Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 19:53:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ooa_13008/04_2023/7ooa_13008_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ooa_13008/04_2023/7ooa_13008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ooa_13008/04_2023/7ooa_13008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ooa_13008/04_2023/7ooa_13008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ooa_13008/04_2023/7ooa_13008_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ooa_13008/04_2023/7ooa_13008_updated.pdb" } resolution = 2.7 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= 0.012 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 7 5.49 5 S 42 5.16 5 C 10171 2.51 5 N 2450 2.21 5 O 2940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 15610 Number of models: 1 Model: "" Number of chains: 14 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: "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: "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: "A" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 25 Chain: "B" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 25 Chain: "C" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 25 Chain: "D" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 25 Chain: "E" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 25 Chain: "F" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 25 Chain: "G" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 25 Time building chain proxies: 8.39, per 1000 atoms: 0.54 Number of scatterers: 15610 At special positions: 0 Unit cell: (98.9055, 98.9055, 138.255, 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 2940 8.00 N 2450 7.00 C 10171 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: 6.71 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 Processing helix chain 'A' and resid 63 through 88 Processing helix chain 'A' and resid 93 through 127 removed outlier: 5.365A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 198 through 210 Processing helix chain 'A' and resid 243 through 264 removed outlier: 3.657A pdb=" N LEU A 246 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLN A 247 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 248 " --> pdb=" O ASP A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 58 Processing helix chain 'B' and resid 63 through 88 Processing helix chain 'B' and resid 93 through 127 removed outlier: 5.365A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 198 through 210 Processing helix chain 'B' and resid 243 through 264 removed outlier: 3.658A pdb=" N LEU B 246 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLN B 247 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN B 248 " --> pdb=" O ASP B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 58 Processing helix chain 'C' and resid 63 through 88 Processing helix chain 'C' and resid 93 through 127 removed outlier: 5.366A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 198 through 210 Processing helix chain 'C' and resid 243 through 264 removed outlier: 3.658A pdb=" N LEU C 246 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLN C 247 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 248 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 58 Processing helix chain 'D' and resid 63 through 88 Processing helix chain 'D' and resid 93 through 127 removed outlier: 5.365A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 172 Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 243 through 264 removed outlier: 3.658A pdb=" N LEU D 246 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLN D 247 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN D 248 " --> pdb=" O ASP D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 58 Processing helix chain 'E' and resid 63 through 88 Processing helix chain 'E' and resid 93 through 127 removed outlier: 5.365A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 172 Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'E' and resid 243 through 264 removed outlier: 3.658A pdb=" N LEU E 246 " --> pdb=" O SER E 243 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLN E 247 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN E 248 " --> pdb=" O ASP E 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 58 Processing helix chain 'F' and resid 63 through 88 Processing helix chain 'F' and resid 93 through 127 removed outlier: 5.365A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N SER F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 172 Processing helix chain 'F' and resid 198 through 210 Processing helix chain 'F' and resid 243 through 264 removed outlier: 3.658A pdb=" N LEU F 246 " --> pdb=" O SER F 243 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLN F 247 " --> pdb=" O GLY F 244 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN F 248 " --> pdb=" O ASP F 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 58 Processing helix chain 'G' and resid 63 through 88 Processing helix chain 'G' and resid 93 through 127 removed outlier: 5.365A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 172 Processing helix chain 'G' and resid 198 through 210 Processing helix chain 'G' and resid 243 through 264 removed outlier: 3.658A pdb=" N LEU G 246 " --> pdb=" O SER G 243 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLN G 247 " --> pdb=" O GLY G 244 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN G 248 " --> pdb=" O ASP G 245 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.713A pdb=" N VAL A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.746A 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: 6.051A pdb=" N VAL A 236 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU A 225 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ARG A 238 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL A 223 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N