Starting phenix.real_space_refine on Thu Sep 18 14:52:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h80_51916/09_2025/9h80_51916.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h80_51916/09_2025/9h80_51916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h80_51916/09_2025/9h80_51916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h80_51916/09_2025/9h80_51916.map" model { file = "/net/cci-nas-00/data/ceres_data/9h80_51916/09_2025/9h80_51916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h80_51916/09_2025/9h80_51916.cif" } resolution = 2.5 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= -0.001 sd= 0.039 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 15 5.16 5 C 11107 2.51 5 N 3199 2.21 5 O 3418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s 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: 17742 Number of models: 1 Model: "" Number of chains: 26 Chain: "M" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3067 Classifications: {'peptide': 391} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 382} Chain: "C" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1187 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "D" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1187 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1187 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "F" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1187 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "G" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1187 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "H" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1187 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "I" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1187 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "J" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1187 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "K" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1187 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "L" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1187 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "A" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1187 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "B" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1187 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "M" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'PTY': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 4.72, per 1000 atoms: 0.27 Number of scatterers: 17742 At special positions: 0 Unit cell: (108.323, 135.222, 132.314, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 3 15.00 O 3418 8.00 N 3199 7.00 C 11107 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=24, symmetry=0 Number of additional bonds: simple=24, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 960.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4030 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 30 sheets defined 31.0% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'M' and resid 804 through 815 Processing helix chain 'M' and resid 816 through 826 Processing helix chain 'M' and resid 830 through 841 Processing helix chain 'M' and resid 843 through 853 removed outlier: 3.535A pdb=" N ALA M 847 " --> pdb=" O HIS M 843 " (cutoff:3.500A) Processing helix chain 'M' and resid 862 through 878 Processing helix chain 'M' and resid 995 through 1001 Processing helix chain 'M' and resid 1077 through 1081 Processing helix chain 'M' and resid 1094 through 1099 removed outlier: 4.152A pdb=" N LEU M1098 " --> pdb=" O ARG M1094 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 65 removed outlier: 3.672A pdb=" N GLU C 65 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 99 removed outlier: 3.711A pdb=" N TRP C 95 " --> pdb=" O ARG C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 169 Processing helix chain 'D' and resid 49 through 65 removed outlier: 3.577A pdb=" N GLU D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 153 through 169 Processing helix chain 'E' and resid 49 through 65 Processing helix chain 'E' and resid 84 through 99 removed outlier: 3.681A pdb=" N TRP E 95 " --> pdb=" O ARG E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 168 Processing helix chain 'F' and resid 49 through 65 removed outlier: 3.554A pdb=" N SER F 60 " --> pdb=" O GLN F 56 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU F 65 " --> pdb=" O VAL F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 84 through 99 Processing helix chain 'F' and resid 153 through 169 Processing helix chain 'G' and resid 49 through 65 Processing helix chain 'G' and resid 84 through 100 Processing helix chain 'G' and resid 153 through 169 Processing helix chain 'H' and resid 49 through 66 Processing helix chain 'H' and resid 84 through 100 Processing helix chain 'H' and resid 153 through 169 Processing helix chain 'I' and resid 49 through 65 Processing helix chain 'I' and resid 84 through 100 Processing helix chain 'I' and resid 153 through 169 Processing helix chain 'J' and resid 49 through 65 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.577A pdb=" N VAL J 83 " --> pdb=" O LEU J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 99 Processing helix chain 'J' and resid 153 through 169 Processing helix chain 'K' and resid 49 through 65 removed outlier: 3.526A pdb=" N GLU K 65 " --> pdb=" O VAL K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 99 Processing helix chain 'K' and resid 153 through 169 Processing helix chain 'L' and resid 49 through 65 Processing helix chain 'L' and resid 84 through 100 Processing helix chain 'L' and resid 153 through 169 Processing helix chain 'A' and resid 49 through 65 Processing helix chain 'A' and resid 84 through 99 removed outlier: 3.650A pdb=" N ARG A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 Processing helix chain 'B' and resid 49 through 65 Processing helix chain 'B' and resid 84 through 99 removed outlier: 3.571A pdb=" N ARG B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 168 Processing sheet with id=AA1, first strand: chain 'M' and resid 921 through 924 removed outlier: 3.505A pdb=" N GLY M 949 " --> pdb=" O LEU M 946 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N HIS M 966 " --> pdb=" O ARG M 990 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG M 990 " --> pdb=" O HIS M 966 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP M 980 " --> pdb=" O LEU M 976 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ARG M1004 " --> pdb=" O HIS M 989 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER M1031 " --> pdb=" O MET M1003 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN M1020 " --> pdb=" O TRP M1048 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TRP M1048 " --> pdb=" O GLN M1020 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER M1022 " --> pdb=" O LEU M1046 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU M1046 " --> pdb=" O SER M1022 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER M1024 " --> pdb=" O