Starting phenix.real_space_refine on Wed Jan 15 01:08:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bcv_44440/01_2025/9bcv_44440.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bcv_44440/01_2025/9bcv_44440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bcv_44440/01_2025/9bcv_44440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bcv_44440/01_2025/9bcv_44440.map" model { file = "/net/cci-nas-00/data/ceres_data/9bcv_44440/01_2025/9bcv_44440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bcv_44440/01_2025/9bcv_44440.cif" } resolution = 3.2 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= 0.002 sd= 0.127 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 17 5.16 5 C 4736 2.51 5 N 1469 2.21 5 O 1499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7729 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1568 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 204} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1580 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 204} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 595 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'TRANS': 118} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 119 Planarities with less than four sites: {'UNK:plan-1': 119} Unresolved non-hydrogen planarities: 119 Chain: "H" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 560 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 112 Planarities with less than four sites: {'UNK:plan-1': 112} Unresolved non-hydrogen planarities: 112 Chain: "J" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 585 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'TRANS': 116} Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 117 Planarities with less than four sites: {'UNK:plan-1': 117} Unresolved non-hydrogen planarities: 117 Chain: "I" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 560 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 112 Planarities with less than four sites: {'UNK:plan-1': 112} Unresolved non-hydrogen planarities: 112 Chain: "C" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 575 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'TRANS': 114} Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'UNK:plan-1': 115} Unresolved non-hydrogen planarities: 115 Chain: "D" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 530 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'TRANS': 105} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'UNK:plan-1': 106} Unresolved non-hydrogen planarities: 106 Chain: "E" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 580 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 116 Planarities with less than four sites: {'UNK:plan-1': 116} Unresolved non-hydrogen planarities: 116 Chain: "F" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 530 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'TRANS': 105} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'UNK:plan-1': 106} Unresolved non-hydrogen planarities: 106 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {' MG': 1, 'G2P': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.68, per 1000 atoms: 0.73 Number of scatterers: 7729 At special positions: 0 Unit cell: (102.34, 128.52, 107.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 17 16.00 P 6 15.00 Mg 2 11.99 O 1499 8.00 N 1469 7.00 C 4736 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 459.8 milliseconds 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 23 sheets defined 45.0% alpha, 119.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 845 through 849 Processing helix chain 'A' and resid 854 through 863 Processing helix chain 'A' and resid 884 through 889 removed outlier: 3.774A pdb=" N LEU A 888 " --> pdb=" O GLY A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 913 removed outlier: 3.660A pdb=" N VAL A 897 " --> pdb=" O THR A 893 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 898 " --> pdb=" O PRO A 894 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 910 " --> pdb=" O THR A 906 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A 911 " --> pdb=" O CYS A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 957 removed outlier: 4.530A pdb=" N CYS A 943 " --> pdb=" O ARG A 939 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 950 " --> pdb=" O ALA A 946 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 957 " --> pdb=" O LEU A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1009 removed outlier: 4.256A pdb=" N ASN A1000 " --> pdb=" O GLY A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1028 removed outlier: 3.538A pdb=" N LYS A1021 " --> pdb=" O SER A1017 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A1023 " --> pdb=" O GLU A1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 846 removed outlier: 4.225A pdb=" N TYR B 846 " --> pdb=" O ALA B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 860 Processing helix chain 'B' and resid 889 through 909 removed outlier: 3.655A pdb=" N ALA B 906 " --> pdb=" O THR B 902 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 907 " --> pdb=" O CYS B 903 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 909 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 952 removed outlier: 4.601A pdb=" N CYS B 939 " --> pdb=" O ARG B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1004 removed outlier: 3.554A pdb=" N GLU B1002 " --> pdb=" O ALA B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1024 removed outlier: 3.756A pdb=" N ALA B1018 " --> pdb=" O SER B1014 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL B1019 " --> pdb=" O GLU B1015 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.771A pdb=" N UNK G 32 " --> pdb=" O UNK G 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.549A pdb=" N UNK C 32 " --> pdb=" O UNK C 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.573A pdb=" N UNK E 32 " --> pdb=" O UNK E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 918 through 923 removed outlier: 7.252A pdb=" N MET A 928 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N THR A 922 " --> pdb=" O ALA A 926 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA A 926 " --> pdb=" O THR A 922 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER A 874 " --> pdb=" O GLY A 978 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY A 978 " --> pdb=" O SER A 874 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR A 876 " --> pdb=" O HIS A 976 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N HIS A 976 " --> pdb=" O THR A 876 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR A 878 " --> pdb=" O GLY A 974 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY A 974 " --> pdb=" O TYR A 878 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER A 880 " --> pdb=" O ARG A 972 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG A 972 " --> pdb=" O SER A 880 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 918 through 923 removed outlier: 7.252A pdb=" N MET A 928 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N THR A 922 " --> pdb=" O ALA A 926 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA A 926 " --> pdb=" O THR A 922 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER A 874 " --> pdb=" O GLY A 978 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY A 978 " --> pdb=" O SER A 874 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR A 876 " --> pdb=" O HIS A 976 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N HIS A 976 " --> pdb=" O THR A 876 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR A 878 " --> pdb=" O GLY A 974 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY A 974 " --> pdb=" O TYR A 878 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER A 880 " --> pdb=" O ARG A 972 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG A 972 " --> pdb=" O SER A 880 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE A 973 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE A1014 " --> pdb=" O LEU A1051 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR A1048 " --> pdb=" O ARG A1035 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU A1031 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 914 through 919 removed outlier: 7.166A pdb=" N MET B 924 " --> pdb=" O VAL B 916 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR B 918 " --> pdb=" O ALA B 922 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA B 922 " --> pdb=" O THR B 918 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ALA B 867 " --> pdb=" O ALA B 978 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ALA B 978 " --> pdb=" O ALA B 867 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASP B 869 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL B 976 " --> pdb=" O ASP B 869 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 914 through 919 removed outlier: 7.166A pdb=" N MET B 924 " --> pdb=" O VAL B 916 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR B 918 " --> pdb=" O ALA B 922 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA B 922 " --> pdb=" O THR B 918 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ALA B 867 " --> pdb=" O ALA B 978 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ALA B 978 " --> pdb=" O ALA B 867 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASP B 869 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL B 976 " --> pdb=" O ASP B 869 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU B 967 " --> pdb=" O LYS B1009 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N HIS B1011 " --> pdb=" O LEU B 967 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 969 " --> pdb=" O HIS B1011 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE B1010 " --> pdb=" O LEU B1047 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LYS B1041 " --> pdb=" O GLU B1035 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLU B1035 " --> pdb=" O LYS B1041 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG B1043 " --> pdb=" O ASP B1033 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP B1033 " --> pdb=" O ARG B1043 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TYR B1045 " --> pdb=" O ARG B1031 