Starting phenix.real_space_refine on Sat Jul 20 20:23:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgo_37228/07_2024/8kgo_37228.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgo_37228/07_2024/8kgo_37228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgo_37228/07_2024/8kgo_37228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgo_37228/07_2024/8kgo_37228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgo_37228/07_2024/8kgo_37228.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgo_37228/07_2024/8kgo_37228.cif" } resolution = 3.4 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= -0.000 sd= 0.003 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 50 5.16 5 C 7813 2.51 5 N 2086 2.21 5 O 2192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 718": "NH1" <-> "NH2" Residue "A ARG 736": "NH1" <-> "NH2" Residue "A ARG 873": "NH1" <-> "NH2" Residue "A ARG 900": "NH1" <-> "NH2" Residue "A ARG 912": "NH1" <-> "NH2" Residue "A ARG 929": "NH1" <-> "NH2" Residue "A ARG 940": "NH1" <-> "NH2" Residue "A ARG 956": "NH1" <-> "NH2" Residue "A ARG 1004": "NH1" <-> "NH2" Residue "A ARG 1006": "NH1" <-> "NH2" Residue "A ARG 1131": "NH1" <-> "NH2" Residue "A PHE 1164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1185": "NH1" <-> "NH2" Residue "B ARG 718": "NH1" <-> "NH2" Residue "B ARG 736": "NH1" <-> "NH2" Residue "B ARG 831": "NH1" <-> "NH2" Residue "B ARG 873": "NH1" <-> "NH2" Residue "B ARG 900": "NH1" <-> "NH2" Residue "B ARG 912": "NH1" <-> "NH2" Residue "B ARG 929": "NH1" <-> "NH2" Residue "B ARG 940": "NH1" <-> "NH2" Residue "B ARG 956": "NH1" <-> "NH2" Residue "B ARG 1004": "NH1" <-> "NH2" Residue "B ARG 1006": "NH1" <-> "NH2" Residue "B ARG 1131": "NH1" <-> "NH2" Residue "B PHE 1164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1185": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 12141 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6072 Classifications: {'peptide': 747} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 716} Chain breaks: 2 Chain: "B" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6069 Classifications: {'peptide': 747} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 716} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.02, per 1000 atoms: 0.58 Number of scatterers: 12141 At special positions: 0 Unit cell: (113.75, 120.25, 111.8, 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 50 16.00 O 2192 8.00 N 2086 7.00 C 7813 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 - 3.50 Amino acid : False - 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: 4.59 Conformation dependent library (CDL) restraints added in 2.2 seconds 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2808 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 18 sheets defined 44.8% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.684A pdb=" N SER A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 513 Processing helix chain 'A' and resid 547 through 560 removed outlier: 3.558A pdb=" N PHE A 559 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 603 removed outlier: 3.806A pdb=" N PHE A 596 " --> pdb=" O TYR A 592 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 601 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN A 603 " --> pdb=" O TRP A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.166A pdb=" N HIS A 620 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 644 through 653 removed outlier: 3.785A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 664 Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 687 through 704 removed outlier: 4.288A pdb=" N THR A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 729 removed outlier: 3.621A pdb=" N LYS A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 729 " --> pdb=" O GLY A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 749 Processing helix chain 'A' and resid 755 through 765 Processing helix chain 'A' and resid 787 through 791 removed outlier: 3.773A pdb=" N LEU A 790 " --> pdb=" O SER A 787 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 791 " --> pdb=" O ARG A 788 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 787 through 791' Processing helix chain 'A' and resid 809 through 814 Processing helix chain 'A' and resid 864 through 866 No H-bonds generated for 'chain 'A' and resid 864 through 866' Processing helix chain 'A' and resid 867 through 877 removed outlier: 3.979A pdb=" N LEU A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 889 removed outlier: 3.885A pdb=" N ALA A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 952 Processing helix chain 'A' and resid 953 through 958 removed outlier: 3.897A pdb=" N THR A 958 " --> pdb=" O SER