Starting phenix.real_space_refine on Wed Sep 17 09:36:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bcv_44440/09_2025/9bcv_44440.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bcv_44440/09_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_44440/09_2025/9bcv_44440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bcv_44440/09_2025/9bcv_44440.map" model { file = "/net/cci-nas-00/data/ceres_data/9bcv_44440/09_2025/9bcv_44440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bcv_44440/09_2025/9bcv_44440.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 6, 'ASP:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 1} 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: {'GLU:plan': 5, 'ASP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1} 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: 2.24, per 1000 atoms: 0.29 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: 0.62 Conformation dependent library (CDL) restraints added in 265.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.39 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: 1.19 Time building geometry restraints manager: 0.84 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: 1.120 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.630 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.290 ------------------------------------------------------------------------------- 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 7780 Z= 0.168 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (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 ARG 0.002 0.000 ARG B1000 TYR 0.010 0.001 TYR A 878 PHE 0.007 0.001 PHE B 868 TRP 0.008 0.002 TRP A1050 HIS 0.006 0.002 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 7779) covalent geometry : angle 0.86030 (10757) hydrogen bonds : bond 0.12439 ( 356) hydrogen bonds : angle 5.70877 ( 1026) Misc. bond : bond 0.00354 ( 1) *********************** 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 : 0.138 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 0.0973 time to fit residues: 4.5525 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 : 0.182 ------------------------------------------------------------------------------- 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 98 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 overall best weight: 4.9186 ------------------------------------------------------------------------------- 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 = 0.175957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.170151 restraints weight = 9426.676| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 0.45 r_work: 0.3782 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.055 7780 Z= 0.393 Angle : 1.129 8.383 10757 Z= 0.506 Chirality : 0.055 0.200 1425 Planarity : 0.004 0.048 1457 Dihedral : 10.574 79.223 1422 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 9.00 % Allowed : 27.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.41), residues: 418 helix: -0.01 (0.41), residues: 162 sheet: 0.36 (0.54), residues: 77 loop : -1.19 (0.47), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1000 TYR 0.014 0.003 TYR A 878 PHE 0.013 0.003 PHE B 868 TRP 0.008 0.002 TRP A1050 HIS 0.011 0.003 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.00905 ( 7779) covalent geometry : angle 1.12908 (10757) hydrogen bonds : bond 0.05494 ( 356) hydrogen bonds : angle 4.85232 ( 1026) Misc. bond : bond 0.00231 ( 1) *********************** 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 60 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 32 time to evaluate : 0.194 Fit side-chains REVERT: A 962 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8094 (ptm160) REVERT: A 995 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: B 936 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7931 (mp) outliers start: 28 outliers final: 21 residues processed: 59 average time/residue: 0.1062 time to fit residues: 8.3524 Evaluate side-chains 54 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 30 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 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 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 33 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.173714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.167593 restraints weight = 9539.355| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 0.47 r_work: 0.3819 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 7780 Z= 0.307 Angle : 0.965 7.178 10757 Z= 0.433 Chirality : 0.049 0.180 1425 Planarity : 0.004 0.047 1457 Dihedral : 10.064 74.013 1422 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 8.04 % Allowed : 28.