LEU M1044 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU M1044 " --> pdb=" O SER M1024 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA M1026 " --> pdb=" O GLU M1042 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU M1042 " --> pdb=" O ALA M1026 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN M1028 " --> pdb=" O ASN M1040 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASN M1040 " --> pdb=" O ASN M1028 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE M1030 " --> pdb=" O LEU M1038 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TRP M1059 " --> pdb=" O LEU M1052 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG M 889 " --> pdb=" O PHE M 896 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 20 through 22 removed outlier: 6.749A pdb=" N SER C 127 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL C 109 " --> pdb=" O SER C 127 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN C 129 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLY C 107 " --> pdb=" O GLN C 129 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL C 105 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU C 42 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU C 111 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 22 removed outlier: 6.749A pdb=" N SER C 127 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL C 109 " --> pdb=" O SER C 127 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN C 129 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLY C 107 " --> pdb=" O GLN C 129 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL C 105 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY C 37 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N GLY C 107 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TRP C 36 " --> pdb=" O ARG C 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 30 through 31 removed outlier: 6.658A pdb=" N LEU C 30 " --> pdb=" O GLU C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 20 through 22 removed outlier: 7.052A pdb=" N ALA D 123 " --> pdb=" O TRP D 112 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP D 112 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLY D 125 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 20 through 22 removed outlier: 7.052A pdb=" N ALA D 123 " --> pdb=" O TRP D 112 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP D 112 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLY D 125 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU D 42 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N GLU D 111 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 20 through 22 removed outlier: 6.984A pdb=" N ALA E 123 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TRP E 112 " --> pdb=" O ALA E 123 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLY E 125 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU E 42 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU E 111 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 37 through 38 Processing sheet with id=AA9, first strand: chain 'F' and resid 20 through 22 removed outlier: 6.806A pdb=" N SER F 127 " --> pdb=" O VAL F 109 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL F 109 " --> pdb=" O SER F 127 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLN F 129 " --> pdb=" O GLY F 107 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY F 107 " --> pdb=" O GLN F 129 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU F 131 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL F 105 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU F 42 " --> pdb=" O VAL F 109 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLU F 111 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 20 through 22 removed outlier: 6.806A pdb=" N SER F 127 " --> pdb=" O VAL F 109 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL F 109 " --> pdb=" O SER F 127 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLN F 129 " --> pdb=" O GLY F 107 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY F 107 " --> pdb=" O GLN F 129 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU F 131 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL F 105 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY F 37 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N GLY F 107 " --> pdb=" O GLY F 37 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N TRP F 36 " --> pdb=" O ARG F 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 30 through 31 removed outlier: 6.828A pdb=" N LEU F 30 " --> pdb=" O GLU F 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 20 through 22 removed outlier: 7.016A pdb=" N ALA G 123 " --> pdb=" O TRP G 112 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP G 112 " --> pdb=" O ALA G 123 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLY G 125 " --> pdb=" O GLU G 110 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU G 42 " --> pdb=" O VAL G 109 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N GLU G 111 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 20 through 22 removed outlier: 7.016A pdb=" N ALA G 123 " --> pdb=" O TRP G 112 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP G 112 " --> pdb=" O ALA G 123 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLY G 125 " --> pdb=" O GLU G 110 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY G 37 " --> pdb=" O VAL G 105 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N GLY G 107 " --> pdb=" O GLY G 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 30 through 31 removed outlier: 6.831A pdb=" N LEU G 30 " --> pdb=" O GLU G 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.793A pdb=" N SER H 127 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL H 109 " --> pdb=" O SER H 127 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLN H 129 " --> pdb=" O GLY H 107 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY H 107 " --> pdb=" O GLN H 129 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU H 131 " --> pdb=" O VAL H 105 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL H 105 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU H 42 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLU H 111 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.793A pdb=" N SER H 127 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL H 109 " --> pdb=" O SER H 127 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLN H 129 " --> pdb=" O GLY H 107 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY H 107 " --> pdb=" O GLN H 129 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU H 131 " --> pdb=" O VAL H 105 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL H 105 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY H 37 " --> pdb=" O VAL H 105 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLY H 107 " --> pdb=" O GLY H 37 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N TRP H 36 " --> pdb=" O ARG H 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 20 through 22 removed outlier: 6.986A pdb=" N