Starting phenix.real_space_refine on Sat Oct 12 19:26:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjl_43288/10_2024/8vjl_43288.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjl_43288/10_2024/8vjl_43288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjl_43288/10_2024/8vjl_43288.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjl_43288/10_2024/8vjl_43288.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjl_43288/10_2024/8vjl_43288.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjl_43288/10_2024/8vjl_43288.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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 2 5.49 5 S 56 5.16 5 C 8846 2.51 5 N 2162 2.21 5 O 2268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 13334 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2353 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 276} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 888 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2353 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 276} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 888 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2353 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 276} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 888 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2353 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 276} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 888 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 116 Unusual residues: {'LMN': 1, 'PEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 116 Unusual residues: {'LMN': 1, 'PEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.05, per 1000 atoms: 0.60 Number of scatterers: 13334 At special positions: 0 Unit cell: (135.16, 108.128, 89.816, 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 56 16.00 P 2 15.00 O 2268 8.00 N 2162 7.00 C 8846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 1.7 seconds 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3072 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 8 sheets defined 67.9% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 Processing helix chain 'A' and resid 14 through 26 removed outlier: 3.980A pdb=" N TRP A 18 " --> pdb=" O HIS A 14 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 19 " --> pdb=" O PRO A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 54 removed outlier: 3.658A pdb=" N HIS A 47 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 89 removed outlier: 3.882A pdb=" N ILE A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 93 through 107 removed outlier: 3.793A pdb=" N LEU A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 130 removed outlier: 3.639A pdb=" N PHE A 115 " --> pdb=" O HIS A 111 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 117 " --> pdb=" O HIS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 4.088A pdb=" N LEU A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 178 Processing helix chain 'A' and resid 181 through 200 removed outlier: 3.905A pdb=" N TRP A 185 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 234 through 240 removed outlier: 3.599A pdb=" N ALA A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 removed outlier: 3.793A pdb=" N VAL A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 47 Processing helix chain 'B' and resid 48 through 58 removed outlier: 3.554A pdb=" N ARG B 52 " --> pdb=" O ASP B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 70 removed outlier: 3.996A pdb=" N VAL B 63 " --> pdb=" O ASN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 94 removed outlier: 4.087A pdb=" N LEU B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 126 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 14 through 28 removed outlier: 3.732A pdb=" N TRP C 18 " --> pdb=" O HIS C 14 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 19 " --> pdb=" O PRO C 15 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 53 removed outlier: 3.965A pdb=" N HIS C 47 " --> pdb=" O HIS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.538A pdb=" N GLU C 83 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 107 removed outlier: 4.228A pdb=" N TRP C 96 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 107 " --> pdb=" O MET C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 removed outlier: 3.568A pdb=" N LEU C 117 " --> pdb=" O HIS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 148 Processing helix chain 'C' and resid 151 through 177 removed outlier: 3.685A pdb=" N ASN C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 160 " --> pdb=" O HIS C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 200 removed outlier: 3.625A pdb=" N TRP C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 removed outlier: 4.081A pdb=" N ILE C 205 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 241 removed outlier: 