A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1004 Processing helix chain 'A' and resid 1027 through 1034 removed outlier: 4.084A pdb=" N ILE A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A1032 " --> pdb=" O TYR A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1038 Processing helix chain 'A' and resid 1039 through 1075 removed outlier: 3.564A pdb=" N ASN A1069 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ALA A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLU A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1079 Processing helix chain 'A' and resid 1081 through 1092 removed outlier: 3.687A pdb=" N ALA A1085 " --> pdb=" O ASP A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1103 removed outlier: 3.645A pdb=" N ILE A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A1103 " --> pdb=" O HIS A1099 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1098 through 1103' Processing helix chain 'A' and resid 1109 through 1116 Processing helix chain 'A' and resid 1134 through 1159 Processing helix chain 'A' and resid 1166 through 1186 removed outlier: 3.578A pdb=" N LEU A1171 " --> pdb=" O ALA A1167 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLU A1172 " --> pdb=" O SER A1168 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU A1173 " --> pdb=" O VAL A1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 451 removed outlier: 3.683A pdb=" N SER B 444 " --> pdb=" O ASP B 440 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 513 Processing helix chain 'B' and resid 547 through 560 removed outlier: 3.558A pdb=" N PHE B 559 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 603 removed outlier: 3.806A pdb=" N PHE B 596 " --> pdb=" O TYR B 592 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 601 " --> pdb=" O ASP B 597 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN B 603 " --> pdb=" O TRP B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.161A pdb=" N HIS B 620 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 629 Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 644 through 653 removed outlier: 3.783A pdb=" N LEU B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 664 Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 687 through 707 removed outlier: 4.266A pdb=" N THR B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE B 703 " --> pdb=" O LYS B 699 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 705 " --> pdb=" O ASP B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 729 removed outlier: 3.657A pdb=" N LYS B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 729 " --> pdb=" O GLY B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 749 Processing helix chain 'B' and resid 755 through 767 Processing helix chain 'B' and resid 787 through 791 removed outlier: 3.772A pdb=" N LEU B 790 " --> pdb=" O SER B 787 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 791 " --> pdb=" O ARG B 788 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 787 through 791' Processing helix chain 'B' and resid 809 through 814 Processing helix chain 'B' and resid 864 through 867 removed outlier: 3.857A pdb=" N ASP B 867 " --> pdb=" O GLN B 864 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 864 through 867' Processing helix chain 'B' and resid 868 through 877 Processing helix chain 'B' and resid 882 through 886 removed outlier: 3.652A pdb=" N LEU B 885 " --> pdb=" O LYS B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 952 Processing helix chain 'B' and resid 953 through 958 removed outlier: 3.897A pdb=" N THR B 958 " --> pdb=" O SER B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1004 Processing helix chain 'B' and resid 1027 through 1034 removed outlier: 4.083A pdb=" N ILE B1031 " --> pdb=" O THR B1027 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU B1032 " --> pdb=" O TYR B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1038 Processing helix chain 'B' and resid 1039 through 1075 removed outlier: 3.564A pdb=" N ASN B1069 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ALA B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU B1073 " --> pdb=" O ASN B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1079 Processing helix chain 'B' and resid 1081 through 1092 removed outlier: 3.688A pdb=" N ALA B1085 " --> pdb=" O ASP B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1103 removed outlier: 3.645A pdb=" N ILE B1102 " --> pdb=" O ASN B1098 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE B1103 " --> pdb=" O HIS B1099 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1098 through 1103' Processing helix chain 'B' and resid 1109 through 1116 Processing helix chain 'B' and resid 1134 through 1159 Processing helix