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG B1031 " --> pdb=" O TYR B1045 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU B1047 " --> pdb=" O GLU B1029 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLU B1029 " --> pdb=" O LEU B1047 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY B1049 " --> pdb=" O GLU B1027 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.548A pdb=" N UNK G 5 " --> pdb=" O UNK G 23 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N UNK G 23 " --> pdb=" O UNK G 5 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 57 through 60 removed outlier: 4.189A pdb=" N UNK G 57 " --> pdb=" O UNK G 52 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N UNK G 59 " --> pdb=" O UNK G 50 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N UNK G 36 " --> pdb=" O UNK G 48 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N UNK G 50 " --> pdb=" O UNK G 34 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N UNK G 34 " --> pdb=" O UNK G 50 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N UNK G 96 " --> pdb=" O UNK G 111 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N UNK G 111 " --> pdb=" O UNK G 96 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N UNK G 98 " --> pdb=" O UNK G 109 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.732A pdb=" N UNK H 92 " --> pdb=" O UNK H 108 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N UNK H 39 " --> pdb=" O UNK H 55 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N UNK H 55 " --> pdb=" O UNK H 39 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N UNK H 41 " --> pdb=" O UNK H 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'J' and resid 58 through 60 removed outlier: 6.782A pdb=" N UNK J 36 " --> pdb=" O UNK J 48 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N UNK J 50 " --> pdb=" O UNK J 34 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N UNK J 34 " --> pdb=" O UNK J 50 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N UNK J 96 " --> pdb=" O UNK J 111 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N UNK J 111 " --> pdb=" O UNK J 96 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N UNK J 98 " --> pdb=" O UNK J 109 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 58 through 60 removed outlier: 6.782A pdb=" N UNK J 36 " --> pdb=" O UNK J 48 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N UNK J 50 " --> pdb=" O UNK J 34 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N UNK J 34 " --> pdb=" O UNK J 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AB4, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.749A pdb=" N UNK I 92 " --> pdb=" O UNK I 108 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N UNK I 43 " --> pdb=" O UNK I 52 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N UNK I 52 " --> pdb=" O UNK I 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.569A pdb=" N UNK C 23 " --> pdb=" O UNK C 5 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 45 through 50 removed outlier: 5.047A pdb=" N UNK C 47 " --> pdb=" O UNK C 38 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N UNK C 38 " --> pdb=" O UNK C 47 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N UNK C 49 " --> pdb=" O UNK C 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.549A pdb=" N UNK D 11 " --> pdb=" O UNK D 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 19 through 22 Processing sheet with id=AB9, first strand: chain 'D' and resid 53 through 54 removed outlier: 5.492A pdb=" N UNK D 46 " --> pdb=" O UNK D 37 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N UNK D 37 " --> pdb=" O UNK D 46 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N UNK D 97 " --> pdb=" O UNK D 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.788A pdb=" N UNK E 99 " --> pdb=" O UNK E 33 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N UNK E 34 " --> pdb=" O UNK E 50 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N UNK E 50 " --> pdb=" O UNK E 34 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N UNK E 36 " --> pdb=" O UNK E 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.535A pdb=" N UNK F 105 " --> pdb=" O UNK F 11 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N UNK F 86 " --> pdb=" O UNK F 102 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N UNK F 84 " --> pdb=" O UNK F 104 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N UNK F 37 " --> pdb=" O UNK F 46 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N UNK F 46 " --> pdb=" O UNK F 37 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.535A pdb=" N UNK F 105 " --> pdb=" O UNK F 11 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N UNK F 86 " --> pdb=" O UNK F 102 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N UNK F 84 " --> pdb=" O UNK F 104 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N UNK F 97 " --> pdb=" O UNK F 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 19 through 24 400 hydrogen bonds defined for protein. 