Starting phenix.real_space_refine (version: dev) on Wed Feb 22 09:32:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onj_12996/02_2023/7onj_12996_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onj_12996/02_2023/7onj_12996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onj_12996/02_2023/7onj_12996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onj_12996/02_2023/7onj_12996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onj_12996/02_2023/7onj_12996_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onj_12996/02_2023/7onj_12996_updated.pdb" } resolution = 2.3 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 ------------------------------------------------------------------------------- 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= 0.009 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 16947 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "G" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "B" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "C" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "D" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "E" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "F" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "A" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 50 Chain: "G" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 50 Chain: "B" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 50 Chain: "C" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 50 Chain: "D" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 50 Chain: "E" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 50 Chain: "F" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 50 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "F" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Time building chain proxies: 9.74, per 1000 atoms: 0.57 Number of scatterers: 16947 At special positions: 0 Unit cell: (98.9055, 98.9055, 137.192, 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 42 16.00 P 7 15.00 O 3493 8.00 N 2450 7.00 C 10955 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.35 Conformation dependent library (CDL) restraints added in 2.2 seconds 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3388 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 14 sheets defined 53.4% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 21 through 58 removed outlier: 3.588A pdb=" N SER A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 88 Processing helix chain 'A' and resid 93 through 127 removed outlier: 5.306A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 198 through 211 Processing helix chain 'A' and resid 243 through 264 removed outlier: 3.614A pdb=" N LEU A 246 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLN A 247 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 253 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 58 removed outlier: 3.587A pdb=" N SER G 26 " --> pdb=" O ALA G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 88 Processing helix chain 'G' and resid 93 through 127 removed outlier: 5.306A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 171 Processing helix chain 'G' and resid 198 through 211 Processing helix chain 'G' and resid 243 through 264 removed outlier: 3.615A pdb=" N LEU G 246 " --> pdb=" O SER G 243 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLN G 247 " --> pdb=" O GLY G 244 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL G 253 " --> pdb=" O TYR G 250 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE G 261 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 58 removed outlier: 3.588A pdb=" N SER B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 88 Processing helix chain 'B' and resid 93 through 127 removed outlier: 5.305A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 198 through 211 Processing helix chain 'B' and resid 243 through 264 removed outlier: 3.615A pdb=" N LEU B 246 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLN B 247 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 253 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 261 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 58 removed outlier: 3.587A pdb=" N SER C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 88 Processing helix chain 'C' and resid 93 through 127 removed outlier: 5.306A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 198 through 211 Processing helix chain 'C' and resid 243 through 264 removed outlier: 3.614A pdb=" N LEU C 246 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLN C 247 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 253 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 261 " --> pdb=" O LYS C 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 58 removed outlier: 3.587A pdb=" N SER D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 88 Processing helix chain 'D' and resid 93 through 127 removed outlier: 5.306A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N SER D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 198 through 211 Processing helix chain 'D' and resid 243 through 264 removed outlier: 3.614A pdb=" N LEU D 246 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLN D 247 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 253 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE D 261 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 58 removed outlier: 3.587A pdb=" N SER E 26 " --> pdb=" O ALA E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 88 Processing helix chain 'E' and resid 93 through 127 removed outlier: 5.305A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'E' and