3.621A pdb=" N VAL C 238 " --> pdb=" O LYS C 234 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU C 241 " --> pdb=" O HIS C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 273 Processing helix chain 'C' and resid 280 through 286 Processing helix chain 'D' and resid 35 through 47 removed outlier: 3.646A pdb=" N LYS D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 58 removed outlier: 3.642A pdb=" N ARG D 52 " --> pdb=" O ASP D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.842A pdb=" N ALA D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS D 65 " --> pdb=" O ARG D 61 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 94 removed outlier: 3.776A pdb=" N LEU D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 removed outlier: 3.538A pdb=" N LYS D 99 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 96 through 100' Processing helix chain 'D' and resid 102 through 126 removed outlier: 3.515A pdb=" N TYR D 106 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'E' and resid 14 through 26 removed outlier: 3.980A pdb=" N TRP E 18 " --> pdb=" O HIS E 14 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE E 19 " --> pdb=" O PRO E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 54 removed outlier: 3.645A pdb=" N HIS E 47 " --> pdb=" O HIS E 43 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 89 removed outlier: 3.883A pdb=" N ILE E 87 " --> pdb=" O GLU E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 93 through 107 removed outlier: 3.780A pdb=" N LEU E 97 " --> pdb=" O GLN E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 130 removed outlier: 3.642A pdb=" N PHE E 115 " --> pdb=" O HIS E 111 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU E 116 " --> pdb=" O GLN E 112 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU E 117 " --> pdb=" O HIS E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 150 removed outlier: 4.104A pdb=" N LEU E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 178 Processing helix chain 'E' and resid 181 through 200 removed outlier: 3.913A pdb=" N TRP E 185 " --> pdb=" O GLN E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 215 Processing helix chain 'E' and resid 234 through 240 removed outlier: 3.550A pdb=" N ALA E 240 " --> pdb=" O TYR E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 274 removed outlier: 3.785A pdb=" N VAL E 267 " --> pdb=" O ASP E 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 47 Processing helix chain 'F' and resid 48 through 58 removed outlier: 3.557A pdb=" N ARG F 52 " --> pdb=" O ASP F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 70 removed outlier: 3.897A pdb=" N VAL F 63 " --> pdb=" O ASN F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 94 removed outlier: 4.105A pdb=" N LEU F 80 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 126 Processing helix chain 'G' and resid 2 through 9 Processing helix chain 'G' and resid 14 through 28 removed outlier: 3.732A pdb=" N TRP G 18 " --> pdb=" O HIS G 14 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE G 19 " --> pdb=" O PRO G 15 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU G 26 " --> pdb=" O ALA G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 53 removed outlier: 3.966A pdb=" N HIS G 47 " --> pdb=" O HIS G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.538A pdb=" N GLU G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 107 removed outlier: 4.227A pdb=" N TRP G 96 " --> pdb=" O LEU G 92 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL G 107 " --> pdb=" O MET G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 removed outlier: 3.572A pdb=" N LEU G 117 " --> pdb=" O HIS G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 148 removed outlier: 3.573A pdb=" N LYS G 148 " --> pdb=" O LEU G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 177 removed outlier: 3.708A pdb=" N ASN G 159 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU G 160 " --> pdb=" O HIS G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 200 removed outlier: 3.610A pdb=" N TRP G 185 " --> pdb=" O GLN G 181 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL G 186 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU G 187 " --> pdb=" O SER G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 215 removed outlier: 4.086A pdb=" N ILE G 205 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS G 206 " --> pdb=" O ARG G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 241 removed outlier: 3.619A pdb=" N VAL G 238 " --> pdb=" O LYS G 234 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU G 241 " --> pdb=" O HIS G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 273 Processing helix chain 'G' and resid 280 through 286 Processing helix chain 'H' and resid 35 through 47 removed outlier: 3.611A pdb=" N LYS H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 58 removed outlier: 