1026 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: 2.61 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2864 1.35 - 1.47: 1689 1.47 - 1.60: 3190 1.60 - 1.73: 6 1.73 - 1.85: 30 Bond restraints: 7779 Sorted by residual: bond pdb=" CA GLY A 938 " pdb=" C GLY A 938 " ideal model delta sigma weight residual 1.530 1.512 0.019 1.04e-02 9.25e+03 3.19e+00 bond pdb=" N GLY A 938 " pdb=" CA GLY A 938 " ideal model delta sigma weight residual 1.464 1.448 0.016 1.12e-02 7.97e+03 2.13e+00 bond pdb=" C UNK C 7 " pdb=" N UNK C 8 " ideal model delta sigma weight residual 1.329 1.341 -0.012 1.40e-02 5.10e+03 7.26e-01 bond pdb=" CA UNK E 101 " pdb=" CB UNK E 101 " ideal model delta sigma weight residual 1.530 1.514 0.016 2.00e-02 2.50e+03 6.32e-01 bond pdb=" CA UNK H 1 " pdb=" CB UNK H 1 " ideal model delta sigma weight residual 1.530 1.514 0.016 2.00e-02 2.50e+03 6.19e-01 ... (remaining 7774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 9574 1.31 - 2.62: 1005 2.62 - 3.93: 143 3.93 - 5.24: 29 5.24 - 6.55: 6 Bond angle restraints: 10757 Sorted by residual: angle pdb=" C UNK I 56 " pdb=" N UNK I 57 " pdb=" CA UNK I 57 " ideal model delta sigma weight residual 121.70 127.17 -5.47 1.80e+00 3.09e-01 9.25e+00 angle pdb=" C UNK J 25 " pdb=" N UNK J 26 " pdb=" CA UNK J 26 " ideal model delta sigma weight residual 121.70 126.94 -5.24 1.80e+00 3.09e-01 8.48e+00 angle pdb=" C UNK I 62 " pdb=" CA UNK I 62 " pdb=" CB UNK I 62 " ideal model delta sigma weight residual 110.08 115.57 -5.49 1.90e+00 2.77e-01 8.35e+00 angle pdb=" C UNK H 71 " pdb=" N UNK H 72 " pdb=" CA UNK H 72 " ideal model delta sigma weight residual 121.70 126.83 -5.13 1.80e+00 3.09e-01 8.13e+00 angle pdb=" C UNK F 65 " pdb=" N UNK F 66 " pdb=" CA UNK F 66 " ideal model delta sigma weight residual 121.70 126.79 -5.09 1.80e+00 3.09e-01 7.99e+00 ... (remaining 10752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.32: 4355 18.32 - 36.63: 215 36.63 - 54.95: 57 54.95 - 73.27: 19 73.27 - 91.59: 15 Dihedral angle restraints: 4661 sinusoidal: 752 harmonic: 3909 Sorted by residual: dihedral pdb=" CA UNK G 7 " pdb=" C UNK G 7 " pdb=" N UNK G 8 " pdb=" CA UNK G 8 " ideal model delta harmonic sigma weight residual 180.00 160.89 19.11 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA UNK G 6 " pdb=" C UNK G 6 " pdb=" N UNK G 7 " pdb=" CA UNK G 7 " ideal model delta harmonic sigma weight residual 180.00 -161.55 -18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA UNK H 6 " pdb=" C UNK H 6 " pdb=" N UNK H 7 " pdb=" CA UNK H 7 " ideal model delta harmonic sigma weight residual -180.00 -163.07 -16.93 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 4658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 948 0.033 - 0.067: 327 0.067 - 0.100: 104 0.100 - 0.133: 40 0.133 - 0.167: 6 Chirality restraints: 1425 Sorted by residual: chirality pdb=" C3' G2P A1102 " pdb=" C2' G2P A1102 " pdb=" C4' G2P A1102 " pdb=" O3' G2P A1102 " both_signs ideal model delta sigma weight residual False -2.71 -2.54 -0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CA VAL B 871 " pdb=" N VAL B 871 " pdb=" C VAL B 871 " pdb=" CB VAL B 871 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA UNK J 26 " pdb=" N UNK J 26 " pdb=" C UNK J 26 " pdb=" CB UNK J 26 " both_signs ideal model delta sigma weight residual False 2.52 2.38 0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 1422 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 893 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO A 894 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 894 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 894 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 889 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO B 890 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 890 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 890 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA UNK C 103 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.51e+00 pdb=" C UNK C 103 " 0.021 2.00e-02 2.50e+03 pdb=" O UNK C 103 " -0.008 2.00e-02 2.50e+03 pdb=" N UNK C 104 " -0.007 2.00e-02 2.50e+03 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 24 2.58 - 3.16: 5744 3.16 - 3.74: 10116 3.74 - 4.32: 12201 4.32 - 4.90: 23131 Nonbonded interactions: 51216 Sorted by model distance: nonbonded pdb=" O1G G2P A1101 " pdb="MG MG A1103 " model vdw 1.994 2.170 nonbonded pdb=" O2B G2P A1102 " pdb="MG MG B1101 " model vdw 2.009 2.170 nonbonded pdb=" OD2 ASP B 921 " pdb="MG MG B1101 " model vdw 2.082 2.170 nonbonded pdb=" O2B G2P A1101 " pdb="MG MG A1103 " model vdw 2.133 2.170 nonbonded pdb=" OH TYR A 905 " pdb=" O GLY A 924 " model vdw 2.181 3.040 ... (remaining 51211 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' and (resid 846 through 858 or (resid 859 and (name N or name CA or na \ me C or name O or name CB )) or resid 860 through 988 or (resid 989 and (name N \ or name CA or name C or name O or name CB )) or resid 990 through 1016 or (resid \ 1017 through 1018 and (name N or name CA or name C or name O or name CB )) or r \ esid 1019 through 1046 or (resid 1047 through 1048 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1049 through 1055)) selection = (chain 'B' and (resid 842 through 908 or (resid 909 and (name N or name CA or na \ me C or name O or name CB )) or resid 910 through 949 or (resid 950 through 951 \ and (name N or name CA or name C or name O or name CB )) or resid 952 through 95 \ 3 or (resid 954 and (name N or name CA or name C or name O or name CB )) or resi \ d 955 through 992 or (resid 993 and (name N or name CA or name C or name O or na \ me CB )) or resid 994 through 1013 or (resid 1014 and (name N or name CA or name \ C or name O or name CB )) or resid 1015 through 1020 or (resid 1021 through 102 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 1023 through \ 1043 or (resid 1044 and (name N or name CA or name C or name O or name CB )) or \ resid 1045 through 1050 or (resid 1051 and (name N or name CA or name C or name \ O or name CB )))) } ncs_group { reference = (chain 'C' and resid 10 through 115) selection = chain 'D' selection = (chain 'E' and resid 11 through 116) selection = chain 'F' selection = (chain 'G' and resid 14 through 119) selection = (chain 'H' and resid 7 through 112) selection = (chain 'I' and resid 7 through 112) selection = (chain 'J' and resid 12 through 117) } 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.810 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 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 : 0.003 0.027 7779 Z= 0.217 Angle : 0.860 6.548 10757 Z= 0.408 Chirality : 0.041 0.167 1425 Planarity : 0.003 0.041 1457 Dihedral : 15.566 91.586 2081 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.64 % Allowed : 30.55 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.40), residues: 418 helix: 0.59 (0.42), residues: 155 sheet: 0.09 (0.46), residues: 95 loop : -1.07 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A1050 HIS 0.006 0.002 HIS A 963 PHE 0.007 0.001 PHE B 868 TYR 0.010 0.001 TYR A 878 ARG 0.002 0.000 ARG B1000 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.561 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 0.2096 time to fit residues: 10.0406 Evaluate side-chains 33 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 952 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.175554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.170644 restraints weight = 9401.583| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 0.39 r_work: 0.3810 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.063 7779 Z= 0.671 Angle : 1.252 9.131 10757 Z= 0.562 Chirality : 0.060 0.228 1425 Planarity : 0.004 0.049 1457 Dihedral : 10.838 79.866 1422 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.35 % Favored : 96.41 % Rotamer: Outliers : 9.97 % Allowed : 26.37 % Favored : 63.67 % 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: -0.88 (0.41), residues: 418 helix: -0.18 (0.41), residues: 163 sheet: 0.32 (0.55), residues: 77 loop : -1.31 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP A1050 HIS 0.013 0.004 HIS A 963 PHE 0.014 0.003 PHE B 868 TYR 0.014 0.003 TYR A 878 ARG 0.007 0.001 ARG B 932 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 32 time to evaluate : 0.566 Fit side-chains REVERT: A 962 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8169 (ptm160) REVERT: A 995 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8175 (m-80) REVERT: A 1005 MET cc_start: 0.9144 (mmt) cc_final: 0.8919 (mmm) REVERT: B 936 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7960 (mp) outliers start: 31 outliers final: 21 residues processed: 62 average time/residue: 0.2250 time to fit residues: 18.5325 Evaluate side-chains 63 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 39 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 878 TYR Chi-restraints excluded: chain A residue 895 MET Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 995 PHE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain B residue 870 SER Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain B residue 939 CYS Chi-restraints excluded: chain B residue 949 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 THR Chi-restraints excluded: chain B residue 1023 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 85 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 25 optimal weight: 0.0570 chunk 92 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 overall best weight: 2.1502 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.179589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.173829 restraints weight = 9450.934| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 0.45 r_work: 0.3880 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7779 Z= 0.269 Angle : 0.768 6.307 10757 Z= 0.343 Chirality : 0.040 0.167 1425 Planarity : 0.003 0.044 1457 Dihedral : 9.610 83.316 1422 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.82 % Allowed : 31.19 % Favored : 63.99 % 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: -0.52 (0.41), residues: 418 helix: 0.32 (0.42), residues: 161 sheet: 0.13 (0.51), residues: 84 loop : -1.16 (0.49), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1050 HIS 0.008 0.002 HIS A 963 PHE 0.010 0.001 PHE B 