chain 'B' and resid 1166 through 1186 removed outlier: 3.578A pdb=" N LEU B1171 " --> pdb=" O ALA B1167 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU B1172 " --> pdb=" O SER B1168 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU B1173 " --> pdb=" O VAL B1169 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 469 Processing sheet with id=AA2, first strand: chain 'A' and resid 570 through 572 Processing sheet with id=AA3, first strand: chain 'A' and resid 577 through 581 Processing sheet with id=AA4, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AA5, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.082A pdb=" N GLU A 833 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU A 827 " --> pdb=" O ARG A 831 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ARG A 831 " --> pdb=" O GLU A 827 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AA7, first strand: chain 'A' and resid 909 through 913 removed outlier: 3.589A pdb=" N HIS A 909 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 916 " --> pdb=" O PHE A 913 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR A 917 " --> pdb=" O LEU A1009 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 922 through 925 removed outlier: 6.339A pdb=" N THR A 922 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 932 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU A 975 " --> pdb=" O ILE A 963 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE A 963 " --> pdb=" O LEU A 975 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS A 977 " --> pdb=" O GLU A 961 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1014 through 1016 removed outlier: 3.529A pdb=" N ILE A1023 " --> pdb=" O PHE A1015 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 465 through 469 Processing sheet with id=AB2, first strand: chain 'B' and resid 570 through 572 Processing sheet with id=AB3, first strand: chain 'B' and resid 577 through 581 Processing sheet with id=AB4, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AB5, first strand: chain 'B' and resid 824 through 826 removed outlier: 4.171A pdb=" N GLU B 833 " --> pdb=" O VAL B 825 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 849 through 850 Processing sheet with id=AB7, first strand: chain 'B' and resid 910 through 913 removed outlier: 3.600A pdb=" N TYR B 916 " --> pdb=" O PHE B 913 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR B 917 " --> pdb=" O LEU B1009 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 922 through 925 removed outlier: 6.344A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE B 932 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU B 975 " --> pdb=" O ILE B 963 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE B 963 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS B 977 " --> pdb=" O GLU B 961 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1014 through 1016 removed outlier: 3.609A pdb=" N ILE B1023 " --> pdb=" O PHE B1015 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.99 Time building geometry restraints manager: 5.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3375 1.33 - 1.45: 2213 1.45 - 1.57: 6765 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 12431 Sorted by residual: bond pdb=" C LEU A 897 " pdb=" N PRO A 898 " ideal model delta sigma weight residual 1.332 1.391 -0.060 1.34e-02 5.57e+03 1.97e+01 bond pdb=" CA SER B 968 " pdb=" C SER B 968 " ideal model delta sigma weight residual 1.526 1.474 0.052 1.37e-02 5.33e+03 1.45e+01 bond pdb=" N ILE B 703 " pdb=" CA ILE B 703 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.77e+00 bond pdb=" CA LEU A 897 " pdb=" C LEU A 897 " ideal model delta sigma weight residual 1.524 1.560 -0.037 1.26e-02 6.30e+03 8.40e+00 bond pdb=" CA SER B 968 " pdb=" CB SER B 968 " ideal model delta sigma weight residual 1.530 1.491 0.040 1.52e-02 4.33e+03 6.86e+00 ... (remaining 12426 not shown) Histogram of bond angle deviations from ideal: 97.20 - 104.57: 178 104.57 - 111.94: 5455 111.94 - 119.31: 4749 119.31 - 126.68: 6239 126.68 - 134.05: 171 Bond angle restraints: 16792 Sorted by residual: angle pdb=" N GLU A 808 " pdb=" CA GLU A 808 " pdb=" C GLU A 808 " ideal model delta sigma weight residual 114.62 107.70 6.92 1.14e+00 7.69e-01 3.69e+01 angle pdb=" C ALA B 889 " pdb=" N ILE B 890 " pdb=" CA ILE B 890 " ideal model delta sigma weight residual 122.66 117.58 5.08 9.70e-01 1.06e+00 2.74e+01 angle pdb=" N LYS A 893 " pdb=" CA LYS A 893 " pdb=" C LYS A 893 " ideal model delta sigma weight residual 111.39 118.51 -7.12 1.38e+00 5.25e-01 2.66e+01 angle pdb=" C LYS B1055 " pdb=" N LEU B1056 " pdb=" CA LEU B1056 " ideal model delta sigma weight residual 121.58 112.51 9.07 1.95e+00 2.63e-01 