ALA I 123 " --> pdb=" O TRP I 112 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TRP I 112 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLY I 125 " --> pdb=" O GLU I 110 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TRP I 36 " --> pdb=" O TYR I 103 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL I 105 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU I 38 " --> pdb=" O VAL I 105 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N GLY I 107 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N VAL I 109 " --> pdb=" O PRO I 40 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU I 42 " --> pdb=" O VAL I 109 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLU I 111 " --> pdb=" O LEU I 42 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N TRP I 36 " --> pdb=" O ARG I 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 30 through 31 removed outlier: 6.931A pdb=" N LEU I 30 " --> pdb=" O GLU I 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'J' and resid 20 through 22 removed outlier: 7.075A pdb=" N ALA J 123 " --> pdb=" O TRP J 112 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP J 112 " --> pdb=" O ALA J 123 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLY J 125 " --> pdb=" O GLU J 110 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU J 42 " --> pdb=" O VAL J 109 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N GLU J 111 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 30 through 31 removed outlier: 6.625A pdb=" N LEU J 30 " --> pdb=" O GLU J 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'J' and resid 37 through 38 Processing sheet with id=AC4, first strand: chain 'K' and resid 20 through 22 removed outlier: 6.703A pdb=" N LEU K 42 " --> pdb=" O VAL K 109 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLU K 111 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 30 through 31 removed outlier: 7.394A pdb=" N LEU K 30 " --> pdb=" O GLU K 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'L' and resid 20 through 22 removed outlier: 6.939A pdb=" N SER L 127 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL L 109 " --> pdb=" O SER L 127 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLN L 129 " --> pdb=" O GLY L 107 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLY L 107 " --> pdb=" O GLN L 129 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU L 131 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL L 105 " --> pdb=" O LEU L 131 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU L 42 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N GLU L 111 " --> pdb=" O LEU L 42 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 20 through 22 removed outlier: 6.939A pdb=" N SER L 127 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL L 109 " --> pdb=" O SER L 127 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLN L 129 " --> pdb=" O GLY L 107 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLY L 107 " --> pdb=" O GLN L 129 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU L 131 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL L 105 " --> pdb=" O LEU L 131 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLY L 37 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N GLY L 107 " --> pdb=" O GLY L 37 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 30 through 31 removed outlier: 7.883A pdb=" N LEU L 30 " --> pdb=" O GLU L 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.893A pdb=" N SER A 127 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL A 109 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLN A 129 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY A 107 " --> pdb=" O GLN A 129 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU A 131 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL A 105 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 42 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N GLU A 111 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AD2, first strand: chain 'B' and resid 20 through 22 removed outlier: 4.045A pdb=" N GLU B 121 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER B 127 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL B 109 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN B 129 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY B 107 " --> pdb=" O GLN B 129 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU B 131 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL B 105 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 20 through 22 removed outlier: 4.045A pdb=" N GLU B 121 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER B 127 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL B 109 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN B 129 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY B 107 " --> pdb=" O GLN B 129 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU B 131 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL B 105 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLY B 37 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N GLY B 107 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TRP B 36 " --> pdb=" O ARG B 70 " (cutoff:3.500A) 949 hydrogen bonds defined for protein. 2796 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.61 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3290 1.32 - 1.45: 4500 1.45 - 1.57: 10226 1.57 - 1.69: 6 1.69 - 1.81: 18 Bond restraints: 18040 Sorted by residual: bond pdb=" C8 PTY C 201 " pdb=" O7 PTY C 201 " ideal model delta sigma weight residual 1.331 1.208 0.123 2.00e-02 2.50e+03 3.81e+01 bond pdb=" N GLY M 803 " pdb=" CA GLY M 803 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.99e+00 bond pdb=" N CYS D 19 " pdb=" CA CYS D 19 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.46e+00 bond pdb=" N CYS C 19 " pdb=" CA CYS C 19 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N CYS L 19 " pdb=" CA CYS L 19 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 ... (remaining 18035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 24018 2.42 - 4.85: 301 4.85 - 7.27: 45 7.27 - 9.69: 1 9.69 - 12.12: 1 Bond angle restraints: 24366 Sorted by residual: angle pdb=" C11 PTY C 201 " pdb=" C8 PTY C 201 " pdb=" O7 PTY C 201 " ideal model delta sigma weight residual 111.29 123.41 -12.12 3.00e+00 1.11e-01 1.63e+01 angle pdb=" N VAL C 83 " pdb=" CA VAL C 83 " pdb=" C VAL C 83 " ideal model delta sigma weight residual 113.53 109.86 3.67 9.80e-01 1.04e+00 1.40e+01 angle pdb=" N GLY M 920 " pdb=" CA GLY M 920 " pdb=" C GLY M 920 " ideal model delta sigma weight residual 110.63 115.98 -5.35 1.45e+00 4.76e-01 1.36e+01 angle pdb=" C ARG M 861 " pdb=" N ASP M 862 " pdb=" CA ASP M 862 " ideal model delta sigma weight residual 121.54 128.21 -6.67 1.91e+00 2.74e-01 1.22e+01 angle pdb=" CA LYS J 100 " pdb=" CB LYS J 100 " pdb=" CG LYS J 100 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 ... (remaining 24361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.27: 9998 25.27 - 50.54: 626 50.54 - 75.81: 232 75.81 - 101.08: 22 101.08 - 126.35: 1 Dihedral angle restraints: 10879 sinusoidal: 4566 harmonic: 6313 Sorted by residual: dihedral pdb=" CA PRO M1125 " pdb=" C PRO M1125 " pdb=" N GLN M1126 " pdb=" CA GLN M1126 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" N1 PTY M1201 " pdb=" C2 PTY M1201 " pdb=" C3 PTY M1201 " pdb=" O11 PTY M1201 " ideal model delta sinusoidal sigma weight residual 65.33 -61.02 126.35 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" CA ALA B 147 " pdb=" C ALA B 147 " pdb=" N GLY B 148 " pdb=" CA GLY B 148 " ideal model delta harmonic sigma weight residual 180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 10876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1768 0.034 - 0.068: 605 0.068 - 0.102: 112 0.102 - 0.136: 98 0.136 - 0.170: 3 Chirality restraints: 2586 Sorted by residual: chirality pdb=" CG LEU D 93 " pdb=" CB LEU D 93 " pdb=" CD1 LEU D 93 " pdb=" CD2 LEU D 93 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA VAL M1076 " pdb=" N VAL M1076 " pdb=" C VAL M1076 " pdb=" CB VAL M1076 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA VAL B 39 " pdb=" N VAL B 39 " pdb=" C VAL B 39 " pdb=" CB VAL B 39 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 2583 not shown) Planarity restraints: 3232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 28 " -0.060 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO D 29 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO D 29 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 29 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP M 862 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C ASP M 862 " 0.056 2.00e-02 2.50e+03 pdb=" O ASP M 862 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN M 863 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 88 " 0.254 9.50e-02 1.11e+02 1.15e-01 9.84e+00 pdb=" NE ARG H 88 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG H 88 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG H 88 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG H 88 " 0.001 2.00e-02 2.50e+03 ... (remaining 3229 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 356 2.68 - 3.24: 16166 3.24 - 3.79: 28263 3.79 - 4.35: 39669 4.35 - 4.90: 65760 Nonbonded interactions: 150214 Sorted by model distance: nonbonded pdb=" OH TYR J 114 " pdb=" OE2 GLU K 111 " model vdw 2.129 3.040 nonbonded pdb=" OH TYR H 114 " pdb=" OE2 GLU I 111 " model vdw 2.133 3.040 nonbonded pdb=" OG SER J 108 " pdb=" OE2 GLU J 110 " model vdw 2.141 3.040 nonbonded pdb=" OG SER J 127 " pdb=" OG SER J 143 " model vdw 2.147 3.040 nonbonded pdb=" OG SER I 127 " pdb=" OG SER I 143 " model vdw 2.153 3.040 ... (remaining 150209 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 19 through 172 or resid 202)) selection = (chain 'B' and (resid 19 through 172 or resid 202)) selection = (chain 'C' and (resid 19 through 172 or (resid 202 and (name C1 or name C11 or n \ ame C30 or name C31 or name C5 or name C6 or name C8 or name O10 or name O30 or \ name O4 or name O7 )))) selection = (chain 'D' and (resid 19 through 172 or (resid 202 and (name C1 or name C11 or n \ ame C30 or name C31 or name C5 or name C6 or name C8 or name O10 or name O30 or \ name O4 or name O7 )))) selection = (chain 'E' and (resid 19 through 172 or (resid 202 and (name C1 or name C11 or n \ ame C30 or name C31 or name C5 or name C6 or name C8 or name O10 or name O30 or \ name O4 or name O7 )))) selection = (chain 'F' and (resid 19 through 172 or (resid 202 and (name C1 or name C11 or n \ ame C30 or name C31 or name C5 or name C6 or name C8 or name O10 or name O30 or \ name O4 or name O7 )))) selection = (chain 'G' and (resid 19 through 172 or (resid 202 and (name C1 or name C11 or n \ ame C30 or name C31 or name C5 or name C6 or name C8 or name O10 or name O30 or \ name O4 or name O7 )))) selection = (chain 'H' and (resid 19 through 172 or (resid 202 and (name C1 or name C11 or n \ ame C30 or name C31 or name C5 or name C6 or name C8 or name O10 or name O30 or \ name O4 or name O7 )))) selection = (chain 'I' and (resid 19 through 172 or (resid 202 and (name C1 or name C11 or n \ ame C30 or name C31 or name C5 or name C6 or name C8 or name O10 or name O30 or \ name O4 or name O7 )))) selection = (chain 'J' and (resid 19 through 172 or (resid 202 and (name C1 or name C11 or n \ ame C30 or name C31 or name C5 or name C6 or name C8 or name O10 or name O30 or \ name O4 or name O7 )))) selection = (chain 'K' and (resid 19 through 172 or (resid 202 and (name C1 or name C11 or n \ ame C30 or name C31 or name C5 or name C6 or name C8 or name O10 or name O30 or \ name O4 or name O7 )))) selection = (chain 'L' and (resid 19 through 172 or resid 202)) } 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: 4.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.770 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:8.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 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 : 0.004 0.152 18064 Z= 0.301 Angle : 0.681 12.116 24366 Z= 0.354 Chirality : 0.039 0.170 2586 Planarity : 0.006 0.115 3232 Dihedral : 18.380 126.351 6849 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.79 % Allowed : 19.40 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 0.60 (0.18), residues: 2213 helix: 2.07 (0.20), residues: 646 sheet: -0.46 (0.19), residues: 753 loop : 0.06 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG H 88 TYR 0.021 0.001 TYR C 72 PHE 0.006 0.001 PHE D 22 TRP 0.009 0.001 TRP M 974 HIS 0.004 0.001 HIS M 859 Details of bonding type rmsd covalent geometry : bond 0.00376 (18040) covalent geometry : angle 0.68075 (24366) hydrogen bonds : bond 0.17631 ( 844) hydrogen bonds : angle 7.63984 ( 2796) Misc. bond : bond 0.06779 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 200 average time/residue: 0.7404 time to fit residues: 163.7468 Evaluate side-chains 149 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 900 THR Chi-restraints excluded: chain J residue 143 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.083604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.059493 restraints weight = 38758.372| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.29 r_work: 0.2682 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 18064 Z= 0.220 Angle : 0.566 6.153 24366 Z= 0.295 Chirality : 0.038 0.259 2586 Planarity : 0.004 0.049 3232 Dihedral : 9.777 129.592 2786 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.95 % Allowed : 17.30 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.18), residues: 2213 helix: 2.07 (0.20), residues: 696 sheet: -0.49 (0.18), residues: 751 loop : -0.11 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 88 TYR 0.023 0.001 TYR F 72 PHE 0.005 0.001 PHE M 950 TRP 0.013 0.001 TRP M 974 HIS 0.003 0.001 HIS M1013 Details of bonding type rmsd covalent geometry : bond 0.00484 (18040) covalent geometry : angle 0.56634 (24366) hydrogen bonds : bond 0.05086 ( 844) hydrogen bonds : angle 5.77974 ( 2796) Misc. bond : bond 0.00069 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 158 