resid 198 through 211 Processing helix chain 'E' and resid 243 through 264 removed outlier: 3.614A pdb=" N LEU E 246 " --> pdb=" O SER E 243 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLN E 247 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 253 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE E 261 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 58 removed outlier: 3.589A pdb=" N SER F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 88 Processing helix chain 'F' and resid 93 through 127 removed outlier: 5.305A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 171 Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 243 through 264 removed outlier: 3.615A pdb=" N LEU F 246 " --> pdb=" O SER F 243 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLN F 247 " --> pdb=" O GLY F 244 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL F 253 " --> pdb=" O TYR F 250 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE F 261 " --> pdb=" O LYS F 258 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.536A pdb=" N VAL A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 183 through 192 removed outlier: 5.896A pdb=" N VAL A 236 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU A 225 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ARG A 238 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL A 223 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N TRP A 240 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N MET A 221 " --> pdb=" O TRP A 240 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 175 through 177 removed outlier: 3.535A pdb=" N VAL G 141 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 183 through 192 removed outlier: 5.896A pdb=" N VAL G 236 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU G 225 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ARG G 238 " --> pdb=" O VAL G 223 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL G 223 " --> pdb=" O ARG G 238 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N TRP G 240 " --> pdb=" O MET G 221 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N MET G 221 " --> pdb=" O TRP G 240 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 175 through 177 removed outlier: 3.535A pdb=" N VAL B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 183 through 192 removed outlier: 5.895A pdb=" N VAL B 236 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU B 225 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ARG B 238 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL B 223 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N TRP B 240 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N MET B 221 " --> pdb=" O TRP B 240 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 175 through 177 removed outlier: 3.536A pdb=" N VAL C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 183 through 192 removed outlier: 5.897A pdb=" N VAL C 236 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU C 225 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ARG C 238 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL C 223 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N TRP C 240 " --> pdb=" O MET C 221 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N MET C 221 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 175 through 177 removed outlier: 3.535A pdb=" N VAL D 141 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 183 through 192 removed outlier: 5.895A pdb=" N VAL D 236 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU D 225 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ARG D 238 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL D 223 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N TRP D 240 " --> pdb=" O MET D 221 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N MET D 221 " --> pdb=" O TRP D 240 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 175 through 177 removed outlier: 3.536A pdb=" N VAL E 141 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 183 through 192 removed outlier: 5.896A pdb=" N VAL E 236 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU E 225 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ARG E 238 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL E 223 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N TRP E 240 " --> pdb=" O MET E 221 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N MET E 221 " --> pdb=" O TRP E 240 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 175 through 177 removed outlier: 3.536A pdb=" N VAL F 141 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 183 through 192 removed outlier: 5.896A pdb=" N VAL F 236 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU F 225 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ARG F 238 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL F 223 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N TRP F 240 " --> pdb=" O MET F 221 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N MET F 221 " --> pdb=" O TRP F 240 " (cutoff:3.500A) 938 hydrogen bonds defined for protein. 