2.16e+01 angle pdb=" C LYS A1055 " pdb=" N LEU A1056 " pdb=" CA LEU A1056 " ideal model delta sigma weight residual 121.58 112.52 9.06 1.95e+00 2.63e-01 2.16e+01 ... (remaining 16787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 6887 15.12 - 30.23: 428 30.23 - 45.35: 122 45.35 - 60.47: 12 60.47 - 75.59: 9 Dihedral angle restraints: 7458 sinusoidal: 3078 harmonic: 4380 Sorted by residual: dihedral pdb=" CA ASP B 867 " pdb=" C ASP B 867 " pdb=" N ILE B 868 " pdb=" CA ILE B 868 " ideal model delta harmonic sigma weight residual 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA ASP A 867 " pdb=" C ASP A 867 " pdb=" N ILE A 868 " pdb=" CA ILE A 868 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA PHE B 629 " pdb=" C PHE B 629 " pdb=" N LYS B 630 " pdb=" CA LYS B 630 " ideal model delta harmonic sigma weight residual 180.00 158.68 21.32 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 7455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1330 0.069 - 0.137: 417 0.137 - 0.206: 58 0.206 - 0.274: 9 0.274 - 0.343: 5 Chirality restraints: 1819 Sorted by residual: chirality pdb=" CA LYS A 893 " pdb=" N LYS A 893 " pdb=" C LYS A 893 " pdb=" CB LYS A 893 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB VAL B 825 " pdb=" CA VAL B 825 " pdb=" CG1 VAL B 825 " pdb=" CG2 VAL B 825 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CB VAL A 803 " pdb=" CA VAL A 803 " pdb=" CG1 VAL A 803 " pdb=" CG2 VAL A 803 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 1816 not shown) Planarity restraints: 2136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1170 " -0.028 2.00e-02 2.50e+03 2.29e-02 1.31e+01 pdb=" CG TRP A1170 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A1170 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A1170 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A1170 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A1170 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1170 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1170 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1170 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A1170 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1170 " 0.028 2.00e-02 2.50e+03 2.28e-02 1.30e+01 pdb=" CG TRP B1170 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP B1170 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B1170 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP B1170 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B1170 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B1170 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1170 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1170 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B1170 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 824 " 0.021 2.00e-02 2.50e+03 2.08e-02 8.61e+00 pdb=" CG TYR A 824 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR A 824 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 824 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 824 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 824 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 824 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 824 " -0.001 2.00e-02 2.50e+03 ... (remaining 2133 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1953 2.76 - 3.29: 10337 3.29 - 3.83: 18939 3.83 - 4.36: 22826 4.36 - 4.90: 40538 Nonbonded interactions: 94593 Sorted by model distance: nonbonded pdb=" NZ LYS B 893 " pdb=" OE1 GLU B1030 " model vdw 2.219 2.520 nonbonded pdb=" OE2 GLU A1161 " pdb=" OG SER A1168 " model vdw 2.283 2.440 nonbonded pdb=" OE2 GLU B1161 " pdb=" OG SER B1168 " model vdw 2.283 2.440 nonbonded pdb=" O SER A 819 " pdb=" OH TYR A 824 " model vdw 2.290 2.440 nonbonded pdb=" O PHE B1094 " pdb=" OH TYR B1122 " model vdw 2.303 2.440 ... (remaining 94588 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 415 through 893 or (resid 894 and (name N or name CA or na \ me C or name O or name CB )) or resid 895 through 1192)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.200 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 : 0.011 0.096 12431 Z= 0.706 Angle : 1.138 16.021 16792 Z= 0.597 Chirality : 0.067 0.343 1819 Planarity : 0.008 0.058 2136 Dihedral : 11.212 75.586 4650 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 0.92 % Allowed : 4.74 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -4.07 (0.18), residues: 1482 helix: -2.90 (0.15), residues: 644 sheet: -1.95 (0.35), residues: 212 loop : -2.58 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.005 TRP A1170 HIS 0.012 0.003 HIS B1099 PHE 0.039 0.005 PHE B 990 TYR 0.051 0.004 TYR A 824 ARG 0.008 0.001 ARG B 956 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 