Starting phenix.real_space_refine on Sat Mar 16 20:32:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ooa_13008/03_2024/7ooa_13008_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ooa_13008/03_2024/7ooa_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_13008/03_2024/7ooa_13008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ooa_13008/03_2024/7ooa_13008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ooa_13008/03_2024/7ooa_13008_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ooa_13008/03_2024/7ooa_13008_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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-dev-5265/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: 133 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: 133 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: 133 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: 133 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: 133 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: 133 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: 133 Unresolved non-hydrogen chiralities: 25 Time building chain proxies: 8.28, per 1000 atoms: 0.53 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: 5.58 Conformation dependent library (CDL) restraints added in 2.5 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: 2.30 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: 4.35 Time building geometry restraints manager: 6.17 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: 10339 25.55 - 51.11: 301 51.11 - 76.66: 112 76.66 - 102.22: 84 102.22 - 127.77: 140 Dihedral angle restraints: 10976 sinusoidal: 5719 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 10973 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: 1.980 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: 6.700 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 40.690 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: 0.000 Load rotamer database and sin/cos tables:10.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.140 ------------------------------------------------------------------------------- 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 : 21.922 127.771 7588 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 % Allowed : 1.89 % Favored : 98.11 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 251 PHE 0.012 0.002 PHE G 178 TYR 0.006 0.001 TYR E 75 ARG 0.003 0.000 ARG D 184 *********************** 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 : 1.603 Fit side-chains REVERT: A 105 LEU cc_start: 0.8773 (tp) cc_final: 0.8553 (tp) REVERT: B 92 GLN cc_start: 0.8454 (mt0) cc_final: 0.8233 (mt0) REVERT: C 54 ARG cc_start: 0.7217 (mtm-85) cc_final: 0.6997 (mtm-85) REVERT: C 149 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8162 (mm110) REVERT: D 75 TYR cc_start: 0.8614 (m-10) cc_final: 0.8359 (m-80) REVERT: E 75 TYR cc_start: 0.8712 (m-10) cc_final: 0.8464 (m-80) REVERT: G 92 GLN cc_start: 0.8355 (mt0) cc_final: 0.8085 (mt0) outliers start: 0 outliers final: 2 residues processed: 274 average time/residue: 1.7654 time to fit residues: 518.4285 Evaluate side-chains 210 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 208 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain G residue 44 ILE 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: 0.8338 moved from start: 0.1108 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= 0.146 Angle : 0.552 7.836 21301 Z= 0.266 Chirality : 0.041 0.149 2681 Planarity : 0.005 0.033 2450 Dihedral : 18.011 128.800 4463 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.48 % Allowed : 10.92 % Favored : 87.60 % 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: 2.15 (0.19), residues: 1820 helix: 2.56 (0.15), residues: 1029 sheet: 0.68 (0.29), residues: 294 loop : -0.60 (0.23), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 251 PHE 0.012 0.002 PHE C 277 TYR 0.005 0.001 TYR A 270 ARG 0.006 0.000 ARG A 59 *********************** 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 263 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 241 time to evaluate : 1.830 Fit side-chains REVERT: A 105 LEU cc_start: 0.8762 (tp) cc_final: 0.8551 (tp) REVERT: B 92 GLN cc_start: 0.8432 (mt0) cc_final: 0.8219 (mt0) REVERT: C 54 ARG cc_start: 0.7207 (mtm-85) cc_final: 0.6949 (mtm-85) REVERT: C 105 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8171 (tt) REVERT: D 75 TYR cc_start: 0.8545 (m-10) cc_final: 0.8270 (m-10) REVERT: D 88 ARG cc_start: 0.7975 (tpp-160) cc_final: 0.7555 (tpt-90) REVERT: E 59 ARG cc_start: 0.7802 (mmt90) cc_final: 0.7450 (mmt90) REVERT: E 209 ILE cc_start: 0.8948 (pt) cc_final: 0.8710 (pt) REVERT: G 92 GLN cc_start: 0.8379 (mt0) cc_final: 0.8067 (mt0) outliers start: 