TRP A 240 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N MET A 221 " --> pdb=" O TRP A 240 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 175 through 177 removed outlier: 3.713A pdb=" N VAL B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 183 through 192 removed outlier: 6.051A pdb=" N VAL B 236 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU B 225 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ARG B 238 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL B 223 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N TRP B 240 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N MET B 221 " --> pdb=" O TRP B 240 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 175 through 177 removed outlier: 3.713A pdb=" N VAL C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 183 through 192 removed outlier: 6.052A pdb=" N VAL C 236 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU C 225 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ARG C 238 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL C 223 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N TRP C 240 " --> pdb=" O MET C 221 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N MET C 221 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 175 through 177 removed outlier: 3.714A pdb=" N VAL D 141 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 183 through 192 removed outlier: 6.051A pdb=" N VAL D 236 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU D 225 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ARG D 238 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL D 223 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N TRP D 240 " --> pdb=" O MET D 221 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N MET D 221 " --> pdb=" O TRP D 240 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 175 through 177 removed outlier: 3.714A pdb=" N VAL E 141 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 183 through 192 removed outlier: 6.051A pdb=" N VAL E 236 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU E 225 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ARG E 238 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL E 223 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N TRP E 240 " --> pdb=" O MET E 221 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N MET E 221 " --> pdb=" O TRP E 240 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 175 through 177 removed outlier: 3.713A pdb=" N VAL F 141 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 183 through 192 removed outlier: 6.051A pdb=" N VAL F 236 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU F 225 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ARG F 238 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL F 223 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N TRP F 240 " --> pdb=" O MET F 221 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N MET F 221 " --> pdb=" O TRP F 240 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 175 through 177 removed outlier: 3.712A pdb=" N VAL G 141 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 183 through 192 removed outlier: 6.051A pdb=" N VAL G 236 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU G 225 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ARG G 238 " --> pdb=" O VAL G 223 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL G 223 " --> pdb=" O ARG G 238 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N TRP G 240 " --> pdb=" O MET G 221 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N MET G 221 " --> pdb=" O TRP G 240 " (cutoff:3.500A) 952 hydrogen bonds defined for protein. 2499 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: 4.61 Time building geometry restraints manager: 7.16 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: 2311 1.32 - 1.44: 3961 1.44 - 1.56: 9443 1.56 - 1.68: 14 1.68 - 1.80: 84 Bond restraints: 15813 Sorted by residual: bond pdb=" C4 PEE G 303 " pdb=" O4P PEE G 303 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C4 PEE B 303 " pdb=" O4P PEE B 303 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" C4 PEE E 303 " pdb=" O4P PEE E 303 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" C4 PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.23e+00 bond pdb=" C4 PEE C 303 " pdb=" O4P PEE C 303 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.21e+00 ... (remaining 15808 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.25: 333 107.25 - 113.94: 9999 113.94 - 120.63: 6010 120.63 - 127.32: 4896 127.32 - 134.01: 63 Bond angle restraints: 21301 Sorted by residual: angle pdb=" O3P PEE A 301 " pdb=" P PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 92.91 105.04 -12.13 3.00e+00 1.11e-01 1.64e+01 angle pdb=" O3P PEE D 303 " pdb=" P PEE D 303 " pdb=" O4P PEE D 303 " ideal model delta sigma weight residual 92.91 105.04 -12.13 3.00e+00 1.11e-01 1.64e+01 angle pdb=" O3P PEE G 303 " pdb=" P PEE G 303 " pdb=" O4P PEE G 303 " ideal model delta sigma weight residual 92.91 105.04 -12.13 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O3P PEE C 303 " pdb=" P PEE C 303 " pdb=" O4P PEE C 303 " ideal model delta sigma weight residual 92.91 105.03 -12.12 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O3P PEE E 303 " pdb=" P PEE E 303 " pdb=" O4P PEE E 303 " ideal model delta sigma weight residual 92.91 105.03 -12.12 3.00e+00 1.11e-01 1.63e+01 ... (remaining 21296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.55: 8981 25.55 - 51.11: 154 51.11 - 76.66: 35 76.66 - 102.22: 14 102.22 - 127.77: 42 Dihedral angle restraints: 9226 sinusoidal: 3969 harmonic: 5257 Sorted by residual: dihedral pdb=" C12 PEE E 303 " pdb=" C10 PEE E 303 " pdb=" C11 PEE E 303 " pdb=" O4 PEE E 303 " ideal model delta sinusoidal sigma weight residual -19.47 -147.24 127.77 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" C12 PEE