190 time to evaluate : 1.422 Fit side-chains REVERT: A 735 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7330 (mt-10) REVERT: A 964 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7541 (tp) REVERT: A 1149 GLN cc_start: 0.8477 (tp40) cc_final: 0.7865 (mt0) REVERT: B 735 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7333 (mt-10) REVERT: B 887 HIS cc_start: 0.5693 (OUTLIER) cc_final: 0.5356 (p90) REVERT: B 964 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7487 (tp) REVERT: B 1149 GLN cc_start: 0.8461 (tp40) cc_final: 0.7847 (mt0) outliers start: 12 outliers final: 2 residues processed: 198 average time/residue: 0.2530 time to fit residues: 71.1906 Evaluate side-chains 129 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 964 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 HIS A 609 HIS A 733 ASN A 883 HIS A 903 ASN A1010 HIS A1069 ASN A1115 GLN B 557 HIS B 609 HIS B 883 HIS B1010 HIS B1069 ASN B1115 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12431 Z= 0.172 Angle : 0.569 8.226 16792 Z= 0.284 Chirality : 0.042 0.146 1819 Planarity : 0.005 0.047 2136 Dihedral : 5.079 33.546 1666 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.84 % Allowed : 7.96 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.48 (0.20), residues: 1482 helix: -1.19 (0.20), residues: 638 sheet: -1.69 (0.36), residues: 208 loop : -1.99 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1170 HIS 0.004 0.001 HIS B1051 PHE 0.014 0.001 PHE B 990 TYR 0.016 0.001 TYR B1067 ARG 0.002 0.000 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 1.476 Fit side-chains REVERT: A 523 GLN cc_start: 0.7623 (tp40) cc_final: 0.7318 (tp40) REVERT: A 701 ASP cc_start: 0.8650 (t70) cc_final: 0.8151 (t0) REVERT: A 749 MET cc_start: 0.8725 (mmt) cc_final: 0.8085 (mmt) REVERT: A 1088 ILE cc_start: 0.7274 (mt) cc_final: 0.7049 (mt) REVERT: A 1149 GLN cc_start: 0.8300 (tp40) cc_final: 0.7816 (mt0) REVERT: B 523 GLN cc_start: 0.7610 (tp40) cc_final: 0.7354 (tp40) REVERT: B 735 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7407 (mt-10) REVERT: B 964 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7440 (tp) REVERT: B 1088 ILE cc_start: 0.7248 (mt) cc_final: 0.7043 (mt) REVERT: B 1149 GLN cc_start: 0.8287 (tp40) cc_final: 0.7804 (mt0) outliers start: 24 outliers final: 12 residues processed: 168 average time/residue: 0.2616 time to fit residues: 62.6875 Evaluate side-chains 141 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 0.0170 chunk 41 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 634 ASN A1115 GLN B 519 HIS B 634 ASN B 903 ASN B1115 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12431 Z= 0.163 Angle : 0.506 7.892 16792 Z= 0.253 Chirality : 0.041 0.137 1819 Planarity : 0.004 0.042 2136 Dihedral : 4.406 33.780 1661 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.14 % Allowed : 9.03 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.60 (0.22), residues: 1482 helix: -0.33 (0.21), residues: 640 sheet: -1.46 (0.37), residues: 208 loop : -1.59 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1170 HIS 0.005 0.001 HIS B1051 PHE 0.012 0.001 PHE A 990 TYR 0.012 0.001 TYR A1067 ARG 0.002 0.000 ARG B 526 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 1.443 Fit side-chains REVERT: A 749 MET cc_start: 0.8743 (mmt) cc_final: 0.8151 (mmt) REVERT: A 1149 GLN cc_start: 0.8352 (tp40) cc_final: 0.7802 (mt0) REVERT: B 735 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7475 (mt-10) REVERT: B 749 MET cc_start: 0.8580 (mmp) cc_final: 0.8168 (mmp) REVERT: B 964 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7430 (tp) REVERT: B 1149 GLN cc_start: 0.8346 (tp40) cc_final: 0.7796 (mt0) outliers start: 28 outliers final: 15 residues processed: 160 average time/residue: 0.2724 time to fit residues: 61.2767 Evaluate side-chains 145 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1102 ILE Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1115 GLN B 690 HIS B1115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12431 Z= 0.300 Angle : 0.586 9.194 16792 Z= 0.293 Chirality : 0.044 0.147 1819 Planarity : 0.005 0.044 2136 Dihedral : 4.701 36.924 1661 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.98 % Allowed : 10.56 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.33 (0.22), residues: 1482 helix: -0.06 (0.22), residues: 638 sheet: -1.28 (0.36), residues: 226 loop : -1.51 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B1170 HIS 0.006 0.001 HIS B1051 PHE 0.016 0.002 PHE A 739 TYR 0.015 0.002 TYR B 637 ARG 0.003 0.000 ARG A1040 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 130 time to evaluate : 1.553 Fit side-chains REVERT: A 1050 