.149 19372 Z= 0.305 Angle : 0.843 18.659 26244 Z= 0.428 Chirality : 0.047 0.263 3088 Planarity : 0.007 0.118 3256 Dihedral : 5.239 45.478 2571 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.23 % Allowed : 10.98 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.16), residues: 2332 helix: -1.25 (0.12), residues: 1580 sheet: -2.92 (0.60), residues: 60 loop : -2.33 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 745 HIS 0.016 0.002 HIS B 753 PHE 0.040 0.003 PHE A 965 TYR 0.029 0.002 TYR D 620 ARG 0.011 0.001 ARG D 821 *********************** 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 312 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 244 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 GLU cc_start: 0.4730 (OUTLIER) cc_final: 0.4435 (mt-10) REVERT: A 641 MET cc_start: 0.2819 (pp-130) cc_final: 0.2613 (pp-130) REVERT: A 845 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.5224 (tpp-160) REVERT: A 983 LEU cc_start: 0.6423 (tt) cc_final: 0.6181 (tt) REVERT: A 1131 MET cc_start: 0.4527 (OUTLIER) cc_final: 0.1294 (mmm) REVERT: B 1015 MET cc_start: 0.8634 (tpp) cc_final: 0.8352 (tpt) REVERT: B 1146 MET cc_start: 0.0994 (OUTLIER) cc_final: 0.0337 (ttt) REVERT: C 630 MET cc_start: 0.1339 (tpp) cc_final: 0.0929 (ttt) REVERT: C 950 ILE cc_start: 0.7167 (mm) cc_final: 0.6466 (mt) REVERT: D 560 THR cc_start: 0.2489 (t) cc_final: 0.1965 (m) REVERT: D 675 ASN cc_start: 0.3369 (p0) cc_final: 0.2805 (m-40) REVERT: D 1012 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.6460 (ptt) outliers start: 68 outliers final: 11 residues processed: 281 average time/residue: 1.1498 time to fit residues: 370.4444 Evaluate side-chains 209 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 193 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 845 ARG Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 876 MET Chi-restraints excluded: chain B residue 1032 GLU Chi-restraints excluded: chain B residue 1146 MET Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain D residue 1012 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 6.9990 chunk 161 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 228 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS A 491 ASN A 540 HIS ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN A 911 GLN A1050 HIS ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 ASN B 543 HIS B 568 HIS B 593 HIS B 753 HIS B 911 GLN ** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 608 ASN C 638 ASN C 742 GLN ** C 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 911 GLN D 962 HIS ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 1.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.191 19372 Z= 0.374 Angle : 0.927 14.328 26244 Z= 0.464 Chirality : 0.050 0.277 3088 Planarity : 0.007 0.087 3256 Dihedral : 5.717 43.287 2571 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.47 % Allowed : 13.36 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.16), residues: 2332 helix: -1.34 (0.12), residues: 1648 sheet: -2.39 (0.65), residues: 60 loop : -2.40 (0.21), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C1061 HIS 0.015 0.002 HIS D 962 PHE 0.034 0.003 PHE D 752 TYR 0.031 0.003 TYR D 621 ARG 0.010 0.001 ARG A 845 *********************** 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 414 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 341 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 933 VAL cc_start: 0.7443 (OUTLIER) cc_final: 0.7163 (t) REVERT: A 956 ILE cc_start: 0.5827 (OUTLIER) cc_final: 0.4940 (mt) REVERT: B 498 ASP cc_start: 0.4688 (t0) cc_final: 0.4202 (m-30) REVERT: B 1009 SER cc_start: 0.8597 (t) cc_final: 0.8276 (m) REVERT: B 1146 MET cc_start: 0.2278 (pmm) cc_final: 0.1136 (ttt) REVERT: C 500 GLU cc_start: 0.3527 (tp30) cc_final: 0.2691 (mm-30) REVERT: C 914 ASP cc_start: 0.6621 (m-30) cc_final: 0.6381 (m-30) REVERT: C 1000 VAL cc_start: 0.7711 (OUTLIER) cc_final: 0.7490 (m) REVERT: C 1068 MET cc_start: 0.5879 (OUTLIER) cc_final: 0.5676 (ppp) REVERT: D 560 THR cc_start: 0.3916 (t) cc_final: 0.3514 (m) REVERT: D 601 MET cc_start: 0.5212 (tmm) cc_final: 0.4644 (tmm) outliers start: 73 outliers final: 12 residues processed: 374 average time/residue: 1.2200 time to fit residues: 515.9530 Evaluate side-chains 251 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 235 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1068 MET Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 844 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 194 optimal weight: 0.2980 chunk 157 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 204 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN A 590 ASN A 648 HIS A 753 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN A1046 GLN ** B 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1136 HIS C 570 HIS C1039 GLN C1136 HIS D 525 HIS D 777 ASN D 911 GLN D1121 GLN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 1.