A 301 " pdb=" C10 PEE A 301 " pdb=" C11 PEE A 301 " pdb=" O4 PEE A 301 " ideal model delta sinusoidal sigma weight residual -19.47 -147.21 127.74 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" C12 PEE D 303 " pdb=" C10 PEE D 303 " pdb=" C11 PEE D 303 " pdb=" O4 PEE D 303 " ideal model delta sinusoidal sigma weight residual -19.47 -147.21 127.74 1 3.00e+01 1.11e-03 1.72e+01 ... (remaining 9223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2074 0.050 - 0.100: 474 0.100 - 0.150: 98 0.150 - 0.199: 18 0.199 - 0.249: 17 Chirality restraints: 2681 Sorted by residual: chirality pdb=" C2 PEE C 303 " pdb=" C1 PEE C 303 " pdb=" C3 PEE C 303 " pdb=" O2 PEE C 303 " both_signs ideal model delta sigma weight residual False -2.33 -2.58 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C2 PEE A 301 " pdb=" C1 PEE A 301 " pdb=" C3 PEE A 301 " pdb=" O2 PEE A 301 " both_signs ideal model delta sigma weight residual False -2.33 -2.58 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C2 PEE D 303 " pdb=" C1 PEE D 303 " pdb=" C3 PEE D 303 " pdb=" O2 PEE D 303 " both_signs ideal model delta sigma weight residual False -2.33 -2.58 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 2678 not shown) Planarity restraints: 2450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 270 " 0.012 5.00e-02 4.00e+02 1.87e-02 5.60e-01 pdb=" N PRO D 271 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO D 271 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO D 271 " 0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 270 " 0.012 5.00e-02 4.00e+02 1.87e-02 5.58e-01 pdb=" N PRO E 271 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO E 271 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO E 271 " 0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 270 " 0.012 5.00e-02 4.00e+02 1.85e-02 5.50e-01 pdb=" N PRO F 271 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO F 271 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO F 271 " 0.010 5.00e-02 4.00e+02 ... (remaining 2447 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2919 2.78 - 3.31: 14986 3.31 - 3.84: 26040 3.84 - 4.37: 30996 4.37 - 4.90: 54493 Nonbonded interactions: 129434 Sorted by model distance: nonbonded pdb=" OD2 ASP B 159 " pdb=" NZ LYS B 161 " model vdw 2.256 2.520 nonbonded pdb=" OD2 ASP E 159 " pdb=" NZ LYS E 161 " model vdw 2.256 2.520 nonbonded pdb=" OD2 ASP D 159 " pdb=" NZ LYS D 161 " model vdw 2.256 2.520 nonbonded pdb=" OD2 ASP G 159 " pdb=" NZ LYS G 161 " model vdw 2.256 2.520 nonbonded pdb=" OD2 ASP A 159 " pdb=" NZ LYS A 161 " model vdw 2.256 2.520 ... (remaining 129429 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 302 or (resid 305 and (name C1 or \ name C2 or name C3 or name C4 or name C5 or name C6 or name CAA or name CAB or n \ ame 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 CBP or name CBQ or name CBR or name CBS or n \ ame CBT or name CCF or name CCH or name CCJ or name CCL or name CCM or name CCQ \ or name O1 or name O2 or name O3 or name O4 or name O5 or name O6 or name OAL or \ name OAN or name OAP or name OBV or name OBX or name OCB)))) selection = (chain 'B' and (resid 19 through 280 or (resid 302 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 305)) selection = (chain 'C' and (resid 19 through 280 or (resid 302 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 305)) selection = (chain 'D' and (resid 19 through 280 or (resid 302 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 305)) selection = (chain 'E' and (resid 19 through 280 or (resid 302 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 305)) selection = (chain 'F' and (resid 19 through 280 or (resid 302 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 305)) selection = (chain 'G' and (resid 19 through 280 or (resid 302 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 305)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.630 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 41.590 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:10.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 : 0.005 0.041 15813 Z= 0.324 Angle : 0.662 12.132 21301 Z= 0.289 Chirality : 0.047 0.249 2681 Planarity : 0.003 0.019 2450 Dihedral : 15.269 127.771 5838 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer Outliers : 0.00 % 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: 2.71 (0.18), residues: 1820 helix: 3.13 (0.15), residues: 1029 sheet: 0.82 (0.29), residues: 280 loop : -0.53 (0.22), residues: 511 *********************** 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 274 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.744 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 274 average time/residue: 1.8569 time to fit residues: 545.0348 Evaluate side-chains 210 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 208 time to evaluate : 1.739 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.1822 time to fit residues: 2.9262 ------------------------------------------------------------------------------- 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: 1.9990 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 47 optimal weight: 0.0470 chunk 93 optimal weight: 0.0870 chunk 73 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 165 optimal weight: 0.0980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN B 149 GLN C 276 ASN D 92 GLN D 112 GLN F 92 GLN F 112 GLN F 149 GLN F 210 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 15813 Z= 0.126 Angle : 0.417 4.478 21301 Z= 0.235 Chirality : 0.039 0.138 2681 Planarity : 0.005 0.029 2450 Dihedral : 16.622 123.716 2709 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer Outliers : 1.48 % 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: 2.19 (0.19), residues: 1820 helix: 2.61 (0.15), residues: 1029 sheet: 0.63 (0.30), residues: 280 loop : -0.52 (0.22), residues: 511 *********************** 