2478 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: 5.13 Time building geometry restraints manager: 7.97 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: 2384 1.32 - 1.44: 4260 1.44 - 1.56: 10163 1.56 - 1.68: 14 1.68 - 1.80: 84 Bond restraints: 16905 Sorted by residual: bond pdb=" O3P PEE C 303 " pdb=" P PEE C 303 " ideal model delta sigma weight residual 1.636 1.588 0.048 2.00e-02 2.50e+03 5.78e+00 bond pdb=" O3P PEE D 303 " pdb=" P PEE D 303 " ideal model delta sigma weight residual 1.636 1.588 0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" O3P PEE E 303 " pdb=" P PEE E 303 " ideal model delta sigma weight residual 1.636 1.588 0.048 2.00e-02 2.50e+03 5.69e+00 bond pdb=" O3P PEE A 301 " pdb=" P PEE A 301 " ideal model delta sigma weight residual 1.636 1.588 0.048 2.00e-02 2.50e+03 5.68e+00 bond pdb=" O3P PEE G 403 " pdb=" P PEE G 403 " ideal model delta sigma weight residual 1.636 1.589 0.047 2.00e-02 2.50e+03 5.60e+00 ... (remaining 16900 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.02: 407 107.02 - 113.77: 10994 113.77 - 120.52: 6454 120.52 - 127.27: 4783 127.27 - 134.02: 63 Bond angle restraints: 22701 Sorted by residual: angle pdb=" O3P PEE E 303 " pdb=" P PEE E 303 " pdb=" O4P PEE E 303 " ideal model delta sigma weight residual 92.91 103.93 -11.02 3.00e+00 1.11e-01 1.35e+01 angle pdb=" O3P PEE G 403 " pdb=" P PEE G 403 " pdb=" O4P PEE G 403 " ideal model delta sigma weight residual 92.91 103.90 -10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" O3P PEE A 301 " pdb=" P PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 92.91 103.90 -10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" O3P PEE B 303 " pdb=" P PEE B 303 " pdb=" O4P PEE B 303 " ideal model delta sigma weight residual 92.91 103.89 -10.98 3.00e+00 1.11e-01 1.34e+01 angle pdb=" O3P PEE F 405 " pdb=" P PEE F 405 " pdb=" O4P PEE F 405 " ideal model delta sigma weight residual 92.91 103.89 -10.98 3.00e+00 1.11e-01 1.34e+01 ... (remaining 22696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.71: 9233 27.71 - 55.42: 308 55.42 - 83.14: 35 83.14 - 110.85: 28 110.85 - 138.56: 49 Dihedral angle restraints: 9653 sinusoidal: 4396 harmonic: 5257 Sorted by residual: dihedral pdb=" CBQ AV0 E 302 " pdb=" CBS AV0 E 302 " pdb=" CCM AV0 E 302 " pdb=" O1 AV0 E 302 " ideal model delta sinusoidal sigma weight residual 70.26 -68.30 138.56 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" CBQ AV0 D 302 " pdb=" CBS AV0 D 302 " pdb=" CCM AV0 D 302 " pdb=" O1 AV0 D 302 " ideal model delta sinusoidal sigma weight residual 70.26 -68.28 138.54 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" CBQ AV0 A 307 " pdb=" CBS AV0 A 307 " pdb=" CCM AV0 A 307 " pdb=" O1 AV0 A 307 " ideal model delta sinusoidal sigma weight residual 70.26 -68.28 138.54 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 9650 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2501 0.075 - 0.149: 327 0.149 - 0.224: 84 0.224 - 0.298: 7 0.298 - 0.373: 7 Chirality restraints: 2926 Sorted by residual: chirality pdb=" C4' LMT E 301 " pdb=" C3' LMT E 301 " pdb=" C5' LMT E 301 " pdb=" O1B LMT E 301 " both_signs ideal model delta sigma weight residual False -2.76 -2.39 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" C4' LMT F 403 " pdb=" C3' LMT F 403 " pdb=" C5' LMT F 403 " pdb=" O1B LMT F 403 " both_signs ideal model delta sigma weight residual False -2.76 -2.39 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" C4' LMT C 301 " pdb=" C3' LMT C 301 " pdb=" C5' LMT C 301 " pdb=" O1B LMT C 301 " both_signs ideal model delta sigma weight residual False -2.76 -2.39 -0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 2923 not shown) Planarity restraints: 2450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 83 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.54e+00 pdb=" C ILE B 83 " -0.021 2.00e-02 2.50e+03 pdb=" O ILE B 83 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA B 84 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 83 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.53e+00 pdb=" C ILE E 83 " -0.021 2.00e-02 2.50e+03 pdb=" O ILE E 83 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA E 84 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 83 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" C ILE G 83 " 0.021 2.00e-02 2.50e+03 pdb=" O ILE G 83 " -0.008 2.00e-02 2.50e+03 pdb=" N ALA G 84 " -0.007 2.00e-02 2.50e+03 ... (remaining 2447 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 612 2.70 - 3.25: 16690 3.25 - 3.80: 28542 3.80 - 4.35: 36722 4.35 - 4.90: 61048 Nonbonded interactions: 143614 Sorted by model distance: nonbonded pdb=" OAR AV0 A 307 " pdb=" OAN AV0 G 405 " model vdw 2.155 2.440 nonbonded pdb=" OAN AV0 B 305 " pdb=" OAR AV0 C 302 " model vdw 2.155 2.440 nonbonded pdb=" OAN AV0 A 303 " pdb=" OAR AV0 B 302 " model vdw 2.155 2.440 nonbonded pdb=" OAN AV0 E 305 " pdb=" OAR AV0 F 404 " model vdw 2.155 2.440 nonbonded pdb=" OAR AV0 G 409 " pdb=" OAN AV0 F 407 " model vdw 2.155 2.440 ... (remaining 143609 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'B' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'C' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'D' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'E' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'F' and (resid 19 through 280 or resid 407 or (resid 409 and (name CAA or \ name CAB or name CAW or name CAX or name CAY or name CAZ or name CBA or name CB \ B or name CBC or name CBD or name CBE or name CBF or name CBG or name CBH or nam \ e CBI or name CBJ or name CBK or name CBL or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCF or name CCH or name CCJ or name CCL or name CC \ M or name CCQ or name O1 or name OAL or name OAN or name OAP or name OBV or name \ OBX or name OCB)))) selection = (chain 'G' and (resid 19 through 280 or (resid 407 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or (resid 409 and (nam \ e CAA or name CAB or name CAW or name CAX or name CAY or name CAZ or name CBA or \ name CBB or name CBC or name CBD or name CBE or name CBF or name CBG or name CB \ H or name CBI or name CBJ or name CBK or name CBL or name CBP or name CBQ or nam \ e CBR or name CBS or name CBT or name CCF or name CCH or name CCJ or name CCL or \ name CCM or name CCQ or name O1 or name OAL or name OAN or name OAP or name OBV \ or name OBX or name OCB)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 42 5.16 5 C 10955 2.51 5 N 2450 2.21 5 O 3493 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.800 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: 5.670 Check model and map are aligned: 0.290 Process input model: 45.650 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.160 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:12.