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8231 (pp20) REVERT: A 1060 MET cc_start: 0.8385 (ttt) cc_final: 0.8142 (ttm) REVERT: A 1149 GLN cc_start: 0.8389 (tp40) cc_final: 0.7821 (mt0) REVERT: B 1050 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8241 (pp20) REVERT: B 1060 MET cc_start: 0.8395 (ttt) cc_final: 0.8158 (ttm) REVERT: B 1149 GLN cc_start: 0.8382 (tp40) cc_final: 0.7812 (mt0) outliers start: 39 outliers final: 23 residues processed: 157 average time/residue: 0.2730 time to fit residues: 60.4396 Evaluate side-chains 150 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1010 HIS Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1010 HIS Chi-restraints excluded: chain B residue 1050 GLU Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1102 ILE Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.1980 chunk 81 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 887 HIS A1115 GLN B1115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12431 Z= 0.129 Angle : 0.477 7.958 16792 Z= 0.235 Chirality : 0.040 0.130 1819 Planarity : 0.004 0.043 2136 Dihedral : 4.004 25.619 1659 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.14 % Allowed : 12.55 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.91 (0.22), residues: 1482 helix: 0.31 (0.22), residues: 640 sheet: -1.11 (0.38), residues: 208 loop : -1.31 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1170 HIS 0.005 0.001 HIS A1051 PHE 0.009 0.001 PHE A 990 TYR 0.010 0.001 TYR B1067 ARG 0.002 0.000 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 1.463 Fit side-chains REVERT: A 1149 GLN cc_start: 0.8361 (tp40) cc_final: 0.7812 (mt0) REVERT: B 1149 GLN cc_start: 0.8346 (tp40) cc_final: 0.7801 (mt0) outliers start: 28 outliers final: 19 residues processed: 147 average time/residue: 0.2845 time to fit residues: 57.8058 Evaluate side-chains 145 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 628 MET Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1076 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 9.9990 chunk 128 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 0.0030 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1115 GLN B1115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12431 Z= 0.154 Angle : 0.470 7.433 16792 Z= 0.234 Chirality : 0.040 0.132 1819 Planarity : 0.004 0.039 2136 Dihedral : 3.918 25.153 1659 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.45 % Allowed : 12.70 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.71 (0.22), residues: 1482 helix: 0.51 (0.22), residues: 640 sheet: -1.03 (0.38), residues: 218 loop : -1.23 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1170 HIS 0.005 0.001 HIS B1051 PHE 0.011 0.001 PHE A 739 TYR 0.010 0.001 TYR A1067 ARG 0.001 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 1.425 Fit side-chains REVERT: A 749 MET cc_start: 0.8953 (mmt) cc_final: 0.8212 (mmt) REVERT: A 1149 GLN cc_start: 0.8370 (tp40) cc_final: 0.7797 (mt0) REVERT: B 1149 GLN cc_start: 0.8358 (tp40) cc_final: 0.7787 (mt0) outliers start: 32 outliers final: 20 residues processed: 160 average time/residue: 0.2745 time to fit residues: 61.4161 Evaluate side-chains 149 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1102 ILE Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 HIS A 930 ASN B 930 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12431 Z= 0.298 Angle : 0.564 8.932 16792 Z= 0.284 Chirality : 0.044 0.140 1819 Planarity : 0.004 0.040 2136 Dihedral : 4.407 36.047 1659 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.06 % Allowed : 12.01 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.85 (0.22), residues: 1482 helix: 0.41 (0.22), residues: 638 sheet: -1.09 (0.37), residues: 230 loop : -1.31 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1170 HIS 0.006 0.001 HIS B1051 PHE 0.017 0.002 PHE B 739 TYR 0.012 0.002 TYR A 824 ARG 0.003 0.000 ARG B1040 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 132 time to evaluate : 1.487 Fit side-chains REVERT: A 833 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7309 (pm20) REVERT: A 1149 GLN cc_start: 0.8396 (tp40) cc_final: 0.8104 (tp40) REVERT: B 1149 GLN cc_start: 0.8389 (tp40) cc_final: 0.8112 (tp40) outliers start: 40 outliers final: 23 residues processed: 167 average time/residue: 0.2652 time to fit residues: 62.5438 Evaluate side-chains 156 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1010 HIS Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1010 HIS Chi-restraints excluded: chain B residue 1050 GLU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1076 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 3.9990 chunk 85 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 129 