868 TYR 0.011 0.002 TYR A 878 ARG 0.002 0.000 ARG B1000 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.522 Fit side-chains REVERT: A 995 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: B 1002 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7979 (tm-30) outliers start: 15 outliers final: 11 residues processed: 58 average time/residue: 0.1674 time to fit residues: 13.8519 Evaluate side-chains 54 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 995 PHE Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 870 SER Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 939 CYS Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1023 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 111 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.172154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.166379 restraints weight = 9513.217| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 0.44 r_work: 0.3801 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 7779 Z= 0.537 Angle : 1.090 8.414 10757 Z= 0.488 Chirality : 0.053 0.192 1425 Planarity : 0.004 0.048 1457 Dihedral : 9.900 72.713 1422 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 11.90 % Allowed : 24.76 % Favored : 63.34 % 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: -0.80 (0.41), residues: 418 helix: -0.03 (0.42), residues: 162 sheet: 0.26 (0.57), residues: 77 loop : -1.29 (0.47), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1050 HIS 0.011 0.003 HIS A 963 PHE 0.012 0.002 PHE B 868 TYR 0.014 0.003 TYR A 878 ARG 0.005 0.001 ARG B1000 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 39 time to evaluate : 0.584 Fit side-chains REVERT: A 962 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8095 (ptm160) REVERT: A 995 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: B 936 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7981 (mp) REVERT: B 1002 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8006 (tm-30) outliers start: 37 outliers final: 29 residues processed: 74 average time/residue: 0.1934 time to fit residues: 19.5863 Evaluate side-chains 70 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 38 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 878 TYR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 895 MET Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 995 PHE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 870 SER Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain B residue 939 CYS Chi-restraints excluded: chain B residue 949 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 THR Chi-restraints excluded: chain B residue 1016 THR Chi-restraints excluded: chain B residue 1023 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 111 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.179495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.173702 restraints weight = 9358.371| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 0.45 r_work: 0.3853 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7779 Z= 0.277 Angle : 0.774 6.355 10757 Z= 0.345 Chirality : 0.041 0.169 1425 Planarity : 0.003 0.045 1457 Dihedral : 8.712 71.786 1422 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 9.32 % Allowed : 27.97 % Favored : 62.70 % 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: -0.59 (0.41), residues: 418 helix: 0.25 (0.42), residues: 162 sheet: 0.06 (0.52), residues: 84 loop : -1.16 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1050 HIS 0.008 0.002 HIS A 963 PHE 0.008 0.001 PHE B 868 TYR 0.011 0.002 TYR A 878 ARG 0.002 0.000 ARG B1000 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 43 time to evaluate : 0.507 Fit side-chains REVERT: A 995 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.8009 (m-80) REVERT: B 1002 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7937 (tm-30) outliers start: 29 outliers final: 24 residues processed: 69 average time/residue: 0.1665 time to fit residues: 16.4178 Evaluate side-chains 68 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 43 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 995 PHE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 870 SER Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 939 CYS Chi-restraints excluded: chain B residue 949 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1016 THR Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain B residue 1022 GLU Chi-restraints excluded: chain B residue 1023 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.178950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.174475 restraints weight = 9436.830| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 0.38 r_work: 0.3840 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7779 Z= 0.405 Angle : 0.931 7.796 10757 Z= 0.415 Chirality : 0.047 0.179 1425 Planarity : 0.003 0.046 1457 Dihedral : 9.063 72.106 1422 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 11.25 % Allowed : 27.01 % Favored : 61.74 % 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: -0.67 (0.41), residues: 418 helix: 0.12 (0.42), residues: 162 sheet: 0.25 (0.57), residues: 77 loop : -1.21 (0.47), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1050 HIS 0.010 0.003 HIS A 963 PHE 0.009 0.002 PHE B 868 TYR 0.013 0.002 TYR B 923 ARG 0.003 0.000 ARG B1000 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 36 time to evaluate : 0.531 Fit side-chains REVERT: A 962 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8063 (ptm160) REVERT: A 995 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8149 (m-80) REVERT: B 1002 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7966 (tm-30) outliers start: 35 outliers final: 29 residues processed: 67 average time/residue: 0.1684 time to fit residues: 15.8507 Evaluate side-chains 67 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 36 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 895 MET Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 995 PHE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 870 SER Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 939 CYS Chi-restraints excluded: chain B residue 949 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 THR Chi-restraints excluded: chain B residue 1016 THR Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain B residue 1022 GLU Chi-restraints excluded: chain B residue 1023 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 3 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.173089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.167316 restraints weight = 9602.620| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 0.44 r_work: 0.3817 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 7779 Z= 0.469 Angle : 1.006 8.984 10757 Z= 0.449 Chirality : 0.050 0.180 1425 Planarity : 0.004 0.047 1457 Dihedral : 9.261 72.904 1422 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 12.54 % Allowed : 25.40 % Favored : 62.06 % 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: -0.86 (0.41), residues: 418 helix: -0.01 (0.42), residues: 162 sheet: 0.16 (0.58), residues: 77 loop : -1.35 (0.46), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A1050 HIS 0.010 0.003 HIS A 963 PHE 0.011 0.002 PHE B 868 TYR 0.015 0.002 TYR B 923 ARG 0.004 0.000 ARG B1000 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 37 time to evaluate : 0.572 Fit side-chains REVERT: A 962 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8076 (ptm160) REVERT: A 995 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.8156 (m-80) REVERT: B 936 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7922 (mp) outliers start: 39 outliers final: 32 residues processed: 72 average time/residue: 0.1740 time to fit residues: 17.7650 Evaluate side-chains 72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 37 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 895 MET Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 995 PHE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain B residue 870 SER Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain B residue 939 CYS Chi-restraints excluded: chain B residue 949 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 THR Chi-restraints excluded: chain B residue 1016 THR Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain B residue 1022 GLU Chi-restraints excluded: chain B residue 1023 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 117 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.178624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.172896 restraints weight = 9494.467| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 0.45 r_work: 0.3853 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3738 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7779 Z= 0.319 Angle : 0.815 6.504 10757 Z= 0.365 Chirality : 0.043 0.170 1425 Planarity : 0.003 0.046 1457 Dihedral : 8.701 72.340 1422 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 10.61 % Allowed : 27.33 % Favored : 62.06 % 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: -0.69 (0.41), residues: 418 helix: 0.14 (0.42), residues: 162 sheet: 0.11 (0.57), residues: 77 loop : -1.20 (0.47), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1050 HIS 0.009 0.002 HIS A 963 PHE 0.009 0.002 PHE B 868 TYR 0.012 0.002 TYR A 878 ARG 0.002 0.000 ARG B1000 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 43 time to evaluate : 0.515 Fit side-chains REVERT: A 962 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8069 (ptm160) REVERT: A 995 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.8085 (m-80) REVERT: B 1002 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7855 (tm-30) outliers start: 33 outliers final: 29 residues processed: 73 average time/residue: 0.1743 time to fit residues: 18.0817 Evaluate side-chains 72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 41 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 995 PHE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 870 SER Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 939 CYS Chi-restraints excluded: chain B residue 949 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 THR Chi-restraints excluded: chain B residue 1016 