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.062 16905 Z= 0.647 Angle : 0.970 11.017 22701 Z= 0.433 Chirality : 0.060 0.373 2926 Planarity : 0.004 0.021 2450 Dihedral : 18.451 138.562 6265 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 1820 helix: -0.33 (0.11), residues: 1043 sheet: 0.31 (0.29), residues: 294 loop : 0.43 (0.25), residues: 483 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 308 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 310 average time/residue: 1.7207 time to fit residues: 579.2864 Evaluate side-chains 247 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 246 time to evaluate : 1.865 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.3517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 142 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN G 92 GLN B 149 GLN B 210 GLN C 92 GLN C 149 GLN C 210 GLN D 149 GLN D 210 GLN E 210 GLN E 276 ASN F 92 GLN F 149 GLN F 203 GLN F 210 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 16905 Z= 0.169 Angle : 0.489 4.607 22701 Z= 0.256 Chirality : 0.039 0.160 2926 Planarity : 0.004 0.028 2450 Dihedral : 20.834 139.268 3136 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.18), residues: 1820 helix: 1.70 (0.15), residues: 1043 sheet: 0.52 (0.29), residues: 280 loop : 0.02 (0.23), residues: 497 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 263 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 4 residues processed: 267 average time/residue: 1.8961 time to fit residues: 545.7494 Evaluate side-chains 261 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 257 time to evaluate : 1.997 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.9908 time to fit residues: 4.7596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 178 optimal weight: 0.7980 chunk 147 optimal weight: 0.5980 chunk 164 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN G 92 GLN B 149 GLN C 92 GLN C 149 GLN D 210 GLN F 92 GLN F 149 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 16905 Z= 0.196 Angle : 0.470 4.645 22701 Z= 0.247 Chirality : 0.039 0.141 2926 Planarity : 0.004 0.030 2450 Dihedral : 19.924 138.781 3136 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.18), residues: 1820 helix: 2.06 (0.15), residues: 1043 sheet: 0.69 (0.29), residues: 280 loop : 0.02 (0.23), residues: 497 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 258 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 266 average time/residue: 1.8425 time to fit residues: 529.2911 Evaluate side-chains 252 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 244 time to evaluate : 1.855 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 2 residues processed: 6 average time/residue: 0.4394 time to fit residues: 5.7757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 166 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 210 GLN G 30 ASN G 92 GLN G 149 GLN B 210 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN C 149 GLN D 210 GLN E 149 GLN F 92 GLN F 149 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 16905 Z= 0.152 Angle : 0.437 4.560 22701 Z= 0.231 Chirality : 0.038 0.128 2926 Planarity : 0.003 0.030 2450 Dihedral : 19.184 135.142 3136 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.19), residues: 1820 helix: 2.23 (0.16), residues: 1043 sheet: 0.72 (0.28), residues: 280 loop : 0.06 (0.24), residues: 497 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 257 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 7 residues processed: 265 average time/residue: 1.9097 time to fit residues: 546.3210 Evaluate side-chains 254 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 247 time to evaluate : 1.997 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 1 residues processed: 6 average time/residue: 0.8261 time to fit residues: 8.2374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.2980 chunk 99 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 72 optimal weight: 0.5980 chunk 150 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN G 30 ASN G 92 GLN B 149 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN C 210 GLN D 210 GLN F 92 GLN F 203 GLN F 207 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 16905 Z= 0.145 Angle : 0.428 4.460 22701 Z= 0.225 Chirality : 0.038 0.128 2926 Planarity : 0.003 0.044 2450 Dihedral : 18.485 130.261 3136 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.19), residues: 1820 helix: 2.34 (0.16), residues: 1043 sheet: 0.70 (0.28), residues: 280 loop : 0.06 (0.24), residues: 497 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 255 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 4 residues processed: 260 average time/residue: 1.8862 time to fit residues: 528.5275 Evaluate side-chains 250 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 246 time to evaluate : 1.861 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.2662 time to fit residues: 3.1170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN D 149 GLN D 210 GLN F 92 GLN F 149 