22 outliers final: 2 residues processed: 245 average time/residue: 1.7724 time to fit residues: 465.8249 Evaluate side-chains 211 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 208 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain G residue 44 ILE 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: 3.9990 chunk 137 optimal weight: 0.0980 chunk 112 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 165 optimal weight: 0.5980 chunk 178 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 112 GLN D 92 GLN D 112 GLN F 92 GLN F 112 GLN F 149 GLN F 210 GLN G 149 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1394 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= 0.179 Angle : 0.466 4.426 21301 Z= 0.243 Chirality : 0.040 0.133 2681 Planarity : 0.005 0.031 2450 Dihedral : 15.319 123.914 4461 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.22 % Allowed : 11.79 % Favored : 85.98 % 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: 0.52 (0.29), residues: 280 loop : -0.49 (0.22), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 251 PHE 0.011 0.002 PHE C 277 TYR 0.009 0.001 TYR B 75 ARG 0.008 0.001 ARG A 59 *********************** 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 262 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 229 time to evaluate : 1.761 Fit side-chains REVERT: A 105 LEU cc_start: 0.8798 (tp) cc_final: 0.8578 (tp) REVERT: A 155 MET cc_start: 0.9148 (ptp) cc_final: 0.8905 (ptm) REVERT: A 210 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.7412 (mp10) REVERT: B 92 GLN cc_start: 0.8366 (mt0) cc_final: 0.8152 (mt0) REVERT: C 105 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8266 (tt) REVERT: C 149 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8368 (mm110) REVERT: D 46 ARG cc_start: 0.7512 (ttp-110) cc_final: 0.7183 (ttp80) REVERT: D 54 ARG cc_start: 0.7288 (mtp180) cc_final: 0.6903 (mtp180) REVERT: E 59 ARG cc_start: 0.7775 (mmt90) cc_final: 0.7444 (mmt90) REVERT: E 210 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7549 (mp10) REVERT: F 155 MET cc_start: 0.9134 (ptp) cc_final: 0.8896 (ptm) REVERT: G 92 GLN cc_start: 0.8405 (mt0) cc_final: 0.8122 (mt0) REVERT: G 210 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.7571 (mp10) outliers start: 33 outliers final: 5 residues processed: 239 average time/residue: 1.7978 time to fit residues: 460.7555 Evaluate side-chains 214 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 205 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 111 optimal weight: 0.0670 chunk 166 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 B 149 GLN C 112 GLN D 92 GLN D 112 GLN F 92 GLN F 112 GLN F 149 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15813 Z= 0.143 Angle : 0.419 4.406 21301 Z= 0.225 Chirality : 0.039 0.134 2681 Planarity : 0.004 0.022 2450 Dihedral : 14.643 123.243 4459 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.42 % Allowed : 12.80 % Favored : 85.78 % 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: 2.33 (0.16), residues: 1029 sheet: 0.56 (0.30), residues: 280 loop : -0.51 (0.22), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 240 PHE 0.010 0.001 PHE C 188 TYR 0.008 0.001 TYR E 75 ARG 0.005 0.000 ARG A 59 *********************** 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 241 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 220 time to evaluate : 1.644 Fit side-chains REVERT: A 105 LEU cc_start: 0.8803 (tp) cc_final: 0.8574 (tp) REVERT: A 210 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.7299 (mp10) REVERT: B 92 GLN cc_start: 0.8354 (mt0) cc_final: 0.8138 (mt0) REVERT: C 105 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8269 (tt) REVERT: C 273 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.7925 (tpp) REVERT: D 54 ARG cc_start: 0.7279 (mtp180) cc_final: 0.6907 (mtp180) REVERT: E 59 ARG cc_start: 0.7762 (mmt90) cc_final: 0.7440 (mmt90) REVERT: F 155 MET cc_start: 0.9081 (ptp) cc_final: 0.8830 (ptm) REVERT: G 92 GLN cc_start: 0.8405 (mt0) cc_final: 0.8078 (mt0) outliers start: 21 outliers final: 5 residues processed: 226 average time/residue: 1.8723 time to fit residues: 454.1454 Evaluate side-chains 215 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 207 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 195 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 121 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN B 276 ASN D 92 GLN F 112 GLN F 149 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15813 Z= 0.286 Angle : 0.515 4.884 21301 Z= 0.269 Chirality : 0.041 0.134 2681 Planarity : 0.005 0.023 2450 Dihedral : 14.932 123.042 4459 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.90 % Allowed : 11.93 % Favored : 85.18 % 