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19372 Z= 0.202 Angle : 0.670 11.826 26244 Z= 0.336 Chirality : 0.042 0.222 3088 Planarity : 0.004 0.057 3256 Dihedral : 4.487 20.618 2568 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.95 % Allowed : 17.40 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.17), residues: 2332 helix: -0.49 (0.13), residues: 1632 sheet: -1.99 (0.69), residues: 60 loop : -2.33 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 745 HIS 0.016 0.001 HIS B 648 PHE 0.019 0.001 PHE D 752 TYR 0.023 0.001 TYR D 623 ARG 0.006 0.001 ARG C1036 *********************** 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 346 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 284 time to evaluate : 2.058 Fit side-chains revert: symmetry clash REVERT: A 617 TYR cc_start: 0.5029 (t80) cc_final: 0.4387 (t80) REVERT: A 931 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8157 (tp) REVERT: B 498 ASP cc_start: 0.4967 (t0) cc_final: 0.4758 (m-30) REVERT: B 589 GLU cc_start: 0.5814 (OUTLIER) cc_final: 0.5535 (tp30) REVERT: B 905 ARG cc_start: 0.7813 (tpt-90) cc_final: 0.7245 (ttt90) REVERT: B 1009 SER cc_start: 0.8597 (t) cc_final: 0.8371 (m) REVERT: B 1030 ASP cc_start: 0.7833 (m-30) cc_final: 0.7613 (m-30) REVERT: D 560 THR cc_start: 0.4134 (t) cc_final: 0.3694 (m) outliers start: 62 outliers final: 14 residues processed: 321 average time/residue: 1.2488 time to fit residues: 453.1455 Evaluate side-chains 248 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 232 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 589 GLU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain C residue 570 HIS Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 659 MET Chi-restraints excluded: chain D residue 861 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.9990 chunk 205 optimal weight: 10.0000 chunk 45 optimal weight: 0.0870 chunk 133 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 228 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 75 optimal weight: 0.2980 chunk 119 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 HIS ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 HIS ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN ** B 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 882 GLN B1144 GLN ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 608 ASN ** C 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1039 GLN ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 GLN D 753 HIS D 962 HIS ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 1.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 19372 Z= 0.186 Angle : 0.622 11.395 26244 Z= 0.317 Chirality : 0.041 0.154 3088 Planarity : 0.004 0.082 3256 Dihedral : 4.253 18.911 2568 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.66 % Allowed : 18.87 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.17), residues: 2332 helix: -0.14 (0.13), residues: 1660 sheet: -1.86 (0.81), residues: 40 loop : -2.14 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 745 HIS 0.014 0.001 HIS C 570 PHE 0.011 0.001 PHE D 923 TYR 0.025 0.001 TYR D 623 ARG 0.015 0.000 ARG B 546 *********************** 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 326 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 270 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 589 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7140 (tp30) REVERT: A 617 TYR cc_start: 0.5469 (t80) cc_final: 0.4553 (t80) REVERT: A 621 TYR cc_start: 0.5660 (OUTLIER) cc_final: 0.5244 (t80) REVERT: A 931 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8125 (tp) REVERT: A 956 ILE cc_start: 0.6189 (OUTLIER) cc_final: 0.5546 (mt) REVERT: A 1122 ARG cc_start: 0.6670 (ttp-110) cc_final: 0.6105 (ttp-110) REVERT: B 599 MET cc_start: 0.5274 (OUTLIER) cc_final: 0.5067 (ttm) REVERT: B 983 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8727 (mt) REVERT: C 1120 ARG cc_start: 0.5797 (OUTLIER) cc_final: 0.5537 (ttm110) REVERT: D 560 THR cc_start: 0.4614 (t) cc_final: 0.4193 (m) REVERT: D 1133 GLU cc_start: 0.6653 (tt0) cc_final: 0.6401 (tt0) outliers start: 56 outliers final: 16 residues processed: 303 average