3.654A pdb=" N ARG H 52 " --> pdb=" O ASP H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 70 removed outlier: 4.410A pdb=" N VAL H 63 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 94 removed outlier: 3.621A pdb=" N LEU H 80 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 100 removed outlier: 3.545A pdb=" N GLY H 100 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 126 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 64 removed outlier: 4.070A pdb=" N ARG A 60 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY A 68 " --> pdb=" O TYR B 22 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LYS B 24 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL A 70 " --> pdb=" O LYS B 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 230 removed outlier: 6.062A pdb=" N LEU A 227 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU A 253 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 229 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 260 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LYS A 254 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LYS A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 63 through 64 removed outlier: 7.375A pdb=" N GLY C 68 " --> pdb=" O TYR D 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 227 through 228 removed outlier: 7.361A pdb=" N LEU C 227 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N GLU C 253 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE C 250 " --> pdb=" O GLN C 261 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN C 261 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE C 252 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN C 257 " --> pdb=" O LYS C 254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 12 through 13 removed outlier: 4.152A pdb=" N ARG E 60 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY E 68 " --> pdb=" O TYR F 22 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LYS F 24 " --> pdb=" O GLY E 68 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL E 70 " --> pdb=" O LYS F 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 227 through 230 removed outlier: 6.056A pdb=" N LEU E 227 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU E 253 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL E 229 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER E 260 " --> pdb=" O ILE E 252 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LYS E 254 " --> pdb=" O LYS E 258 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS E 258 " --> pdb=" O LYS E 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 63 through 64 removed outlier: 7.363A pdb=" N GLY G 68 " --> pdb=" O TYR H 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 227 through 228 removed outlier: 7.365A pdb=" N LEU G 227 " --> pdb=" O ILE G 251 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N GLU G 253 " --> pdb=" O LEU G 227 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE G 250 " --> pdb=" O GLN G 261 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLN G 261 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE G 252 " --> pdb=" O LEU G 259 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN G 257 " --> pdb=" O LYS G 254 " (cutoff:3.500A) 748 hydrogen bonds defined for protein. 2220 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: 3.39 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2012 1.31 - 1.43: 3620 1.43 - 1.56: 7896 1.56 - 1.68: 64 1.68 - 1.81: 88 Bond restraints: 13680 Sorted by residual: bond pdb=" C1 LMN E 401 " pdb=" O5 LMN E 401 " ideal model delta sigma weight residual 1.403 1.537 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C1 LMN A 401 " pdb=" O5 LMN A 401 " ideal model delta sigma weight residual 1.403 1.537 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C1 LMN C 401 " pdb=" O5 LMN C 401 " ideal model delta sigma weight residual 1.403 1.537 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C1 LMN G 401 " pdb=" O5 LMN G 401 " ideal model delta sigma weight residual 1.403 1.537 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" CBS LMN E 401 " pdb=" CCM LMN E 401 " ideal model delta sigma weight residual 1.529 1.630 -0.101 2.00e-02 2.50e+03 2.55e+01 ... (remaining 13675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 18176 2.98 - 5.97: 310 5.97 - 8.95: 20 8.95 - 11.94: 10 11.94 - 14.92: 2 Bond angle restraints: 18518 Sorted by residual: angle pdb=" O3P PEF A 402 " pdb=" P PEF A 402 " pdb=" O4P PEF A 402 " ideal model delta sigma weight residual 93.96 108.88 -14.92 3.00e+00 1.11e-01 2.47e+01 angle pdb=" O3P PEF E 402 " pdb=" P PEF E 402 " pdb=" O4P PEF E 402 " ideal model delta sigma weight residual 93.96 108.86 -14.90 3.00e+00 1.11e-01 2.47e+01 angle pdb=" O1P PEF A 402 " pdb=" P PEF A 402 " pdb=" O2P PEF A 402 " ideal model delta sigma weight residual 119.53 109.21 10.32 3.00e+00 1.11e-01 1.18e+01 