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 825 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8190 (mm-30) REVERT: M 836 GLU cc_start: 0.8988 (tp30) cc_final: 0.8522 (tp30) REVERT: M 1169 GLN cc_start: 0.8752 (tt0) cc_final: 0.8447 (tt0) REVERT: M 1188 SER cc_start: 0.9166 (OUTLIER) cc_final: 0.8715 (p) REVERT: D 94 ASP cc_start: 0.8900 (m-30) cc_final: 0.8656 (m-30) REVERT: G 94 ASP cc_start: 0.9005 (m-30) cc_final: 0.8767 (m-30) REVERT: I 59 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9172 (mt) REVERT: I 93 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9291 (mp) REVERT: J 99 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8836 (mp10) REVERT: K 84 ASP cc_start: 0.8408 (t0) cc_final: 0.8127 (t0) REVERT: B 87 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8348 (pt0) outliers start: 52 outliers final: 15 residues processed: 198 average time/residue: 0.6174 time to fit residues: 137.5381 Evaluate side-chains 167 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 900 THR Chi-restraints excluded: chain M residue 1044 LEU Chi-restraints excluded: chain M residue 1065 ILE Chi-restraints excluded: chain M residue 1188 SER Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 160 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 143 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 201 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 809 GLN G 99 GLN H 116 ASN K 116 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.083367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.059494 restraints weight = 38957.528| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.28 r_work: 0.2689 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18064 Z= 0.198 Angle : 0.536 6.806 24366 Z= 0.277 Chirality : 0.038 0.240 2586 Planarity : 0.004 0.039 3232 Dihedral : 9.430 129.959 2785 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.89 % Allowed : 17.87 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 0.62 (0.18), residues: 2213 helix: 2.20 (0.20), residues: 697 sheet: -0.51 (0.18), residues: 733 loop : -0.15 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 86 TYR 0.018 0.001 TYR E 72 PHE 0.005 0.001 PHE M1030 TRP 0.013 0.001 TRP B 112 HIS 0.003 0.001 HIS M 859 Details of bonding type rmsd covalent geometry : bond 0.00436 (18040) covalent geometry : angle 0.53594 (24366) hydrogen bonds : bond 0.04618 ( 844) hydrogen bonds : angle 5.39245 ( 2796) Misc. bond : bond 0.00057 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 807 GLU cc_start: 0.8668 (mp0) cc_final: 0.8353 (mp0) REVERT: M 825 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8180 (mm-30) REVERT: M 836 GLU cc_start: 0.9000 (tp30) cc_final: 0.8542 (tp30) REVERT: M 1169 GLN cc_start: 0.8716 (tt0) cc_final: 0.8360 (tt0) REVERT: C 99 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.9001 (mp10) REVERT: D 90 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8079 (tp-100) REVERT: D 94 ASP cc_start: 0.8868 (m-30) cc_final: 0.8412 (m-30) REVERT: D 99 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8285 (mp10) REVERT: F 121 GLU cc_start: 0.8982 (pm20) cc_final: 0.8662 (pm20) REVERT: G 94 ASP cc_start: 0.9080 (m-30) cc_final: 0.8837 (m-30) REVERT: I 93 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9265 (mp) REVERT: J 99 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8853 (mp10) REVERT: K 84 ASP cc_start: 0.8495 (t0) cc_final: 0.8065 (t0) REVERT: B 87 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8382 (pt0) outliers start: 51 outliers final: 17 residues processed: 199 average time/residue: 0.6591 time to fit residues: 146.9678 Evaluate side-chains 165 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 884 LEU Chi-restraints excluded: chain M residue 1044 LEU Chi-restraints excluded: chain M residue 1065 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 93 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 63 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.084161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.060298 restraints weight = 38790.284| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.30 r_work: 0.2708 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18064 Z= 0.148 Angle : 0.519 6.036 24366 Z= 0.267 Chirality : 0.037 0.250 2586 Planarity : 0.003 0.045 3232 Dihedral : 9.129 126.568 2784 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.67 % Allowed : 17.98 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 0.70 (0.18), residues: 2213 helix: 2.28 (0.19), residues: 697 sheet: -0.51 (0.18), residues: 752 loop : -0.04 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 86 TYR 0.016 0.001 TYR F 72 PHE 0.005 0.001 PHE M1030 TRP 0.013 0.001 TRP C 112 HIS 0.003 0.001 HIS M 859 Details of bonding type rmsd covalent geometry : bond 0.00322 (18040) covalent geometry : angle 0.51861 (24366) hydrogen bonds : bond 0.04233 ( 844) hydrogen bonds : angle 5.18290 ( 2796) Misc. bond : bond 0.00036 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 807 GLU cc_start: 0.8662 (mp0) cc_final: 0.8404 (mp0) REVERT: M 825 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8153 (mm-30) REVERT: M 826 ARG cc_start: 0.8613 (mtm-85) cc_final: 0.8389 (ttm110) REVERT: M 836 GLU cc_start: 0.8991 (tp30) cc_final: 0.8387 (tp30) REVERT: M 1188 SER cc_start: 0.9174 (OUTLIER) cc_final: 0.8742 (p) REVERT: C 99 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.8973 (mp10) REVERT: D 84 ASP cc_start: 0.8849 (t0) cc_final: 0.8616 (t0) REVERT: D 87 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8539 (pt0) REVERT: D 90 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8074 (tp-100) REVERT: D 94 ASP cc_start: 0.8917 (m-30) cc_final: 0.8446 (m-30) REVERT: D 99 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8371 (mp10) REVERT: F 121 GLU cc_start: 0.8965 (pm20) cc_final: 0.8674 (pm20) REVERT: G 94 ASP cc_start: 0.9084 (m-30) cc_final: 0.8833 (m-30) REVERT: G 132 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7893 (tm-30) REVERT: I 93 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9271 (mp) REVERT: J 86 ARG cc_start: 0.8714 (tpp80) cc_final: 0.8176 (mmm160) REVERT: K 84 ASP cc_start: 0.8542 (t0) cc_final: 0.8139 (t0) REVERT: B 87 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8335 (pt0) REVERT: B 98 GLN cc_start: 0.9267 (tm-30) cc_final: 0.9064 (tm-30) outliers start: 47 outliers final: 18 residues processed: 195 average time/residue: 0.6405 time to fit residues: 140.1827 Evaluate side-chains 170 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 884 LEU Chi-restraints excluded: chain M residue 1044 LEU Chi-restraints excluded: chain M residue 1065 ILE Chi-restraints excluded: chain M residue 1188 SER Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 131 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 133 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 21 optimal weight: 0.0980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 46 GLN G 99 GLN H 116 ASN J 35 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.083636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.059267 