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 16905 Z= 0.159 Angle : 0.431 4.468 22701 Z= 0.227 Chirality : 0.038 0.129 2926 Planarity : 0.003 0.029 2450 Dihedral : 18.095 126.621 3136 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.19), residues: 1820 helix: 2.38 (0.16), residues: 1043 sheet: 0.71 (0.28), residues: 280 loop : 0.03 (0.24), residues: 497 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 248 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 253 average time/residue: 1.9222 time to fit residues: 523.6103 Evaluate side-chains 246 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 1.849 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.3163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 210 GLN ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN C 210 GLN D 210 GLN F 92 GLN F 203 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 16905 Z= 0.169 Angle : 0.436 4.528 22701 Z= 0.231 Chirality : 0.038 0.130 2926 Planarity : 0.003 0.020 2450 Dihedral : 17.745 123.491 3136 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.19), residues: 1820 helix: 2.38 (0.16), residues: 1043 sheet: 0.74 (0.28), residues: 280 loop : 0.00 (0.24), residues: 497 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 252 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 256 average time/residue: 1.9113 time to fit residues: 527.7910 Evaluate side-chains 251 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 245 time to evaluate : 1.701 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 5 average time/residue: 0.2097 time to fit residues: 3.8390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 104 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 0.0670 chunk 111 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN A 276 ASN G 30 ASN G 92 GLN G 149 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN C 210 GLN D 149 GLN D 210 GLN E 112 GLN F 92 GLN F 203 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 16905 Z= 0.147 Angle : 0.425 4.464 22701 Z= 0.225 Chirality : 0.038 0.128 2926 Planarity : 0.003 0.026 2450 Dihedral : 17.478 122.842 3136 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.19), residues: 1820 helix: 2.41 (0.16), residues: 1043 sheet: 0.71 (0.28), residues: 280 loop : -0.01 (0.24), residues: 497 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 249 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 253 average time/residue: 1.9559 time to fit residues: 533.8866 Evaluate side-chains 247 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 246 time to evaluate : 1.856 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.2111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 147 optimal weight: 0.0270 chunk 154 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 210 GLN G 30 ASN G 112 GLN G 149 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN C 112 GLN D 149 GLN D 210 GLN ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN F 92 GLN F 203 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 16905 Z= 0.141 Angle : 0.419 4.461 22701 Z= 0.222 Chirality : 0.037 0.128 2926 Planarity : 0.003 0.020 2450 Dihedral : 17.164 122.590 3136 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.19), residues: 1820 helix: 2.43 (0.16), residues: 1043 sheet: 0.71 (0.28), residues: 280 loop : -0.06 (0.24), residues: 497 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 247 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 250 average time/residue: 1.9468 time to fit residues: 523.9392 Evaluate side-chains 247 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 243 time to evaluate : 1.825 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 1.2385 time to fit residues: 5.0571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 chunk 181 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN G 112 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN C 112 GLN D 210 GLN E 30 ASN E 112 GLN F 92 GLN F 203 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 16905 Z= 0.146 Angle : 0.419 4.434 22701 Z= 0.223 Chirality : 0.037 0.128 2926 Planarity : 0.003 0.020 2450 Dihedral : 16.966 123.639 3136 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.19), residues: 1820 helix: 2.44 (0.16), residues: 1043 sheet: 0.72 (0.28), residues: 280 loop : -0.08 (0.24), residues: 497 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 245 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 249 average time/residue: 1.9905 time to fit residues: 534.2097 Evaluate side-chains 246 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 244 time to evaluate : 1.802 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.2713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 112 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN C 112 GLN ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN F 92 GLN F 203 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.117678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.082616 restraints weight = 19198.895| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.47 r_work: 0.2704 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 16905 Z= 0.153 Angle : 0.425 4.712 22701 Z= 0.226 Chirality : 0.037 0.130 2926 Planarity : 0.003 0.023 2450 Dihedral : 16.796 123.300 3136 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.19), residues: 1820 helix: 2.44 (0.16), residues: 1043 sheet: 0.73 (0.28), residues: 280 loop : -0.07 (0.24), residues: 497 =============================================================================== Job complete usr+sys time: 7620.48 seconds wall clock time: 135 minutes 24.15 seconds (8124.15 seconds total)