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 260 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 238 time to evaluate : 1.730 Fit side-chains outliers start: 22 outliers final: 5 residues processed: 244 average time/residue: 1.9229 time to fit residues: 503.4310 Evaluate side-chains 211 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 206 time to evaluate : 1.730 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 3 average time/residue: 0.6515 time to fit residues: 4.6649 ------------------------------------------------------------------------------- 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: 3.9990 chunk 51 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 165 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 0.3980 chunk 164 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN B 30 ASN B 149 GLN D 92 GLN D 112 GLN F 30 ASN F 92 GLN F 112 GLN F 210 GLN G 149 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 15813 Z= 0.160 Angle : 0.417 4.410 21301 Z= 0.230 Chirality : 0.039 0.134 2681 Planarity : 0.004 0.028 2450 Dihedral : 15.879 120.145 2709 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer Outliers : 2.16 % 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: 1.95 (0.19), residues: 1820 helix: 2.37 (0.16), residues: 1029 sheet: 0.53 (0.30), residues: 280 loop : -0.51 (0.22), residues: 511 *********************** 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 259 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 227 time to evaluate : 1.880 Fit side-chains outliers start: 32 outliers final: 7 residues processed: 240 average time/residue: 1.8619 time to fit residues: 480.1221 Evaluate side-chains 216 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 209 time to evaluate : 1.732 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 4 average time/residue: 0.9827 time to fit residues: 6.6631 ------------------------------------------------------------------------------- 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: 0.9980 chunk 124 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN B 149 GLN D 92 GLN D 112 GLN F 92 GLN F 112 GLN F 149 GLN G 149 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 15813 Z= 0.199 Angle : 0.453 4.539 21301 Z= 0.244 Chirality : 0.040 0.133 2681 Planarity : 0.005 0.042 2450 Dihedral : 15.795 119.626 2709 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer Outliers : 2.36 % 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: 1.83 (0.19), residues: 1820 helix: 2.24 (0.16), residues: 1029 sheet: 0.52 (0.29), residues: 280 loop : -0.51 (0.22), residues: 511 *********************** 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 260 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 225 time to evaluate : 1.653 Fit side-chains outliers start: 35 outliers final: 8 residues processed: 237 average time/residue: 1.8679 time to fit residues: 474.7317 Evaluate side-chains 217 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 209 time to evaluate : 1.878 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 4 average time/residue: 1.0149 time to fit residues: 6.8869 ------------------------------------------------------------------------------- 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: 4.9990 chunk 99 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 121 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 0.0470 chunk 157 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN D 92 GLN F 92 GLN F 112 GLN F 149 GLN G 149 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 15813 Z= 0.134 Angle : 0.401 4.413 21301 Z= 0.222 Chirality : 0.039 0.134 2681 Planarity : 0.004 0.034 2450 Dihedral : 15.320 118.734 2709 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer Outliers : 1.75 % 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: 1.88 (0.19), residues: 1820 helix: 2.30 (0.16), residues: 1029 sheet: 0.54 (0.30), residues: 280 loop : -0.53 (0.22), residues: 511 *********************** 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 249 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 223 time to evaluate : 1.776 Fit side-chains outliers start: 26 outliers final: 10 residues processed: 234 average time/residue: 1.8361 time to fit residues: 460.7520 Evaluate side-chains 217 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 207 time to evaluate : 1.809 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 1.3450 time to fit residues: 8.2346 ------------------------------------------------------------------------------- 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: 0.6980 chunk 158 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 103 optimal weight: 0.0770 chunk 43 optimal weight: 4.9990 chunk 176 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN D 92 GLN F 112 GLN F 149 GLN G 149 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 15813 Z= 0.125 Angle : 0.395 4.697 21301 Z= 0.218 Chirality : 0.039 0.132 2681 Planarity : 0.004 0.036 2450 Dihedral : 14.851 118.719 2709 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer Outliers : 1.55 % 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 (0.19), residues: 1820 helix: 2.34 (0.16), residues: 1029 sheet: 0.55 (0.30), residues: 280 loop : -0.53 (0.22), residues: 511 *********************** 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 251 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 228 time to evaluate : 1.847 Fit side-chains outliers start: 23 outliers final: 7 residues processed: 240 average time/residue: 1.8739 time to fit residues: 482.0564 Evaluate side-chains 215 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 208 time to evaluate : 1.744 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.9555 time to fit residues: 4.4644 ------------------------------------------------------------------------------- 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: 