time/residue: 1.1379 time to fit residues: 394.7134 Evaluate side-chains 266 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 243 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 852 GLN Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 599 MET Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1120 ARG Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 1049 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 192 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 138 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN A 753 HIS B 525 HIS B 540 HIS B 568 HIS ** B 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 608 ASN ** C 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1137 HIS C1144 GLN ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 GLN D1050 HIS ** D1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 1.7341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 19372 Z= 0.251 Angle : 0.734 14.400 26244 Z= 0.372 Chirality : 0.045 0.302 3088 Planarity : 0.005 0.061 3256 Dihedral : 4.482 24.496 2568 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.71 % Allowed : 19.63 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.17), residues: 2332 helix: -0.05 (0.13), residues: 1644 sheet: -1.89 (0.81), residues: 40 loop : -2.27 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 903 HIS 0.014 0.002 HIS C 518 PHE 0.032 0.002 PHE D 766 TYR 0.027 0.002 TYR D 623 ARG 0.007 0.001 ARG B 546 *********************** 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 426 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 369 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 MET cc_start: 0.8448 (mmt) cc_final: 0.8126 (mmt) REVERT: A 841 LEU cc_start: 0.7777 (tm) cc_final: 0.7450 (tp) REVERT: A 910 LEU cc_start: 0.8886 (tt) cc_final: 0.8592 (mp) REVERT: A 931 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8408 (tp) REVERT: A 956 ILE cc_start: 0.7008 (OUTLIER) cc_final: 0.6468 (mt) REVERT: A 1020 MET cc_start: 0.8597 (mmm) cc_final: 0.8351 (mmp) REVERT: B 554 MET cc_start: 0.8767 (ptm) cc_final: 0.8482 (mtm) REVERT: B 599 MET cc_start: 0.6108 (OUTLIER) cc_final: 0.5856 (ttm) REVERT: B 686 LYS cc_start: 0.7192 (mtpp) cc_final: 0.6896 (mtpt) REVERT: B 839 ILE cc_start: 0.7744 (mm) cc_final: 0.7509 (mp) REVERT: B 845 ARG cc_start: 0.6996 (tpp80) cc_final: 0.6721 (ttm170) REVERT: B 986 VAL cc_start: 0.9014 (m) cc_final: 0.8758 (t) REVERT: C 659 MET cc_start: 0.5173 (OUTLIER) cc_final: 0.4723 (ppp) REVERT: C 661 LYS cc_start: 0.6028 (mmtt) cc_final: 0.5822 (pttp) REVERT: D 560 THR cc_start: 0.6304 (t) cc_final: 0.5929 (m) REVERT: D 1020 MET cc_start: 0.8596 (mmm) cc_final: 0.8385 (mmp) REVERT: D 1126 ARG cc_start: 0.7390 (ttt-90) cc_final: 0.7073 (ttt-90) REVERT: D 1133 GLU cc_start: 0.7269 (tt0) cc_final: 0.6938 (mt-10) outliers start: 57 outliers final: 13 residues processed: 399 average time/residue: 1.3092 time to fit residues: 587.3936 Evaluate side-chains 307 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 290 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 852 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 599 MET Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 1071 ILE Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1129 SER Chi-restraints excluded: chain C residue 659 MET 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 861 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 206 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 693 GLN A 753 HIS ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 HIS ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 HIS B 648 HIS ** C 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1144 GLN ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN D 738 GLN D 991 ASN D1046 GLN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1144 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 1.8079 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= 0.193 Angle : 0.655 12.849 26244 Z= 0.330 Chirality : 0.042 0.266 3088 Planarity : 0.004 0.048 3256 Dihedral : 4.236 26.063 2568 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.47 % Allowed : 23.00 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.17), residues: 2332 helix: 0.14 (0.13), residues: 1688 sheet: -1.76 (0.84), residues: 40 loop : -2.60 (0.21), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 867 HIS 0.008 0.001 HIS B 648 PHE 0.016 0.001 PHE D 752 TYR 0.026 0.002 TYR B1073 ARG 0.008 0.001 ARG B1126 *********************** 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 