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: 1.69 (0.18), residues: 1820 helix: 2.12 (0.16), residues: 1029 sheet: 0.27 (0.37), residues: 175 loop : -0.32 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 251 PHE 0.019 0.002 PHE F 277 TYR 0.012 0.002 TYR B 75 ARG 0.006 0.001 ARG F 184 *********************** 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 258 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 215 time to evaluate : 1.281 Fit side-chains REVERT: A 105 LEU cc_start: 0.8795 (tp) cc_final: 0.8584 (tp) REVERT: A 155 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8934 (ptm) REVERT: A 210 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7302 (mp10) REVERT: B 20 ASN cc_start: 0.2282 (OUTLIER) cc_final: 0.2016 (p0) REVERT: B 92 GLN cc_start: 0.8292 (mt0) cc_final: 0.8029 (mt0) REVERT: B 278 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.7223 (mtmt) REVERT: C 273 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.7896 (tpp) REVERT: D 54 ARG cc_start: 0.7298 (mtp180) cc_final: 0.6922 (mtp180) REVERT: D 155 MET cc_start: 0.9204 (ptp) cc_final: 0.8956 (ptm) REVERT: E 210 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.7527 (mp10) REVERT: E 260 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7475 (mm-30) REVERT: F 20 ASN cc_start: 0.2187 (OUTLIER) cc_final: 0.1749 (p0) REVERT: F 260 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7649 (mm-30) REVERT: G 92 GLN cc_start: 0.8389 (mt0) cc_final: 0.8086 (mt0) REVERT: G 210 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7506 (mp10) outliers start: 43 outliers final: 11 residues processed: 240 average time/residue: 1.7847 time to fit residues: 459.1753 Evaluate side-chains 225 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 206 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 211 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 112 GLN F 149 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15813 Z= 0.154 Angle : 0.430 4.719 21301 Z= 0.233 Chirality : 0.039 0.134 2681 Planarity : 0.004 0.034 2450 Dihedral : 14.423 121.183 4459 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.82 % Allowed : 13.14 % Favored : 85.04 % 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: 1.79 (0.19), residues: 1820 helix: 2.21 (0.16), residues: 1029 sheet: 0.50 (0.29), residues: 280 loop : -0.53 (0.22), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 240 PHE 0.011 0.002 PHE C 188 TYR 0.008 0.001 TYR D 75 ARG 0.009 0.000 ARG E 59 *********************** 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 248 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 221 time to evaluate : 1.495 Fit side-chains revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8828 (tp) cc_final: 0.8607 (tp) REVERT: B 92 GLN cc_start: 0.8306 (mt0) cc_final: 0.8040 (mt0) REVERT: B 278 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7141 (mtmt) REVERT: C 20 ASN cc_start: 0.1760 (OUTLIER) cc_final: 0.1469 (p0) REVERT: C 88 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7366 (tpt90) REVERT: C 273 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.7860 (tpp) REVERT: D 54 ARG cc_start: 0.7299 (mtp180) cc_final: 0.6930 (mtp180) REVERT: D 88 ARG cc_start: 0.8031 (tpp-160) cc_final: 0.7635 (tpt-90) REVERT: F 155 MET cc_start: 0.9049 (ptp) cc_final: 0.8812 (ptm) REVERT: G 92 GLN cc_start: 0.8376 (mt0) cc_final: 0.8075 (mt0) outliers start: 27 outliers final: 9 residues processed: 234 average time/residue: 1.7390 time to fit residues: 437.1710 Evaluate side-chains 218 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 205 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 211 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 3.9990 chunk 19 optimal weight: 0.0370 chunk 100 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15813 Z= 0.279 Angle : 0.505 5.550 21301 Z= 0.265 Chirality : 0.041 0.135 2681 Planarity : 0.005 0.027 2450 Dihedral : 14.787 121.996 4459 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.90 % Allowed : 12.26 % Favored : 84.84 % 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: 1.66 (0.18), residues: 1820 helix: 2.07 (0.16), residues: 1029 sheet: 0.50 (0.29), residues: 280 loop : -0.52 (0.22), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 240 PHE 0.014 0.002 PHE B 178 TYR 0.012 0.001 TYR B 75 ARG 0.007 0.001 ARG E 59 *********************** 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 252 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 209 time to evaluate : 1.514 Fit side-chains REVERT: A 210 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7271 (mp10) REVERT: B 20 ASN cc_start: 0.1869 (OUTLIER) cc_final: 0.1661 (p0) REVERT: B 92 GLN cc_start: 0.8296 (mt0) cc_final: 0.8039 (mt0) REVERT: B 