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.41), residues: 418 helix: 0.08 (0.42), residues: 162 sheet: 0.09 (0.52), residues: 84 loop : -1.25 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1000 TYR 0.013 0.002 TYR A 878 PHE 0.012 0.002 PHE B 868 TRP 0.010 0.002 TRP A1050 HIS 0.010 0.003 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.00710 ( 7779) covalent geometry : angle 0.96518 (10757) hydrogen bonds : bond 0.04761 ( 356) hydrogen bonds : angle 4.53810 ( 1026) Misc. bond : bond 0.00194 ( 1) *********************** 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 60 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 35 time to evaluate : 0.187 Fit side-chains REVERT: A 995 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8018 (m-80) REVERT: B 936 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7917 (mp) REVERT: B 991 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8604 (m-80) outliers start: 25 outliers final: 18 residues processed: 58 average time/residue: 0.0870 time to fit residues: 6.8969 Evaluate side-chains 60 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 39 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 878 TYR Chi-restraints excluded: chain A residue 895 MET Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 995 PHE Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1020 THR 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 991 PHE Chi-restraints excluded: chain B residue 994 THR 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 2 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.177972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.172163 restraints weight = 9582.208| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 0.45 r_work: 0.3843 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 7780 Z= 0.242 Angle : 0.854 6.670 10757 Z= 0.382 Chirality : 0.044 0.173 1425 Planarity : 0.003 0.046 1457 Dihedral : 9.245 71.691 1422 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 10.61 % Allowed : 25.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.41), residues: 418 helix: 0.19 (0.42), residues: 162 sheet: 0.03 (0.51), residues: 84 loop : -1.22 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1004 TYR 0.013 0.002 TYR A 878 PHE 0.010 0.002 PHE B 868 TRP 0.010 0.002 TRP A1050 HIS 0.009 0.002 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 7779) covalent geometry : angle 0.85400 (10757) hydrogen bonds : bond 0.04137 ( 356) hydrogen bonds : angle 4.27140 ( 1026) Misc. bond : bond 0.00168 ( 1) *********************** 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 75 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 42 time to evaluate : 0.183 Fit side-chains REVERT: A 962 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8057 (ptm160) REVERT: A 995 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8217 (m-80) REVERT: B 1002 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8028 (tm-30) outliers start: 33 outliers final: 24 residues processed: 71 average time/residue: 0.0695 time to fit residues: 7.0424 Evaluate side-chains 67 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 41 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 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 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 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 1023 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 = 0.176516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.170342 restraints weight = 9546.231| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 0.48 r_work: 0.3816 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 7780 Z= 0.273 Angle : 0.924 7.017 10757 Z= 0.413 Chirality : 0.047 0.176 1425 Planarity : 0.003 0.046 1457 Dihedral : 9.409 72.161 1422 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 2.28 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.41), residues: 418 helix: 0.13 (0.42), residues: 162 sheet: 0.28 (0.57), residues: 77 loop : -1.24 (0.47), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1000 TYR 0.012 0.002 TYR A 878 PHE 0.010 0.002 PHE B 868 TRP 0.009 0.002 TRP A1050 HIS 0.009 0.003 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.00631 ( 7779) covalent geometry : angle 0.92424 (10757) hydrogen bonds : bond 0.04490 ( 356) hydrogen bonds : angle 4.44060 ( 1026) Misc. bond : bond 0.00136 ( 1) *********************** 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 79 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 42 time to evaluate : 0.197 Fit side-chains REVERT: A 962 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8091 (ptm160) REVERT: A 995 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: B 936 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7960 (mp) REVERT: B 1002 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8006 (tm-30) outliers start: 37 outliers final: 28 residues processed: 75 average time/residue: 0.0732 time to fit residues: 7.9763 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 : 0.152 ------------------------------------------------------------------------------- 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 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 1016 THR Chi-restraints excluded: chain B residue 1021 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 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 107 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 = 0.178699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.173007 restraints weight = 9515.127| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 0.44 r_work: 0.3858 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7780 Z= 0.218 Angle : 0.808 6.436 10757 Z= 0.362 Chirality : 0.042 0.170 1425 Planarity : 0.003 0.045 1457 Dihedral : 9.039 72.013 1422 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 9.97 % Allowed : 27.