4.9990 chunk 19 optimal weight: 0.0570 chunk 100 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 175 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN F 112 GLN F 149 GLN G 149 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 15813 Z= 0.182 Angle : 0.435 4.941 21301 Z= 0.235 Chirality : 0.039 0.133 2681 Planarity : 0.004 0.033 2450 Dihedral : 15.053 119.406 2709 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer Outliers : 1.89 % 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: 1.87 (0.19), residues: 1820 helix: 2.28 (0.16), residues: 1029 sheet: 0.52 (0.30), residues: 280 loop : -0.47 (0.22), residues: 511 *********************** 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 238 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 210 time to evaluate : 1.856 Fit side-chains outliers start: 28 outliers final: 9 residues processed: 225 average time/residue: 1.9708 time to fit residues: 474.9294 Evaluate side-chains 213 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 204 time to evaluate : 1.902 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 1.9344 time to fit residues: 8.8417 ------------------------------------------------------------------------------- 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: 6.9990 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 0.0770 chunk 111 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN D 92 GLN F 92 GLN F 112 GLN F 149 GLN ** G 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 15813 Z= 0.214 Angle : 0.466 9.348 21301 Z= 0.248 Chirality : 0.040 0.181 2681 Planarity : 0.004 0.034 2450 Dihedral : 15.371 119.463 2709 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer Outliers : 1.35 % 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: 1.80 (0.19), residues: 1820 helix: 2.20 (0.16), residues: 1029 sheet: 0.50 (0.30), residues: 280 loop : -0.47 (0.22), residues: 511 *********************** 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 233 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 213 time to evaluate : 1.905 Fit side-chains outliers start: 20 outliers final: 7 residues processed: 227 average time/residue: 1.9163 time to fit residues: 465.9681 Evaluate side-chains 213 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 206 time to evaluate : 1.767 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.1841 time to fit residues: 2.6505 ------------------------------------------------------------------------------- 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: 0.9980 chunk 168 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 163 optimal weight: 0.1980 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN F 112 GLN F 149 GLN ** G 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 15813 Z= 0.148 Angle : 0.421 6.366 21301 Z= 0.229 Chirality : 0.040 0.256 2681 Planarity : 0.004 0.036 2450 Dihedral : 15.071 119.252 2709 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: 1.83 (0.19), residues: 1820 helix: 2.24 (0.16), residues: 1029 sheet: 0.52 (0.30), residues: 280 loop : -0.50 (0.22), residues: 511 *********************** 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 222 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 205 time to evaluate : 1.813 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 217 average time/residue: 1.9208 time to fit residues: 446.1583 Evaluate side-chains 212 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 203 time to evaluate : 1.674 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 1.1511 time to fit residues: 6.0491 ------------------------------------------------------------------------------- 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: 0.8980 chunk 172 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 120 optimal weight: 0.4980 chunk 181 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN C 112 GLN ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN F 112 GLN F 149 GLN G 149 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 15813 Z= 0.152 Angle : 0.425 6.408 21301 Z= 0.231 Chirality : 0.040 0.244 2681 Planarity : 0.004 0.035 2450 Dihedral : 14.970 119.483 2709 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: 1.81 (0.19), residues: 1820 helix: 2.22 (0.16), residues: 1029 sheet: 0.50 (0.30), residues: 280 loop : -0.49 (0.22), residues: 511 ********************** 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 219 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 202 time to evaluate : 1.815 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 214 average time/residue: 2.0242 time to fit residues: 463.6599 Evaluate side-chains 209 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 202 time to evaluate : 1.580 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.2005 time to fit residues: 2.6797 ------------------------------------------------------------------------------- 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: 0.7980 chunk 153 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN B 149 GLN ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN F 112 GLN F 149 GLN G 149 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.117453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.091482 restraints weight = 17582.686| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.18 r_work: 0.2734 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 15813 Z= 0.170 Angle : 0.447 9.877 21301 Z= 0.238 Chirality : 0.040 0.245 2681 Planarity : 0.004 0.033 2450 Dihedral : 15.016 119.825 2709 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.19), residues: 1820 helix: 2.18 (0.16), residues: 1029 sheet: 0.49 (0.29), residues: 280 loop : -0.49 (0.23), residues: 511 =============================================================================== Job complete usr+sys time: 6871.15 seconds wall clock time: 122 minutes 27.55 seconds (7347.55 seconds total)