389 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 337 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 TYR cc_start: 0.4922 (m-10) cc_final: 0.4436 (m-80) REVERT: A 686 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7959 (ptmm) REVERT: A 841 LEU cc_start: 0.7752 (tm) cc_final: 0.7469 (tp) REVERT: A 847 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.6954 (tp) REVERT: A 849 GLN cc_start: 0.6710 (tp40) cc_final: 0.6486 (tp40) REVERT: A 914 ASP cc_start: 0.6875 (t0) cc_final: 0.6665 (m-30) REVERT: A 931 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8350 (tp) REVERT: A 956 ILE cc_start: 0.7189 (OUTLIER) cc_final: 0.6672 (mt) REVERT: A 1020 MET cc_start: 0.8554 (mmm) cc_final: 0.8329 (mmp) REVERT: B 554 MET cc_start: 0.8707 (ptm) cc_final: 0.8355 (mtm) REVERT: B 730 GLU cc_start: 0.7644 (tp30) cc_final: 0.7261 (pt0) REVERT: B 839 ILE cc_start: 0.7686 (mm) cc_final: 0.7437 (mp) REVERT: B 986 VAL cc_start: 0.9044 (m) cc_final: 0.8797 (t) REVERT: B 1122 ARG cc_start: 0.7431 (ttp80) cc_final: 0.7041 (ptm160) REVERT: B 1130 ARG cc_start: 0.7366 (ttp-170) cc_final: 0.7087 (ptm160) REVERT: C 839 ILE cc_start: 0.7941 (mp) cc_final: 0.7526 (mp) REVERT: D 1126 ARG cc_start: 0.7417 (ttt-90) cc_final: 0.7094 (ttt180) REVERT: D 1133 GLU cc_start: 0.7324 (tt0) cc_final: 0.7024 (mt-10) outliers start: 52 outliers final: 15 residues processed: 366 average time/residue: 1.2505 time to fit residues: 518.4398 Evaluate side-chains 310 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 291 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain B residue 486 ARG Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 211 optimal weight: 0.0070 chunk 127 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 166 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 200 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 224 optimal weight: 0.9980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 HIS ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 HIS ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 HIS ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN D1046 GLN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 1.8949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19372 Z= 0.182 Angle : 0.658 11.709 26244 Z= 0.328 Chirality : 0.042 0.237 3088 Planarity : 0.004 0.064 3256 Dihedral : 4.113 27.948 2568 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.71 % Allowed : 24.62 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2332 helix: 0.35 (0.13), residues: 1652 sheet: -1.66 (0.83), residues: 40 loop : -2.56 (0.20), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 867 HIS 0.007 0.001 HIS D 525 PHE 0.023 0.001 PHE A 483 TYR 0.021 0.001 TYR D 623 ARG 0.010 0.001 ARG B1122 *********************** 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 387 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 351 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 ILE cc_start: 0.7181 (tt) cc_final: 0.6847 (pt) REVERT: A 686 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7948 (ptmm) REVERT: A 774 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8214 (ttt) REVERT: A 841 LEU cc_start: 0.7659 (tm) cc_final: 0.7433 (tp) REVERT: A 849 GLN cc_start: 0.6839 (tp40) cc_final: 0.6477 (tp40) REVERT: A 914 ASP cc_start: 0.6982 (t0) cc_final: 0.6750 (m-30) REVERT: A 931 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8375 (tp) REVERT: A 956 ILE cc_start: 0.7226 (OUTLIER) cc_final: 0.6761 (mt) REVERT: A 1020 MET cc_start: 0.8530 (mmm) cc_final: 0.8305 (mmp) REVERT: B 554 MET cc_start: 0.8572 (ptm) cc_final: 0.8291 (mtm) REVERT: B 730 GLU cc_start: 0.7675 (tp30) cc_final: 0.7408 (pt0) REVERT: B 876 MET cc_start: 0.8848 (ttp) cc_final: 0.8480 (ptm) REVERT: B 1122 ARG cc_start: 0.7477 (ttp80) cc_final: 0.6934 (ttm170) REVERT: C 601 MET cc_start: 0.5247 (tmm) cc_final: 0.4205 (mtt) REVERT: C 839 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7686 (mp) REVERT: C 979 MET cc_start: 0.8765 (ttt) cc_final: 0.8372 (ttp) REVERT: C 1020 MET cc_start: 0.8536 (mmm) cc_final: 0.8281 (mmp) REVERT: C 1045 MET cc_start: 0.7515 (tpp) cc_final: 0.7281 (ttp) REVERT: D 478 GLU cc_start: 0.6967 (pt0) cc_final: 0.6714 (pm20) REVERT: D 1126 ARG cc_start: 0.7411 (ttt-90) cc_final: 0.7082 (ttt180) REVERT: D 1133 GLU cc_start: 0.7268 (tt0) cc_final: 0.7050 (mt-10) outliers start: 36 outliers final: 14 residues processed: 368 average time/residue: 1.2232 time to fit residues: 508.7607 Evaluate side-chains 319 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 300 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 1000 VAL Chi-restraints excluded: chain D residue 651 VAL 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 136 optimal weight: 2.9990 chunk 106 optimal weight: 0.0980 chunk 155 optimal weight: 2.9990 chunk 235 optimal weight: 0.6980 chunk 216 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 199 optimal weight: 20.