angle pdb=" O1P PEF E 402 " pdb=" P PEF E 402 " pdb=" O2P PEF E 402 " ideal model delta sigma weight residual 119.53 109.28 10.25 3.00e+00 1.11e-01 1.17e+01 angle pdb=" CCQ LMN A 401 " pdb=" OCB LMN A 401 " pdb=" CCS LMN A 401 " ideal model delta sigma weight residual 119.65 109.45 10.20 3.00e+00 1.11e-01 1.16e+01 ... (remaining 18513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.01: 7582 25.01 - 50.02: 602 50.02 - 75.04: 123 75.04 - 100.05: 35 100.05 - 125.06: 68 Dihedral angle restraints: 8410 sinusoidal: 3682 harmonic: 4728 Sorted by residual: dihedral pdb=" O2 LMN C 401 " pdb=" C2 LMN C 401 " pdb=" C3 LMN C 401 " pdb=" O3 LMN C 401 " ideal model delta sinusoidal sigma weight residual 295.11 170.05 125.06 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" O2 LMN G 401 " pdb=" C2 LMN G 401 " pdb=" C3 LMN G 401 " pdb=" O3 LMN G 401 " ideal model delta sinusoidal sigma weight residual 295.11 170.08 125.03 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C1 LMN C 401 " pdb=" C2 LMN C 401 " pdb=" C3 LMN C 401 " pdb=" O3 LMN C 401 " ideal model delta sinusoidal sigma weight residual 174.26 50.75 123.51 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 8407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1609 0.043 - 0.085: 424 0.085 - 0.128: 88 0.128 - 0.170: 13 0.170 - 0.213: 8 Chirality restraints: 2142 Sorted by residual: chirality pdb=" C1 LMN C 401 " pdb=" C2 LMN C 401 " pdb=" O1 LMN C 401 " pdb=" O5 LMN C 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.50 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C1 LMN G 401 " pdb=" C2 LMN G 401 " pdb=" O1 LMN G 401 " pdb=" O5 LMN G 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.50 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C1 LMN E 401 " pdb=" C2 LMN E 401 " pdb=" O1 LMN E 401 " pdb=" O5 LMN E 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.49 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2139 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 178 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO C 179 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 178 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO G 179 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO G 179 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 179 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 64 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO C 65 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 65 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 65 " 0.019 5.00e-02 4.00e+02 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1742 2.75 - 3.29: 12845 3.29 - 3.83: 20777 3.83 - 4.36: 22337 4.36 - 4.90: 40334 Nonbonded interactions: 98035 Sorted by model distance: nonbonded pdb=" OG SER D 33 " pdb=" OE1 GLU D 36 " model vdw 2.215 3.040 nonbonded pdb=" ND1 HIS A 94 " pdb=" OD1 ASN A 122 " model vdw 2.245 3.120 nonbonded pdb=" ND1 HIS E 94 " pdb=" OD1 ASN E 122 " model vdw 2.245 3.120 nonbonded pdb=" OD1 ASP E 233 " pdb=" N LYS E 234 " model vdw 2.255 3.120 nonbonded pdb=" O LYS B 90 " pdb=" OG SER B 94 " model vdw 2.265 3.040 ... (remaining 98030 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 1 through 288 or resid 401)) selection = chain 'C' selection = (chain 'E' and (resid 1 through 288 or resid 401)) selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.800 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.134 13680 Z= 0.507 Angle : 0.793 14.922 18518 Z= 0.339 Chirality : 0.041 0.213 2142 Planarity : 0.004 0.040 2220 Dihedral : 22.663 125.060 5338 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.81 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1600 helix: 1.60 (0.17), residues: 1044 sheet: 1.75 (0.62), residues: 48 loop : -2.13 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 96 HIS 0.011 0.001 HIS H 65 PHE 0.011 0.001 PHE D 11 TYR 0.012 0.001 TYR D 95 ARG 0.002 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.466 Fit side-chains REVERT: E 233 ASP cc_start: 0.7214 (t0) cc_final: 0.6976 (t0) REVERT: G 274 ASP cc_start: 0.7415 (m-30) cc_final: 0.7202 (m-30) REVERT: H 14 LYS cc_start: 0.7854 (tptp) cc_final: 0.7602 (pttp) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.2660 time to fit residues: 90.1498 Evaluate side-chains 199 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 0.0980 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 HIS A 265 ASN B 118 HIS ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN F 118 HIS ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13680 Z= 0.278 Angle : 0.692 10.083 18518 Z= 0.328 Chirality : 0.045 0.284 2142 Planarity : 0.004 0.041 2220 Dihedral : 18.400 95.193 2306 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.19 % Favored : 92.31 % Rotamer: Outliers : 0.96 % Allowed : 9.22 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.22), residues: 1600 helix: 1.40 (0.16), residues: 