restraints weight = 38932.995| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.33 r_work: 0.2695 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18064 Z= 0.189 Angle : 0.536 8.117 24366 Z= 0.276 Chirality : 0.037 0.280 2586 Planarity : 0.004 0.047 3232 Dihedral : 9.074 128.179 2784 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.84 % Allowed : 18.66 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 0.68 (0.18), residues: 2213 helix: 2.25 (0.19), residues: 697 sheet: -0.49 (0.18), residues: 732 loop : -0.12 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 86 TYR 0.018 0.001 TYR F 72 PHE 0.005 0.001 PHE M1030 TRP 0.011 0.001 TRP C 112 HIS 0.003 0.001 HIS M 859 Details of bonding type rmsd covalent geometry : bond 0.00418 (18040) covalent geometry : angle 0.53642 (24366) hydrogen bonds : bond 0.04320 ( 844) hydrogen bonds : angle 5.16133 ( 2796) Misc. bond : bond 0.00047 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 149 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 807 GLU cc_start: 0.8636 (mp0) cc_final: 0.8380 (mp0) REVERT: M 825 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8164 (mm-30) REVERT: M 826 ARG cc_start: 0.8595 (mtm-85) cc_final: 0.8384 (ttm110) REVERT: M 836 GLU cc_start: 0.9008 (tp30) cc_final: 0.8550 (tp30) REVERT: M 1188 SER cc_start: 0.9179 (OUTLIER) cc_final: 0.8734 (p) REVERT: C 99 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.9024 (mp10) REVERT: D 84 ASP cc_start: 0.8852 (t0) cc_final: 0.8618 (t0) REVERT: D 87 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8587 (pt0) REVERT: D 90 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8135 (tp-100) REVERT: D 94 ASP cc_start: 0.8896 (m-30) cc_final: 0.8338 (m-30) REVERT: D 99 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8371 (mp10) REVERT: E 55 GLU cc_start: 0.8989 (tt0) cc_final: 0.8621 (tt0) REVERT: E 72 TYR cc_start: 0.8099 (p90) cc_final: 0.7531 (p90) REVERT: F 121 GLU cc_start: 0.8996 (pm20) cc_final: 0.8691 (pm20) REVERT: G 94 ASP cc_start: 0.9101 (m-30) cc_final: 0.8843 (m-30) REVERT: G 132 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7906 (tm-30) REVERT: H 86 ARG cc_start: 0.8445 (mmm160) cc_final: 0.8141 (mmm160) REVERT: I 93 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9273 (mp) REVERT: I 98 GLN cc_start: 0.9234 (tt0) cc_final: 0.8960 (tm-30) REVERT: J 86 ARG cc_start: 0.8740 (tpp80) cc_final: 0.8239 (mmm160) REVERT: K 84 ASP cc_start: 0.8496 (t0) cc_final: 0.8069 (t0) REVERT: L 121 GLU cc_start: 0.8866 (pm20) cc_final: 0.8478 (pm20) REVERT: B 84 ASP cc_start: 0.8876 (t0) cc_final: 0.8590 (OUTLIER) REVERT: B 87 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8282 (pt0) outliers start: 50 outliers final: 19 residues processed: 186 average time/residue: 0.6466 time to fit residues: 134.9117 Evaluate side-chains 168 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 884 LEU Chi-restraints excluded: chain M residue 1044 LEU Chi-restraints excluded: chain M residue 1065 ILE Chi-restraints excluded: chain M residue 1188 SER Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 87 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 50 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 172 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 201 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 152 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 99 GLN H 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.084430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.060610 restraints weight = 38615.175| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.29 r_work: 0.2724 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18064 Z= 0.135 Angle : 0.526 10.710 24366 Z= 0.268 Chirality : 0.038 0.353 2586 Planarity : 0.003 0.044 3232 Dihedral : 8.821 123.068 2784 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.50 % Allowed : 19.17 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 0.78 (0.18), residues: 2213 helix: 2.35 (0.20), residues: 697 sheet: -0.46 (0.18), residues: 737 loop : -0.03 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 86 TYR 0.016 0.001 TYR C 72 PHE 0.005 0.001 PHE M1030 TRP 0.013 0.001 TRP C 112 HIS 0.003 0.001 HIS M 859 Details of bonding type rmsd covalent geometry : bond 0.00296 (18040) covalent geometry : angle 0.52592 (24366) hydrogen bonds : bond 0.04033 ( 844) hydrogen bonds : angle 5.00738 ( 2796) Misc. bond : bond 0.00029 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 158 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 807 GLU cc_start: 0.8663 (mp0) cc_final: 0.8445 (mp0) REVERT: M 825 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8019 (mm-30) REVERT: M 826 ARG cc_start: 0.8570 (mtm-85) cc_final: 0.8369 (ttm110) REVERT: M 836 GLU cc_start: 0.8986 (tp30) cc_final: 0.8383 (tp30) REVERT: M 1188 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8738 (p) REVERT: C 99 GLN cc_start: 0.9272 (OUTLIER) cc_final: 0.9012 (mp10) REVERT: D 84 ASP cc_start: 0.8843 (t0) cc_final: 0.8566 (t0) REVERT: D 87 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8579 (pt0) REVERT: D 90 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8087 (tp-100) REVERT: D 94 ASP cc_start: 0.8901 (m-30) cc_final: 0.8395 (m-30) REVERT: D 99 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8339 (mp10) REVERT: E 55 GLU cc_start: 0.8997 (tt0) cc_final: 0.8605 (tt0) REVERT: E 72 TYR cc_start: 0.8184 (p90) cc_final: 0.7612 (p90) REVERT: F 121 GLU cc_start: 0.8982 (pm20) cc_final: 0.8678 (pm20) REVERT: G 132 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7914 (tm-30) REVERT: I 93 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9268 (mp) REVERT: I 98 GLN cc_start: 0.9230 (tt0) cc_final: 0.8980 (tm-30) REVERT: J 86 ARG cc_start: 0.8719 (tpp80) cc_final: 0.8259 (mmm160) REVERT: K 84 ASP cc_start: 0.8481 (t0) cc_final: 0.8035 (t0) REVERT: L 121 GLU cc_start: 0.8860 (pm20) cc_final: 0.8476 (pm20) REVERT: A 131 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8862 (mt) REVERT: B 84 ASP cc_start: 0.8897 (t0) cc_final: 0.8619 (t0) REVERT: B 87 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: B 98 GLN cc_start: 0.9309 (tm-30) cc_final: 0.8918 (pp30) outliers start: 44 outliers final: 20 residues processed: 191 average time/residue: 0.6642 time to fit residues: 142.3353 Evaluate side-chains 177 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 884 LEU Chi-restraints excluded: chain M residue 1044 LEU Chi-restraints excluded: chain M residue 1065 ILE Chi-restraints excluded: chain M residue 1188 SER Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 93 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 22 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 98 GLN G 99 GLN H 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.083569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.059215 restraints weight = 39237.011| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.36 r_work: 0.2694 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18064 Z= 0.189 Angle : 0.552 9.369 