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.41), residues: 418 helix: 0.25 (0.42), residues: 162 sheet: 0.21 (0.56), residues: 77 loop : -1.18 (0.47), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1000 TYR 0.012 0.002 TYR A 878 PHE 0.009 0.002 PHE B 868 TRP 0.010 0.002 TRP A1050 HIS 0.009 0.002 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.00503 ( 7779) covalent geometry : angle 0.80827 (10757) hydrogen bonds : bond 0.03921 ( 356) hydrogen bonds : angle 4.16828 ( 1026) Misc. bond : bond 0.00160 ( 1) *********************** 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 73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 42 time to evaluate : 0.177 Fit side-chains REVERT: A 962 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8036 (ptm160) REVERT: A 995 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.8151 (m-80) REVERT: B 1002 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7942 (tm-30) outliers start: 31 outliers final: 26 residues processed: 71 average time/residue: 0.0695 time to fit residues: 7.0773 Evaluate side-chains 69 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 41 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 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 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 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 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 53 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.180468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.174730 restraints weight = 9510.345| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 0.45 r_work: 0.3860 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7780 Z= 0.172 Angle : 0.718 6.125 10757 Z= 0.322 Chirality : 0.039 0.166 1425 Planarity : 0.003 0.044 1457 Dihedral : 8.652 71.520 1422 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 9.65 % Allowed : 27.33 % Favored : 63.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.41), residues: 418 helix: 0.51 (0.43), residues: 159 sheet: -0.01 (0.50), residues: 90 loop : -1.19 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1000 TYR 0.011 0.001 TYR A 878 PHE 0.009 0.001 PHE B 868 TRP 0.011 0.002 TRP A1050 HIS 0.008 0.002 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 7779) covalent geometry : angle 0.71753 (10757) hydrogen bonds : bond 0.03468 ( 356) hydrogen bonds : angle 3.97061 ( 1026) Misc. bond : bond 0.00168 ( 1) *********************** 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 72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 42 time to evaluate : 0.185 Fit side-chains REVERT: A 962 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7879 (ptm160) REVERT: A 995 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8090 (m-80) REVERT: B 1002 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8046 (tm-30) outliers start: 30 outliers final: 22 residues processed: 68 average time/residue: 0.0808 time to fit residues: 7.7408 Evaluate side-chains 65 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 41 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 907 CYS 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 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 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 1023 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 56 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 99 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.172188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.166358 restraints weight = 9715.475| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 0.45 r_work: 0.3769 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.061 7780 Z= 0.453 Angle : 1.216 9.608 10757 Z= 0.546 Chirality : 0.059 0.211 1425 Planarity : 0.004 0.048 1457 Dihedral : 10.064 73.256 1422 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.11 % Favored : 96.41 % Rotamer: Outliers : 11.90 % Allowed : 25.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.40), residues: 418 helix: -0.21 (0.40), residues: 162 sheet: 0.21 (0.62), residues: 68 loop : -1.42 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1000 TYR 0.016 0.003 TYR A 878 PHE 0.016 0.003 PHE B 868 TRP 0.006 0.002 TRP B1046 HIS 0.012 0.004 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.01045 ( 7779) covalent geometry : angle 1.21596 (10757) hydrogen bonds : bond 0.05805 ( 356) hydrogen bonds : angle 4.89712 ( 1026) Misc. bond : bond 0.00065 ( 1) *********************** 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 77 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 40 time to evaluate : 0.187 Fit side-chains REVERT: A 962 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8129 (ptm160) REVERT: A 995 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.8236 (m-80) REVERT: B 874 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.8692 (t80) REVERT: B 877 ASP cc_start: 0.8401 (p0) cc_final: 0.8100 (p0) REVERT: B 936 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7988 (mp) outliers start: 37 outliers final: 30 residues processed: 74 average time/residue: 0.0864 time to fit residues: 8.7422 Evaluate side-chains 73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 39 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 878 TYR 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 907 CYS Chi-restraints excluded: chain A residue 923 ILE 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 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 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 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 127 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.176598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.170978 restraints weight = 9503.147| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 0.44 r_work: 0.3830 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 7780 Z= 0.276 Angle : 0.921 6.976 10757 Z= 0.413 Chirality : 0.047 0.173 1425 Planarity : 0.003 0.047 1457 Dihedral : 9.322 72.893 1422 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 10.29 % Allowed : 27.