1064 sheet: 1.54 (0.62), residues: 48 loop : -2.28 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 96 HIS 0.005 0.001 HIS C 47 PHE 0.014 0.001 PHE C 62 TYR 0.007 0.001 TYR D 22 ARG 0.002 0.000 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 196 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 281 MET cc_start: 0.6569 (ppp) cc_final: 0.4631 (ptp) REVERT: B 68 LYS cc_start: 0.7508 (ttpp) cc_final: 0.7247 (ttpt) REVERT: C 274 ASP cc_start: 0.7544 (m-30) cc_final: 0.7049 (m-30) REVERT: E 281 MET cc_start: 0.6737 (ppp) cc_final: 0.4871 (ptp) REVERT: G 274 ASP cc_start: 0.7710 (m-30) cc_final: 0.7465 (m-30) outliers start: 13 outliers final: 10 residues processed: 203 average time/residue: 0.2877 time to fit residues: 82.6352 Evaluate side-chains 197 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 187 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 172 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 126 optimal weight: 0.0050 chunk 140 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 113 optimal weight: 5.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 HIS B 118 HIS ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN F 118 HIS ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13680 Z= 0.171 Angle : 0.603 11.710 18518 Z= 0.285 Chirality : 0.041 0.306 2142 Planarity : 0.004 0.035 2220 Dihedral : 13.211 87.670 2306 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.75 % Favored : 92.75 % Rotamer: Outliers : 1.03 % Allowed : 11.73 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.22), residues: 1600 helix: 1.56 (0.16), residues: 1064 sheet: 1.67 (0.63), residues: 48 loop : -2.28 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 96 HIS 0.007 0.001 HIS H 65 PHE 0.012 0.001 PHE G 99 TYR 0.007 0.001 TYR H 106 ARG 0.001 0.000 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 211 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.6566 (ppp) cc_final: 0.4769 (ptp) REVERT: B 68 LYS cc_start: 0.7394 (ttpp) cc_final: 0.7190 (ttpt) REVERT: C 274 ASP cc_start: 0.7532 (m-30) cc_final: 0.6998 (m-30) REVERT: E 281 MET cc_start: 0.6618 (ppp) cc_final: 0.4818 (ptp) REVERT: G 281 MET cc_start: 0.6704 (pmm) cc_final: 0.6243 (pmm) outliers start: 14 outliers final: 7 residues processed: 219 average time/residue: 0.2770 time to fit residues: 86.1240 Evaluate side-chains 193 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 186 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 172 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 20.0000 chunk 150 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 HIS C 77 ASN F 118 HIS ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13680 Z= 0.368 Angle : 0.710 11.553 18518 Z= 0.341 Chirality : 0.045 0.362 2142 Planarity : 0.004 0.039 2220 Dihedral : 12.175 83.215 2306 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.25 % Favored : 92.25 % Rotamer: Outliers : 2.14 % Allowed : 13.79 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1600 helix: 1.24 (0.16), residues: 1064 sheet: 1.46 (0.61), residues: 48 loop : -2.35 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 134 HIS 0.006 0.001 HIS G 47 PHE 0.017 0.001 PHE C 62 TYR 0.011 0.001 TYR E 271 ARG 0.004 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 185 time to evaluate : 1.860 Fit side-chains revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7458 (tt) REVERT: A 281 MET cc_start: 0.6606 (ppp) cc_final: 0.4650 (ptp) REVERT: C 230 LYS cc_start: 0.7909 (mmmt) cc_final: 0.7679 (mmmt) REVERT: C 274 ASP cc_start: 0.7655 (m-30) cc_final: 0.7148 (m-30) REVERT: D 90 LYS cc_start: 0.6764 (mttp) cc_final: 0.6542 (mttm) REVERT: E 164 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7433 (tt) REVERT: E 281 MET cc_start: 0.6637 (ppp) cc_final: 0.4654 (ptp) REVERT: G 281 MET cc_start: 0.7020 (pmm) cc_final: 0.6619 (pmm) outliers start: 29 outliers final: 19 residues processed: 209 average time/residue: 0.2952 time to fit residues: 89.2189 Evaluate side-chains 200 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 179 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 172 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 HIS B 118 HIS ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 HIS F 118 HIS ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13680 Z= 0.181 Angle : 0.574 12.692 18518 Z= 0.279 Chirality : 0.040 0.356 2142 Planarity : 0.004 0.035 2220 Dihedral : 10.683 82.832 2306 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.50 % Favored : 93.00 % Rotamer: Outliers : 1.25 % Allowed : 16.45 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.22), residues: 1600 helix: 1.57 (0.16), residues: 1060 sheet: 0.77 (0.64), residues: 56 loop : -2.18 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 96 HIS 0.006 0.001 HIS B 65 PHE 0.017 0.001 PHE C 99 TYR 0.011 0.001 TYR H 106 ARG 0.003 0.000 ARG C 