24366 Z= 0.281 Chirality : 0.038 0.298 2586 Planarity : 0.003 0.057 3232 Dihedral : 8.853 124.375 2784 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.72 % Allowed : 19.23 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 0.75 (0.18), residues: 2213 helix: 2.32 (0.20), residues: 697 sheet: -0.57 (0.18), residues: 763 loop : 0.11 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 86 TYR 0.018 0.001 TYR F 72 PHE 0.005 0.001 PHE M 950 TRP 0.010 0.001 TRP M 974 HIS 0.003 0.001 HIS M 859 Details of bonding type rmsd covalent geometry : bond 0.00419 (18040) covalent geometry : angle 0.55188 (24366) hydrogen bonds : bond 0.04196 ( 844) hydrogen bonds : angle 5.08092 ( 2796) Misc. bond : bond 0.00044 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 807 GLU cc_start: 0.8657 (mp0) cc_final: 0.8425 (mp0) REVERT: M 825 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7946 (mm-30) REVERT: M 836 GLU cc_start: 0.9002 (tp30) cc_final: 0.8396 (tp30) REVERT: M 983 GLU cc_start: 0.9110 (tt0) cc_final: 0.8815 (tt0) REVERT: M 1188 SER cc_start: 0.9176 (OUTLIER) cc_final: 0.8746 (p) REVERT: C 99 GLN cc_start: 0.9272 (OUTLIER) cc_final: 0.9024 (mp10) REVERT: D 84 ASP cc_start: 0.8863 (t0) cc_final: 0.8584 (t0) REVERT: D 87 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8583 (pt0) REVERT: D 90 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8085 (tp-100) REVERT: D 94 ASP cc_start: 0.8899 (m-30) cc_final: 0.8375 (m-30) REVERT: D 99 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8371 (mp10) REVERT: E 55 GLU cc_start: 0.9032 (tt0) cc_final: 0.8698 (tt0) REVERT: E 72 TYR cc_start: 0.8271 (p90) cc_final: 0.7748 (p90) REVERT: F 99 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7356 (mp10) REVERT: F 121 GLU cc_start: 0.9010 (pm20) cc_final: 0.8666 (pm20) REVERT: G 132 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7947 (tm-30) REVERT: H 86 ARG cc_start: 0.8442 (mmm160) cc_final: 0.8157 (mmm160) REVERT: I 93 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9265 (mp) REVERT: I 98 GLN cc_start: 0.9271 (tt0) cc_final: 0.9026 (tm-30) REVERT: J 86 ARG cc_start: 0.8740 (tpp80) cc_final: 0.8271 (mmm160) REVERT: K 84 ASP cc_start: 0.8430 (t0) cc_final: 0.8000 (t0) REVERT: L 121 GLU cc_start: 0.8895 (pm20) cc_final: 0.8501 (pm20) REVERT: B 84 ASP cc_start: 0.8924 (t0) cc_final: 0.8685 (t0) REVERT: B 87 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8259 (pt0) REVERT: B 98 GLN cc_start: 0.9342 (tm-30) cc_final: 0.9061 (tm-30) outliers start: 48 outliers final: 21 residues processed: 187 average time/residue: 0.6095 time to fit residues: 128.1018 Evaluate side-chains 176 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 884 LEU Chi-restraints excluded: chain M residue 1044 LEU Chi-restraints excluded: chain M residue 1065 ILE Chi-restraints excluded: chain M residue 1188 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 93 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 40 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 202 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 99 GLN H 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.084381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.060140 restraints weight = 38835.351| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.34 r_work: 0.2718 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18064 Z= 0.143 Angle : 0.550 9.722 24366 Z= 0.279 Chirality : 0.037 0.255 2586 Planarity : 0.004 0.081 3232 Dihedral : 8.683 120.980 2784 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.10 % Allowed : 20.19 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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 (0.18), residues: 2213 helix: 2.39 (0.20), residues: 697 sheet: -0.42 (0.18), residues: 737 loop : 0.00 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG M 826 TYR 0.021 0.001 TYR C 72 PHE 0.005 0.001 PHE M 950 TRP 0.013 0.001 TRP C 112 HIS 0.003 0.001 HIS M 859 Details of bonding type rmsd covalent geometry : bond 0.00316 (18040) covalent geometry : angle 0.55018 (24366) hydrogen bonds : bond 0.03983 ( 844) hydrogen bonds : angle 4.99168 ( 2796) Misc. bond : bond 0.00029 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 807 GLU cc_start: 0.8663 (mp0) cc_final: 0.8458 (mp0) REVERT: M 825 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7949 (mm-30) REVERT: M 836 GLU cc_start: 0.8994 (tp30) cc_final: 0.8381 (tp30) REVERT: M 983 GLU cc_start: 0.9109 (tt0) cc_final: 0.8847 (tt0) REVERT: M 1188 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8742 (p) REVERT: C 99 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8997 (mp10) REVERT: D 84 ASP cc_start: 0.8861 (t0) cc_final: 0.8559 (t0) REVERT: D 87 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8564 (pt0) REVERT: D 90 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8096 (tp-100) REVERT: D 94 ASP cc_start: 0.8923 (m-30) cc_final: 0.8427 (m-30) REVERT: D 99 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8334 (mp10) REVERT: F 99 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7405 (mp10) REVERT: F 121 GLU cc_start: 0.8996 (pm20) cc_final: 0.8558 (pm20) REVERT: G 132 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7951 (tm-30) REVERT: H 86 ARG cc_start: 0.8492 (mmm160) cc_final: 0.8165 (mmm160) REVERT: I 93 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9262 (mp) REVERT: I 98 GLN cc_start: 0.9288 (tt0) cc_final: 0.9017 (tm-30) REVERT: J 86 ARG cc_start: 0.8723 (tpp80) cc_final: 0.8265 (mmm160) REVERT: K 84 ASP cc_start: 0.8389 (t0) cc_final: 0.7954 (t0) REVERT: L 121 GLU cc_start: 0.8882 (pm20) cc_final: 0.8498 (pm20) REVERT: B 84 ASP cc_start: 0.8938 (t0) cc_final: 0.8713 (t0) REVERT: B 87 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8262 (pt0) REVERT: B 98 GLN cc_start: 0.9363 (tm-30) cc_final: 0.8926 (pp30) outliers start: 37 outliers final: 20 residues processed: 182 average time/residue: 0.6041 time to fit residues: 123.6024 Evaluate side-chains 180 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 884 LEU Chi-restraints excluded: chain M residue 1044 LEU Chi-restraints excluded: chain M residue 1065 ILE Chi-restraints excluded: chain M residue 1188 SER Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 93 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 100 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 134 optimal weight: 0.0170 chunk 24 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 99 GLN H 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.083339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.058997 restraints weight = 39133.837| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.34 r_work: 0.2693 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 18064 Z= 0.204 Angle : 0.577 10.204 24366 Z= 0.293 Chirality : 0.038 0.232 2586 Planarity : 0.004 0.061 3232 Dihedral : 8.786 124.117 2784 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.93 % Allowed : 20.42 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 0.76 (0.18), residues: 2213 helix: 2.32 (0.20), residues: 697 sheet: -0.58 (0.18), residues: 768 loop : 0.15 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG G 86 TYR 0.019 0.001 TYR F 72 PHE 0.005 0.001 PHE M 950 TRP 0.014 0.001 TRP J 95 HIS 0.003 0.001 HIS M1013 Details of bonding type rmsd covalent geometry : bond 0.00455 (18040) covalent geometry : angle 0.57717 (24366) hydrogen bonds : bond 0.04229 ( 844) hydrogen bonds : angle 5.10036 ( 2796) Misc. bond : bond 0.00046 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 807 GLU cc_start: 0.8657 (mp0) cc_final: 0.8432 (mp0) REVERT: M 825 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7928 (mm-30) REVERT: M 836 GLU cc_start: 0.9009 (tp30) cc_final: 0.8400 (tp30) REVERT: M 983 GLU cc_start: 0.9130 (tt0) cc_final: 0.8849 (tt0) REVERT: M 1188 SER cc_start: 0.9181 (OUTLIER) cc_final: 0.8753 (p) REVERT: C 99 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.9023 (mp10) REVERT: D 84 ASP cc_start: 0.8847 (t0) cc_final: 0.8548 (t0) REVERT: D 87 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8562 (pt0) REVERT: D 90 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8082 (tp-100) REVERT: D 94 ASP cc_start: 0.8933 (m-30) cc_final: 0.8417 (m-30) REVERT: D 99 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8274 (mp10) REVERT: F 99 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7379 (mp10) REVERT: G 132 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7957 (tm-30) REVERT: H 86 ARG cc_start: 0.8566 (mmm160) cc_final: 0.8214 (mmm160) REVERT: I 93 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9264 (mp) REVERT: I 98 GLN cc_start: 0.9289 (tt0) cc_final: 0.9016 (tm-30) REVERT: J 86 ARG cc_start: 0.8714 (tpp80) cc_final: 0.8264 (mmm160) REVERT: K 84 ASP cc_start: 0.8303 (t0) cc_final: 0.7878 (t0) REVERT: L 121 GLU cc_start: 0.8898 (pm20) cc_final: 0.8509 (pm20) REVERT: B 84 ASP cc_start: 0.8959 (t0) cc_final: 0.8744 (t0) REVERT: B 87 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8291 (pt0) REVERT: B 98 GLN cc_start: 0.9365 (tm-30) cc_final: 0.9070 (tm-30) outliers start: 34 outliers final: 21 residues processed: 178 average time/residue: 0.6018 time to fit residues: 120.0836 Evaluate side-chains 174 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 884 LEU Chi-restraints excluded: chain M residue 1044 LEU Chi-restraints excluded: chain M residue 1065 ILE Chi-restraints excluded: chain M residue 1188 SER Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 93 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 126 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 169 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 99 GLN H 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.083572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.058992 restraints weight = 38772.486| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.36 r_work: 0.2690 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18064 Z= 0.190 Angle : 0.586 11.012 24366 Z= 0.298 Chirality : 0.038 0.216 2586 Planarity : 0.004 0.090 3232 Dihedral : 8.790 125.922 2784 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.93 % Allowed : 20.36 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 0.77 (0.18), residues: 2213 helix: 2.32 (0.20), residues: 697 sheet: -0.59 (0.18), residues: 774 loop : 0.19 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG M 826 TYR 0.022 0.001 TYR C 72 PHE 0.005 0.001 PHE M 950 TRP 0.012 0.001 TRP J 95 HIS 0.003 0.001 HIS M1013 Details of bonding type rmsd covalent geometry : bond 0.00426 (18040) covalent geometry : angle 0.58559 (24366) hydrogen bonds : bond 0.04208 ( 844) hydrogen bonds : angle 5.08343 ( 2796) Misc. bond : bond 0.00042 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 807 GLU cc_start: 0.8655 (mp0) cc_final: 0.8445 (mp0) REVERT: M 825 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7934 (mm-30) REVERT: M 826 ARG cc_start: 0.8834 (ttm110) cc_final: 0.8577 (mtp-110) REVERT: M 836 GLU cc_start: 0.9007 (tp30) cc_final: 0.8473 (tp30) REVERT: M 888 LYS cc_start: 0.9040 (tmtp) cc_final: 0.8809 (ptmt) REVERT: M 983 GLU cc_start: 0.9127 (tt0) cc_final: 0.8840 (tt0) REVERT: M 1075 ARG cc_start: 0.7881 (tpp-160) cc_final: 0.7656 (tpm170) REVERT: M 1188 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8750 (p) REVERT: C 99 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.9003 (mp10) REVERT: D 84 ASP cc_start: 0.8844 (t0) cc_final: 0.8526 (t0) REVERT: D 87 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8559 (pt0) REVERT: D 90 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8061 (tp-100) REVERT: D 94 ASP cc_start: 0.8938 (m-30) cc_final: 0.8435 (m-30) REVERT: D 99 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8242 (mp10) REVERT: F 99 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7404 (mp10) REVERT: G 132 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7945 (tm-30) REVERT: I 93 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9279 (mp) REVERT: I 98 GLN cc_start: 0.9303 (tt0) cc_final: 0.9041 (tm-30) REVERT: J 86 ARG cc_start: 0.8707 (tpp80) cc_final: 0.8258 (mmm160) REVERT: K 84 ASP cc_start: 0.8283 (t0) cc_final: 0.7863 (t0) REVERT: L 121 GLU cc_start: 0.8894 (pm20) cc_final: 0.8502 (pm20) REVERT: B 84 ASP cc_start: 0.8969 (t0) cc_final: 0.8757 (t0) REVERT: B 87 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8291 (pt0) REVERT: B 98 GLN cc_start: 0.9365 (tm-30) cc_final: 0.9069 (tm-30) outliers start: 34 outliers final: 22 residues processed: 176 average time/residue: 0.5459 time to fit residues: 108.0922 Evaluate side-chains 176 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 884 LEU Chi-restraints excluded: chain M residue 1044 LEU Chi-restraints excluded: chain M residue 1065 ILE Chi-restraints excluded: chain M residue 1188 SER Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 93 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 162 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 99 GLN H 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.084056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.060299 restraints weight = 39021.753| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 3.27 r_work: 0.2714 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18064 Z= 0.154 Angle : 0.582 11.760 24366 Z= 0.294 Chirality : 0.038 0.203 2586 Planarity : 0.004 0.084 3232 Dihedral : 8.649 123.419 2784 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.93 % Allowed : 20.19 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 0.81 (0.18), residues: 2213 helix: 2.37 (0.20), residues: 697 sheet: -0.46 (0.18), residues: 738 loop : 0.01 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG G 86 TYR 0.020 0.001 TYR C 72 PHE 0.005 0.001 PHE M 950 TRP 0.013 0.001 TRP J 95 HIS 0.002 0.001 HIS M1013 Details of bonding type rmsd covalent geometry : bond 0.00344 (18040) covalent geometry : angle 0.58224 (24366) hydrogen bonds : bond 0.04024 ( 844) hydrogen bonds : angle 5.00591 ( 2796) Misc. bond : bond 0.00031 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5889.58 seconds wall clock time: 101 minutes 9.88 seconds (6069.88 seconds total)