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.41), residues: 418 helix: -0.01 (0.41), residues: 162 sheet: 0.12 (0.58), residues: 77 loop : -1.33 (0.46), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1000 TYR 0.013 0.002 TYR A 878 PHE 0.011 0.002 PHE B 868 TRP 0.010 0.002 TRP A1050 HIS 0.009 0.003 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.00636 ( 7779) covalent geometry : angle 0.92071 (10757) hydrogen bonds : bond 0.04453 ( 356) hydrogen bonds : angle 4.39906 ( 1026) Misc. bond : bond 0.00125 ( 1) *********************** 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 73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 41 time to evaluate : 0.199 Fit side-chains REVERT: A 962 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8070 (ptm160) REVERT: A 995 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: B 874 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8711 (t80) REVERT: B 991 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8607 (m-80) REVERT: B 1002 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7907 (tm-30) outliers start: 32 outliers final: 28 residues processed: 70 average time/residue: 0.0785 time to fit residues: 7.8792 Evaluate side-chains 66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 34 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 907 CYS Chi-restraints excluded: chain A residue 923 ILE 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 852 SER Chi-restraints excluded: chain B residue 870 SER 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 991 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 67 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.175725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.169502 restraints weight = 9579.344| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 0.49 r_work: 0.3805 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 7780 Z= 0.301 Angle : 0.970 7.121 10757 Z= 0.434 Chirality : 0.048 0.181 1425 Planarity : 0.004 0.047 1457 Dihedral : 9.439 73.025 1422 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 10.29 % Allowed : 27.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.41), residues: 418 helix: -0.04 (0.41), residues: 162 sheet: 0.11 (0.58), residues: 77 loop : -1.37 (0.46), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1000 TYR 0.013 0.002 TYR A 878 PHE 0.011 0.002 PHE B 868 TRP 0.008 0.002 TRP A1050 HIS 0.009 0.003 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.00693 ( 7779) covalent geometry : angle 0.97013 (10757) hydrogen bonds : bond 0.04673 ( 356) hydrogen bonds : angle 4.49648 ( 1026) Misc. bond : bond 0.00117 ( 1) ********************** 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 66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 34 time to evaluate : 0.207 Fit side-chains REVERT: A 962 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8120 (ptm160) REVERT: A 995 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.8198 (m-80) REVERT: B 874 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.8755 (t80) REVERT: B 991 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8618 (m-80) REVERT: B 1002 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7989 (tm-30) outliers start: 32 outliers final: 28 residues processed: 64 average time/residue: 0.0746 time to fit residues: 6.8076 Evaluate side-chains 66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 34 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 907 CYS Chi-restraints excluded: chain A residue 923 ILE 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 852 SER Chi-restraints excluded: chain B residue 870 SER 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 991 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 83 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 78 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.176297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.169740 restraints weight = 9520.138| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 0.53 r_work: 0.3790 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 7780 Z= 0.283 Angle : 0.937 6.959 10757 Z= 0.419 Chirality : 0.047 0.177 1425 Planarity : 0.003 0.046 1457 Dihedral : 9.363 72.999 1422 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.41), residues: 418 helix: 0.01 (0.41), residues: 162 sheet: 0.14 (0.58), residues: 77 loop : -1.35 (0.46), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1000 TYR 0.013 0.002 TYR A 878 PHE 0.010 0.002 PHE B 868 TRP 0.009 0.002 TRP A1050 HIS 0.009 0.003 HIS A 963 Details of bonding type rmsd covalent geometry : bond 0.00652 ( 7779) covalent geometry : angle 0.93667 (10757) hydrogen bonds : bond 0.04510 ( 356) hydrogen bonds : angle 4.42723 ( 1026) Misc. bond : bond 0.00122 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1671.79 seconds wall clock time: 29 minutes 9.83 seconds (1749.83 seconds total)