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 187 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.6481 (ppp) cc_final: 0.4585 (ptp) REVERT: C 274 ASP cc_start: 0.7670 (m-30) cc_final: 0.7133 (m-30) REVERT: E 281 MET cc_start: 0.6406 (ppp) cc_final: 0.4599 (ptp) REVERT: G 281 MET cc_start: 0.6900 (pmm) cc_final: 0.6310 (pmm) outliers start: 17 outliers final: 14 residues processed: 200 average time/residue: 0.2867 time to fit residues: 81.9181 Evaluate side-chains 190 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 176 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain H residue 65 HIS Chi-restraints excluded: chain H residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 150 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 HIS F 118 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13680 Z= 0.171 Angle : 0.556 14.103 18518 Z= 0.273 Chirality : 0.039 0.318 2142 Planarity : 0.004 0.034 2220 Dihedral : 10.017 85.197 2306 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.56 % Favored : 92.94 % Rotamer: Outliers : 1.77 % Allowed : 17.26 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.22), residues: 1600 helix: 1.65 (0.16), residues: 1060 sheet: 0.68 (0.65), residues: 56 loop : -2.17 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 96 HIS 0.004 0.001 HIS H 65 PHE 0.008 0.001 PHE C 62 TYR 0.010 0.001 TYR A 215 ARG 0.001 0.000 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 192 time to evaluate : 1.384 Fit side-chains revert: symmetry clash REVERT: A 281 MET cc_start: 0.6425 (ppp) cc_final: 0.4640 (ptp) REVERT: B 42 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7955 (mt-10) REVERT: C 274 ASP cc_start: 0.7680 (m-30) cc_final: 0.7160 (m-30) REVERT: E 281 MET cc_start: 0.6332 (ppp) cc_final: 0.4477 (ptp) REVERT: G 281 MET cc_start: 0.6879 (pmm) cc_final: 0.6295 (pmm) outliers start: 24 outliers final: 18 residues processed: 212 average time/residue: 0.2785 time to fit residues: 83.6002 Evaluate side-chains 193 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 175 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain H residue 65 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS C 77 ASN F 65 HIS F 118 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13680 Z= 0.173 Angle : 0.563 14.782 18518 Z= 0.277 Chirality : 0.039 0.263 2142 Planarity : 0.004 0.034 2220 Dihedral : 9.729 87.484 2306 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.50 % Favored : 93.00 % Rotamer: Outliers : 1.99 % Allowed : 17.18 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.22), residues: 1600 helix: 1.67 (0.16), residues: 1060 sheet: 0.64 (0.65), residues: 56 loop : -2.14 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 96 HIS 0.004 0.001 HIS H 65 PHE 0.016 0.001 PHE G 99 TYR 0.015 0.001 TYR H 106 ARG 0.003 0.000 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 182 time to evaluate : 1.669 Fit side-chains revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7242 (tt) REVERT: A 281 MET cc_start: 0.6415 (ppp) cc_final: 0.4760 (ptp) REVERT: C 274 ASP cc_start: 0.7672 (m-30) cc_final: 0.7433 (m-30) REVERT: D 102 LYS cc_start: 0.4746 (tppt) cc_final: 0.4467 (tptm) REVERT: E 164 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7215 (tt) REVERT: E 281 MET cc_start: 0.6288 (ppp) cc_final: 0.4435 (ptp) REVERT: F 68 LYS cc_start: 0.7492 (ttpp) cc_final: 0.7238 (ttpt) REVERT: G 281 MET cc_start: 0.6859 (pmm) cc_final: 0.6221 (pmm) outliers start: 27 outliers final: 22 residues processed: 205 average time/residue: 0.2774 time to fit residues: 80.5199 Evaluate side-chains 199 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 175 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 70 PHE Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain H residue 65 HIS Chi-restraints excluded: chain H residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS C 77 ASN E 265 ASN F 118 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13680 Z= 0.163 Angle : 0.558 14.232 18518 Z= 0.276 Chirality : 0.038 0.212 2142 Planarity : 0.004 0.034 2220 Dihedral : 9.535 89.369 2306 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.56 % Favored : 92.94 % Rotamer: Outliers : 2.21 % Allowed : 16.74 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.22), residues: 1600 helix: 1.73 (0.16), residues: 1056 sheet: 0.61 (0.66), residues: 56 loop : -2.14 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 96 HIS 0.005 0.001 HIS F 65 PHE 0.008 0.001 PHE D 70 TYR 0.012 0.001 TYR A 215 ARG 0.003 0.000 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 187 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7200 (tt) REVERT: A 281 MET cc_start: 0.6390 (ppp) cc_final: 0.4738 (ptp) REVERT: C 274 ASP cc_start: 0.7662 (m-30) cc_final: 0.7453 (m-30) REVERT: E 164 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7183 (tt) REVERT: E 281 MET cc_start: 0.6282 (ppp) cc_final: 0.4434 (ptp) REVERT: F 68 LYS cc_start: 0.7465 (ttpp) cc_final: 0.7216 (ttpt) REVERT: G 281 MET cc_start: 0.6841 (pmm) cc_final: 0.6193 (pmm) outliers start: 30 outliers final: 20 residues processed: 211 average time/residue: 0.2750 time to fit residues: 82.6803 Evaluate side-chains 203 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 181 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain H residue 65 HIS Chi-restraints excluded: chain H residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 144 optimal weight: 0.0470 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS C 77 ASN F 118 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13680 Z= 0.189 Angle : 0.591 15.478 18518 Z= 0.290 Chirality : 0.039 0.166 2142 Planarity : 0.004 0.034 2220 Dihedral : 9.555 88.155 2306 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.75 % Favored : 92.75 % Rotamer: Outliers : 1.70 % Allowed : 17.70 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.22), residues: 1600 helix: 1.67 (0.16), residues: 1056 sheet: 0.47 (0.66), residues: 56 loop : -2.14 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 96 HIS 0.006 0.001 HIS G 269 PHE 0.015 0.001 PHE C 99 TYR 0.013 0.001 TYR A 271 ARG 0.004 0.000 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 182 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7229 (tt) REVERT: A 271 TYR cc_start: 0.8097 (t80) cc_final: 0.7880 (t80) REVERT: A 281 MET cc_start: 0.6343 (ppp) cc_final: 0.4435 (ptp) REVERT: C 274 ASP cc_start: 0.7651 (m-30) cc_final: 0.7422 (m-30) REVERT: E 164 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7208 (tt) REVERT: E 281 MET cc_start: 0.6286 (ppp) cc_final: 0.4461 (ptp) REVERT: F 68 LYS cc_start: 0.7566 (ttpp) cc_final: 0.7360 (ttpt) outliers start: 23 outliers final: 21 residues processed: 202 average time/residue: 0.2742 time to fit residues: 79.7271 Evaluate side-chains 195 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 172 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain H residue 65 HIS Chi-restraints excluded: chain H residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 143 optimal weight: 9.9990 chunk 123 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS C 77 ASN E 265 ASN F 118 HIS G 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13680 Z= 0.325 Angle : 0.685 15.846 18518 Z= 0.334 Chirality : 0.042 0.160 2142 Planarity : 0.004 0.036 2220 Dihedral : 10.131 88.769 2306 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.50 % Favored : 92.00 % Rotamer: Outliers : 1.92 % Allowed : 17.40 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1600 helix: 1.40 (0.16), residues: 1056 sheet: 0.21 (0.64), residues: 56 loop : -2.21 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 134 HIS 0.020 0.001 HIS C 75 PHE 0.016 0.001 PHE C 62 TYR 0.024 0.001 TYR B 106 ARG 0.007 0.000 ARG C 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 174 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7409 (tt) REVERT: A 237 HIS cc_start: 0.7867 (t-170) cc_final: 0.7564 (t-170) REVERT: A 271 TYR cc_start: 0.8133 (t80) cc_final: 0.7894 (t80) REVERT: A 281 MET cc_start: 0.6519 (ppp) cc_final: 0.4547 (ptp) REVERT: C 274 ASP cc_start: 0.7708 (m-30) cc_final: 0.7492 (m-30) REVERT: E 164 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7390 (tt) REVERT: E 281 MET cc_start: 0.6370 (ppp) cc_final: 0.4454 (ptp) outliers start: 26 outliers final: 22 residues processed: 197 average time/residue: 0.2665 time to fit residues: 75.2749 Evaluate side-chains 196 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 172 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain H residue 65 HIS Chi-restraints excluded: chain H residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 chunk 123 optimal weight: 0.0270 chunk 51 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 HIS G 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.188373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.142458 restraints weight = 17724.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.140434 restraints weight = 11204.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.140873 restraints weight = 9312.499| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13680 Z= 0.168 Angle : 0.590 15.067 18518 Z= 0.290 Chirality : 0.038 0.165 2142 Planarity : 0.004 0.035 2220 Dihedral : 9.548 87.264 2306 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.00 % Favored : 93.50 % Rotamer: Outliers : 1.77 % Allowed : 17.85 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1600 helix: 1.62 (0.16), residues: 1056 sheet: 0.35 (0.66), residues: 56 loop : -2.16 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 96 HIS 0.004 0.001 HIS H 65 PHE 0.017 0.001 PHE G 99 TYR 0.023 0.001 TYR B 106 ARG 0.012 0.000 ARG C 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2531.12 seconds wall clock time: 47 minutes 26.58 seconds (2846.58 seconds total)