THR Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain B residue 1022 GLU Chi-restraints excluded: chain B residue 1023 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 15 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 119 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.178307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.172495 restraints weight = 9564.798| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 0.45 r_work: 0.3864 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7779 Z= 0.329 Angle : 0.832 6.668 10757 Z= 0.372 Chirality : 0.043 0.171 1425 Planarity : 0.003 0.045 1457 Dihedral : 8.698 72.076 1422 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 10.61 % Allowed : 26.69 % Favored : 62.70 % 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: -0.64 (0.41), residues: 418 helix: 0.17 (0.42), residues: 162 sheet: 0.12 (0.57), residues: 77 loop : -1.15 (0.47), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1050 HIS 0.009 0.002 HIS A 963 PHE 0.009 0.002 PHE B 868 TYR 0.011 0.002 TYR A 878 ARG 0.002 0.000 ARG B1000 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 41 time to evaluate : 0.540 Fit side-chains REVERT: A 962 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8054 (ptm160) REVERT: A 995 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.8128 (m-80) REVERT: B 1002 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7928 (tm-30) outliers start: 33 outliers final: 30 residues processed: 70 average time/residue: 0.1762 time to fit residues: 17.6541 Evaluate side-chains 73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 41 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 995 PHE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 870 SER Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 939 CYS Chi-restraints excluded: chain B residue 949 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1016 THR Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain B residue 1022 GLU Chi-restraints excluded: chain B residue 1023 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 56 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.173073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.167288 restraints weight = 9650.468| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 0.44 r_work: 0.3819 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 7779 Z= 0.461 Angle : 0.997 8.907 10757 Z= 0.446 Chirality : 0.049 0.183 1425 Planarity : 0.004 0.046 1457 Dihedral : 9.160 72.814 1422 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 11.25 % Allowed : 26.05 % Favored : 62.70 % 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: -0.83 (0.41), residues: 418 helix: -0.02 (0.41), residues: 162 sheet: 0.16 (0.58), residues: 77 loop : -1.30 (0.46), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A1050 HIS 0.010 0.003 HIS A 963 PHE 0.011 0.002 PHE B 868 TYR 0.013 0.002 TYR B 923 ARG 0.004 0.000 ARG B1000 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 35 time to evaluate : 0.563 Fit side-chains REVERT: A 962 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8084 (ptm160) REVERT: A 995 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8162 (m-80) REVERT: B 874 TYR cc_start: 0.8960 (OUTLIER) cc_final: 0.8551 (t80) REVERT: B 1002 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7935 (tm-30) outliers start: 35 outliers final: 31 residues processed: 66 average time/residue: 0.1687 time to fit residues: 15.9267 Evaluate side-chains 69 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 35 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 895 MET Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 995 PHE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 870 SER Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 874 TYR Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 939 CYS Chi-restraints excluded: chain B residue 949 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1016 THR Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain B residue 1022 GLU Chi-restraints excluded: chain B residue 1023 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 32 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.183773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.172493 restraints weight = 9387.199| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.22 r_work: 0.3790 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7779 Z= 0.153 Angle : 0.597 5.804 10757 Z= 0.270 Chirality : 0.034 0.156 1425 Planarity : 0.003 0.045 1457 Dihedral : 7.925 70.883 1422 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 5.79 % Allowed : 31.51 % Favored : 62.70 % 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: -0.28 (0.42), residues: 418 helix: 0.76 (0.43), residues: 157 sheet: -0.01 (0.51), residues: 90 loop : -1.12 (0.49), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1050 HIS 0.004 0.001 HIS A 963 PHE 0.006 0.001 PHE B 868 TYR 0.009 0.001 TYR B 874 ARG 0.001 0.000 ARG A 939 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3260.76 seconds wall clock time: 58 minutes 46.98 seconds (3526.98 seconds total)