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12431 Z= 0.151 Angle : 0.484 7.565 16792 Z= 0.240 Chirality : 0.041 0.182 1819 Planarity : 0.004 0.040 2136 Dihedral : 3.976 25.277 1659 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.30 % Allowed : 13.47 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.64 (0.22), residues: 1482 helix: 0.58 (0.22), residues: 640 sheet: -0.95 (0.39), residues: 208 loop : -1.23 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1170 HIS 0.005 0.001 HIS A1051 PHE 0.010 0.001 PHE A1164 TYR 0.010 0.001 TYR B1067 ARG 0.002 0.000 ARG B 736 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 1.414 Fit side-chains REVERT: A 749 MET cc_start: 0.8968 (mmt) cc_final: 0.8203 (mmt) REVERT: A 1149 GLN cc_start: 0.8364 (tp40) cc_final: 0.7805 (mt0) REVERT: B 1149 GLN cc_start: 0.8352 (tp40) cc_final: 0.7785 (mt0) outliers start: 30 outliers final: 24 residues processed: 152 average time/residue: 0.2797 time to fit residues: 59.3735 Evaluate side-chains 151 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1050 GLU Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 132 optimal weight: 0.3980 chunk 80 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 120 optimal weight: 0.2980 chunk 125 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12431 Z= 0.116 Angle : 0.448 6.825 16792 Z= 0.221 Chirality : 0.040 0.160 1819 Planarity : 0.003 0.039 2136 Dihedral : 3.617 18.436 1659 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.91 % Allowed : 14.46 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.39 (0.23), residues: 1482 helix: 0.84 (0.22), residues: 630 sheet: -0.83 (0.38), residues: 218 loop : -1.12 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1170 HIS 0.004 0.001 HIS B1051 PHE 0.010 0.001 PHE A1164 TYR 0.007 0.001 TYR B1067 ARG 0.004 0.000 ARG B 734 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 1.381 Fit side-chains REVERT: A 991 LYS cc_start: 0.8291 (mmtm) cc_final: 0.7951 (mmmt) REVERT: A 1149 GLN cc_start: 0.8368 (tp40) cc_final: 0.8079 (tp40) REVERT: B 991 LYS cc_start: 0.8273 (mmtm) cc_final: 0.7933 (mmmt) REVERT: B 1149 GLN cc_start: 0.8356 (tp40) cc_final: 0.7806 (mt0) outliers start: 25 outliers final: 22 residues processed: 162 average time/residue: 0.2803 time to fit residues: 62.7363 Evaluate side-chains 154 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1050 GLU Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 97 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 135 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12431 Z= 0.196 Angle : 0.488 7.583 16792 Z= 0.243 Chirality : 0.041 0.156 1819 Planarity : 0.003 0.039 2136 Dihedral : 3.869 27.891 1659 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.84 % Allowed : 14.61 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.42 (0.23), residues: 1482 helix: 0.75 (0.22), residues: 642 sheet: -0.78 (0.38), residues: 216 loop : -1.11 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1170 HIS 0.005 0.001 HIS A1051 PHE 0.013 0.001 PHE B 785 TYR 0.011 0.001 TYR B1067 ARG 0.002 0.000 ARG B 420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.429 Fit side-chains REVERT: A 991 LYS cc_start: 0.8320 (mmtm) cc_final: 0.7952 (mmmt) REVERT: A 1149 GLN cc_start: 0.8390 (tp40) cc_final: 0.8094 (tp40) REVERT: B 991 LYS cc_start: 0.8298 (mmtm) cc_final: 0.7937 (mmmt) REVERT: B 1149 GLN cc_start: 0.8374 (tp40) cc_final: 0.8086 (tp40) outliers start: 24 outliers final: 23 residues processed: 148 average time/residue: 0.2798 time to fit residues: 57.9251 Evaluate side-chains 151 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1050 GLU Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1102 ILE Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 120 optimal weight: 0.0670 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.146085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.117772 restraints weight = 15202.383| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.51 r_work: 0.3284 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12431 Z= 0.129 Angle : 0.454 6.860 16792 Z= 0.225 Chirality : 0.040 0.152 1819 Planarity : 0.003 0.039 2136 Dihedral : 3.658 21.687 1659 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.91 % Allowed : 14.46 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.26 (0.23), residues: 1482 helix: 0.91 (0.22), residues: 630 sheet: -0.79 (0.38), residues: 218 loop : -1.00 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1170 HIS 0.005 0.001 HIS A1051 PHE 0.010 0.001 PHE A1164 TYR 0.008 0.001 TYR B1067 ARG 0.002 0.000 ARG B 420 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2547.70 seconds wall clock time: 46 minutes 12.06 seconds (2772.06 seconds total)