278 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7189 (mtmt) REVERT: C 20 ASN cc_start: 0.1857 (OUTLIER) cc_final: 0.1536 (p0) REVERT: C 88 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7451 (tpt90) REVERT: C 273 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.7882 (tpp) REVERT: D 54 ARG cc_start: 0.7301 (mtp180) cc_final: 0.6927 (mtp180) REVERT: D 260 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7520 (mm-30) REVERT: E 20 ASN cc_start: 0.2434 (OUTLIER) cc_final: 0.1194 (p0) REVERT: E 35 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8266 (mm) REVERT: F 155 MET cc_start: 0.9106 (ptp) cc_final: 0.8839 (ptm) REVERT: G 92 GLN cc_start: 0.8378 (mt0) cc_final: 0.8077 (mt0) REVERT: G 210 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.7403 (mp10) outliers start: 43 outliers final: 13 residues processed: 238 average time/residue: 1.7487 time to fit residues: 446.9297 Evaluate side-chains 223 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 201 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 211 SER 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: 0.7980 chunk 104 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 137 optimal weight: 0.0870 overall best weight: 0.8960 ------------------------------------------------------------------------------- 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 112 GLN F 149 GLN G 149 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15813 Z= 0.169 Angle : 0.443 5.456 21301 Z= 0.238 Chirality : 0.040 0.142 2681 Planarity : 0.004 0.037 2450 Dihedral : 14.411 121.551 4459 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.16 % Allowed : 13.21 % Favored : 84.64 % 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: 1.74 (0.19), residues: 1820 helix: 2.20 (0.16), residues: 1022 sheet: 0.51 (0.29), residues: 280 loop : -0.61 (0.22), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 240 PHE 0.011 0.002 PHE C 188 TYR 0.007 0.001 TYR D 75 ARG 0.009 0.000 ARG E 59 *********************** 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 244 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 212 time to evaluate : 1.464 Fit side-chains REVERT: A 88 ARG cc_start: 0.8229 (tpp-160) cc_final: 0.7865 (tpt90) REVERT: A 210 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.7215 (mp10) REVERT: B 92 GLN cc_start: 0.8288 (mt0) cc_final: 0.8038 (mt0) REVERT: B 278 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7127 (mtmt) REVERT: C 20 ASN cc_start: 0.2023 (OUTLIER) cc_final: 0.1738 (p0) REVERT: C 88 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7408 (tpt90) REVERT: C 273 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.7861 (tpp) REVERT: D 54 ARG cc_start: 0.7241 (mtp180) cc_final: 0.6870 (mtp180) REVERT: D 88 ARG cc_start: 0.8073 (tpp-160) cc_final: 0.7660 (tpt-90) REVERT: D 155 MET cc_start: 0.9178 (ptp) cc_final: 0.8936 (ptm) REVERT: E 35 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8284 (mm) REVERT: F 20 ASN cc_start: 0.1903 (OUTLIER) cc_final: 0.0658 (p0) REVERT: F 155 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8797 (ptm) REVERT: G 92 GLN cc_start: 0.8368 (mt0) cc_final: 0.8065 (mt0) outliers start: 32 outliers final: 11 residues processed: 231 average time/residue: 1.8135 time to fit residues: 449.5063 Evaluate side-chains 219 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 200 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 211 SER 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: 0.7980 chunk 153 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 0.0970 chunk 50 optimal weight: 2.9990 chunk 147 optimal weight: 0.0770 chunk 154 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 overall best weight: 0.5536 ------------------------------------------------------------------------------- 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 G 276 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15813 Z= 0.134 Angle : 0.413 5.176 21301 Z= 0.225 Chirality : 0.039 0.132 2681 Planarity : 0.004 0.035 2450 Dihedral : 13.781 121.744 4459 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.89 % Allowed : 13.75 % Favored : 84.37 % 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: 2.27 (0.16), residues: 1022 sheet: 0.55 (0.30), residues: 280 loop : -0.60 (0.22), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 240 PHE 0.009 0.001 PHE C 188 TYR 0.006 0.001 TYR G 75 ARG 0.009 0.000 ARG E 59 *********************** 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 246 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 218 time to evaluate : 1.714 Fit side-chains REVERT: A 88 ARG cc_start: 0.8204 (tpp-160) cc_final: 0.7812 (tpt90) REVERT: A 210 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.7231 (mp10) REVERT: B 92 GLN cc_start: 0.8281 (mt0) cc_final: 0.8036 (mt0) REVERT: C 20 ASN cc_start: 0.2096 (OUTLIER) cc_final: 0.1859 (p0) REVERT: C 105 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8269 (tt) REVERT: C 260 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7311 (mm-30) REVERT: C 273 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7837 (tpp) REVERT: D 54 ARG cc_start: 0.7225 (mtp180) cc_final: 0.6864 (mtp180) REVERT: D 260 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7328 (mm-30) REVERT: E 35 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8302 (mm) REVERT: F 20 ASN cc_start: 0.1898 (OUTLIER) cc_final: 0.0652 (p0) REVERT: F 155 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8807 (ptm) REVERT: F 273 MET cc_start: 0.8414 (ttm) cc_final: 0.7884 (ttm) REVERT: G 92 GLN cc_start: 0.8366 (mt0) cc_final: 0.8057 (mt0) REVERT: G 210 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.7311 (mp10) outliers start: 28 outliers final: 7 residues processed: 236 average time/residue: 1.8784 time to fit residues: 474.3587 Evaluate side-chains 219 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 204 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 211 SER 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: 4.9990 chunk 105 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.8385 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15813 Z= 0.199 Angle : 0.459 5.356 21301 Z= 0.246 Chirality : 0.040 0.144 2681 Planarity : 0.004 0.032 2450 Dihedral : 13.886 123.498 4459 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.48 % Allowed : 14.22 % Favored : 84.30 % 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: 1.76 (0.19), residues: 1820 helix: 2.19 (0.16), residues: 1022 sheet: 0.53 (0.30), residues: 280 loop : -0.54 (0.22), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 251 PHE 0.011 0.002 PHE C 188 TYR 0.007 0.001 TYR D 75 ARG 0.009 0.000 ARG E 59 ********************** 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 229 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 207 time to evaluate : 1.615 Fit side-chains REVERT: A 35 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8340 (mm) REVERT: A 88 ARG cc_start: 0.8199 (tpp-160) cc_final: 0.7820 (tpt90) REVERT: A 210 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7251 (mp10) REVERT: A 260 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7632 (mm-30) REVERT: B 92 GLN cc_start: 0.8278 (mt0) cc_final: 0.8029 (mt0) REVERT: C 20 ASN cc_start: 0.1928 (OUTLIER) cc_final: 0.1693 (p0) REVERT: C 260 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7338 (mm-30) REVERT: C 273 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.7854 (tpp) REVERT: D 35 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8346 (mm) REVERT: D 54 ARG cc_start: 0.7245 (mtp180) cc_final: 0.6879 (mtp180) REVERT: D 88 ARG cc_start: 0.7999 (tpp-160) cc_final: 0.7598 (tpt-90) REVERT: D 155 MET cc_start: 0.9192 (ptp) cc_final: 0.8944 (ptm) REVERT: D 260 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7367 (mm-30) REVERT: E 20 ASN cc_start: 0.2549 (OUTLIER) cc_final: 0.1291 (p0) REVERT: E 35 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8300 (mm) REVERT: F 20 ASN cc_start: 0.2120 (OUTLIER) cc_final: 0.0864 (p0) REVERT: F 273 MET cc_start: 0.8418 (ttm) cc_final: 0.7878 (ttm) REVERT: G 92 GLN cc_start: 0.8370 (mt0) cc_final: 0.8063 (mt0) REVERT: G 210 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.7341 (mp10) outliers start: 22 outliers final: 9 residues processed: 220 average time/residue: 1.9402 time to fit residues: 455.9359 Evaluate side-chains 223 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 205 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 211 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.116664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.090997 restraints weight = 17605.002| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.13 r_work: 0.2731 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2053 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 : 0.442 5.623 21301 Z= 0.238 Chirality : 0.040 0.153 2681 Planarity : 0.004 0.034 2450 Dihedral : 13.759 123.855 4459 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.42 % Allowed : 14.15 % Favored : 84.43 % 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: 1.75 (0.19), residues: 1820 helix: 2.20 (0.16), residues: 1022 sheet: 0.51 (0.30), residues: 280 loop : -0.56 (0.22), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 240 PHE 0.011 0.002 PHE B 178 TYR 0.007 0.001 TYR D 75 ARG 0.009 0.000 ARG E 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6683.96 seconds wall clock time: 118 minutes 35.21 seconds (7115.21 seconds total)