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 HIS A 753 HIS A 777 ASN A 962 HIS ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 823 ASN ** D 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1046 GLN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 1.9812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19372 Z= 0.209 Angle : 0.688 14.746 26244 Z= 0.343 Chirality : 0.043 0.244 3088 Planarity : 0.004 0.046 3256 Dihedral : 4.168 18.875 2568 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.38 % Allowed : 26.95 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.17), residues: 2332 helix: 0.49 (0.13), residues: 1616 sheet: -1.32 (0.89), residues: 40 loop : -2.35 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 867 HIS 0.008 0.001 HIS C 584 PHE 0.029 0.001 PHE B 504 TYR 0.025 0.002 TYR C 487 ARG 0.010 0.001 ARG B1122 ********************** 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 383 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 354 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 ILE cc_start: 0.7743 (tt) cc_final: 0.7499 (pt) REVERT: A 617 TYR cc_start: 0.7730 (m-80) cc_final: 0.6814 (t80) REVERT: A 620 TYR cc_start: 0.8631 (t80) cc_final: 0.8349 (t80) REVERT: A 686 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8075 (ptmm) REVERT: A 774 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8165 (ttt) REVERT: A 841 LEU cc_start: 0.7726 (tm) cc_final: 0.7370 (mm) REVERT: A 849 GLN cc_start: 0.6771 (tp40) cc_final: 0.6390 (tm-30) REVERT: A 931 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8377 (tp) REVERT: A 956 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7172 (mt) REVERT: A 1122 ARG cc_start: 0.7638 (ttp80) cc_final: 0.7080 (ttm170) REVERT: B 554 MET cc_start: 0.8591 (ptm) cc_final: 0.8238 (mtm) REVERT: B 841 LEU cc_start: 0.7862 (tt) cc_final: 0.7508 (tp) REVERT: B 1130 ARG cc_start: 0.7524 (ttp-170) cc_final: 0.7123 (ptm160) REVERT: C 514 MET cc_start: 0.4794 (tpt) cc_final: 0.0510 (ptm) REVERT: C 601 MET cc_start: 0.5363 (tmm) cc_final: 0.4738 (mtt) REVERT: C 743 MET cc_start: 0.7953 (tmm) cc_final: 0.7385 (ttp) REVERT: C 979 MET cc_start: 0.8780 (ttt) cc_final: 0.8359 (ttp) REVERT: C 1020 MET cc_start: 0.8580 (mmm) cc_final: 0.8360 (mmp) REVERT: C 1045 MET cc_start: 0.7758 (tpp) cc_final: 0.7455 (ttp) REVERT: D 478 GLU cc_start: 0.7225 (pt0) cc_final: 0.7017 (pm20) REVERT: D 1126 ARG cc_start: 0.7455 (ttt-90) cc_final: 0.7133 (ttt180) REVERT: D 1133 GLU cc_start: 0.7329 (tt0) cc_final: 0.7120 (mt-10) outliers start: 29 outliers final: 12 residues processed: 369 average time/residue: 1.1543 time to fit residues: 483.3572 Evaluate side-chains 329 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 313 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 928 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 670 CYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 651 VAL 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 57 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN A 584 HIS A 753 HIS A1046 GLN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1144 GLN B 721 ASN C 608 ASN C1046 GLN D 507 ASN D 753 HIS D1046 GLN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.172167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.132132 restraints weight = 21476.792| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.97 r_work: 0.3053 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 2.0491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 19372 Z= 0.214 Angle : 0.683 11.494 26244 Z= 0.344 Chirality : 0.043 0.249 3088 Planarity : 0.004 0.048 3256 Dihedral : 4.141 25.979 2568 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.38 % Allowed : 27.61 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.18), residues: 2332 helix: 0.56 (0.13), residues: 1632 sheet: -1.33 (0.88), residues: 40 loop : -2.48 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 867 HIS 0.007 0.001 HIS D 525 PHE 0.017 0.001 PHE D 909 TYR 0.038 0.002 TYR B 607 ARG 0.011 0.001 ARG B1122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7148.35 seconds wall clock time: 126 minutes 20.04 seconds (7580.04 seconds total)