Starting phenix.real_space_refine on Fri Feb 16 17:36:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo0_13003/02_2024/7oo0_13003_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo0_13003/02_2024/7oo0_13003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo0_13003/02_2024/7oo0_13003.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo0_13003/02_2024/7oo0_13003.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo0_13003/02_2024/7oo0_13003_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo0_13003/02_2024/7oo0_13003_updated.pdb" } resolution = 3.1 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= 0.013 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 10402 2.51 5 N 2450 2.21 5 O 3115 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16016 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: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 292 Unusual residues: {'LMT': 7, 'PEE': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 292 Unusual residues: {'LMT': 7, 'PEE': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 292 Unusual residues: {'LMT': 7, 'PEE': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 292 Unusual residues: {'LMT': 7, 'PEE': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 292 Unusual residues: {'LMT': 7, 'PEE': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 257 Unusual residues: {'LMT': 6, 'PEE': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 327 Unusual residues: {'LMT': 8, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 8.79, per 1000 atoms: 0.55 Number of scatterers: 16016 At special positions: 0 Unit cell: (97.842, 98.9055, 137.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 7 15.00 O 3115 8.00 N 2450 7.00 C 10402 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: 6.26 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 53.8% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 21 through 59 removed outlier: 3.509A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 88 Processing helix chain 'A' and resid 93 through 127 removed outlier: 5.421A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.261A 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: 3.738A pdb=" N LEU A 246 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLN A 247 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN A 248 " --> pdb=" O ASP A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 59 removed outlier: 3.509A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 88 Processing helix chain 'B' and resid 93 through 127 removed outlier: 5.421A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.261A 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: 3.737A pdb=" N LEU B 246 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLN B 247 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN B 248 " --> pdb=" O ASP B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 59 removed outlier: 3.509A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 88 Processing helix chain 'C' and resid 93 through 127 removed outlier: 5.420A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.261A 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: 3.738A pdb=" N LEU C 246 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLN C 247 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN C 248 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 59 removed outlier: 3.509A pdb=" N ARG D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 88 Processing helix chain 'D' and resid 93 through 127 removed outlier: 5.421A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.261A 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: 3.737A pdb=" N LEU D 246 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLN D 247 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 248 " --> pdb=" O ASP D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 59 removed outlier: 3.509A pdb=" N ARG E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 88 Processing helix chain 'E' and resid 93 through 127 removed outlier: 5.421A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.261A 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: 3.738A pdb=" N LEU E 246 " --> pdb=" O SER E 243 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLN E 247 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN E 248 " --> pdb=" O ASP E 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 59 removed outlier: 3.509A pdb=" N ARG F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 88 Processing helix chain 'F' and resid 93 through 127 removed outlier: 5.421A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 5.261A 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: 3.738A pdb=" N LEU F 246 " --> pdb=" O SER F 243 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLN F 247 " --> pdb=" O GLY F 244 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN F 248 " --> pdb=" O ASP F 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 59 removed outlier: 3.509A pdb=" N ARG G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 88 Processing helix chain 'G' and resid 93 through 127 removed outlier: 5.421A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.261A 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: 3.737A pdb=" N LEU G 246 " --> pdb=" O SER G 243 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLN G 247 " --> pdb=" O GLY G 244 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN G 248 " --> pdb=" O ASP G 245 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 135 through 138 removed outlier: 3.889A pdb=" N VAL A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 7.074A 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: 6.054A pdb=" N VAL A 236 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU A 225 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG A 238 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL A 223 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N TRP A 240 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET A 221 " --> pdb=" O TRP A 240 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 135 through 138 removed outlier: 3.889A pdb=" N VAL B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 7.074A 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: 6.054A pdb=" N VAL B 236 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU B 225 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG B 238 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL B 223 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N TRP B 240 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET B 221 " --> pdb=" O TRP B 240 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 135 through 138 removed outlier: 3.889A pdb=" N VAL C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 7.074A 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: 6.053A pdb=" N VAL C 236 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU C 225 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG C 238 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL C 223 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N TRP C 240 " --> pdb=" O MET C 221 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N MET C 221 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 135 through 138 removed outlier: 3.889A pdb=" N VAL D 141 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 7.074A 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: 6.053A pdb=" N VAL D 236 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU D 225 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG D 238 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL D 223 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N TRP D 240 " --> pdb=" O MET D 221 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET D 221 " --> pdb=" O TRP D 240 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 135 through 138 removed outlier: 3.889A pdb=" N VAL E 141 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 7.075A 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: 6.053A pdb=" N VAL E 236 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU E 225 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG E 238 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL E 223 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N TRP E 240 " --> pdb=" O MET E 221 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET E 221 " --> pdb=" O TRP E 240 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 135 through 138 removed outlier: 3.889A pdb=" N VAL F 141 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 7.075A 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: 6.053A pdb=" N VAL F 236 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU F 225 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG F 238 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL F 223 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N TRP F 240 " --> pdb=" O MET F 221 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET F 221 " --> pdb=" O TRP F 240 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 135 through 138 removed outlier: 3.888A pdb=" N VAL G 141 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 7.075A 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: 6.053A pdb=" N VAL G 236 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU G 225 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG G 238 " --> pdb=" O VAL G 223 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL G 223 " --> pdb=" O ARG G 238 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N TRP G 240 " --> pdb=" O MET G 221 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET G 221 " --> pdb=" O TRP G 240 " (cutoff:3.500A) 938 hydrogen bonds defined for protein. 2457 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: 4.74 Time building geometry restraints manager: 6.82 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: 2312 1.32 - 1.44: 4180 1.44 - 1.56: 9643 1.56 - 1.68: 14 1.68 - 1.80: 84 Bond restraints: 16233 Sorted by residual: bond pdb=" C4 PEE D 302 " pdb=" O4P PEE D 302 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.15e+00 bond pdb=" C4 PEE E 302 " pdb=" O4P PEE E 302 " ideal model delta sigma weight residual 1.409 1.449 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C4 PEE F 302 " pdb=" O4P PEE F 302 " ideal model delta sigma weight residual 1.409 1.449 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C4 PEE B 302 " pdb=" O4P PEE B 302 " ideal model delta sigma weight residual 1.409 1.449 -0.040 2.00e-02 2.50e+03 3.98e+00 bond pdb=" C4 PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 1.409 1.449 -0.040 2.00e-02 2.50e+03 3.94e+00 ... (remaining 16228 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.32: 189 106.32 - 113.26: 10006 113.26 - 120.20: 5978 120.20 - 127.14: 5611 127.14 - 134.08: 63 Bond angle restraints: 21847 Sorted by residual: angle pdb=" O3P PEE E 302 " pdb=" P PEE E 302 " pdb=" O4P PEE E 302 " ideal model delta sigma weight residual 92.91 104.27 -11.36 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3P PEE D 302 " pdb=" P PEE D 302 " pdb=" O4P PEE D 302 " ideal model delta sigma weight residual 92.91 104.26 -11.35 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3P PEE A 301 " pdb=" P PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 92.91 104.25 -11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3P PEE F 302 " pdb=" P PEE F 302 " pdb=" O4P PEE F 302 " ideal model delta sigma weight residual 92.91 104.24 -11.33 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3P PEE C 302 " pdb=" P PEE C 302 " pdb=" O4P PEE C 302 " ideal model delta sigma weight residual 92.91 104.24 -11.33 3.00e+00 1.11e-01 1.43e+01 ... (remaining 21842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.61: 10884 30.61 - 61.22: 407 61.22 - 91.84: 147 91.84 - 122.45: 280 122.45 - 153.06: 77 Dihedral angle restraints: 11795 sinusoidal: 6538 harmonic: 5257 Sorted by residual: dihedral pdb=" O2 PEE D 302 " pdb=" C1 PEE D 302 " pdb=" C2 PEE D 302 " pdb=" O3P PEE D 302 " ideal model delta sinusoidal sigma weight residual -59.96 93.10 -153.06 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" O2 PEE F 302 " pdb=" C1 PEE F 302 " pdb=" C2 PEE F 302 " pdb=" O3P PEE F 302 " ideal model delta sinusoidal sigma weight residual -59.96 93.10 -153.06 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" O2 PEE E 302 " pdb=" C1 PEE E 302 " pdb=" C2 PEE E 302 " pdb=" O3P PEE E 302 " ideal model delta sinusoidal sigma weight residual -59.96 93.09 -153.05 1 3.00e+01 1.11e-03 2.02e+01 ... (remaining 11792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1715 0.038 - 0.075: 813 0.075 - 0.113: 254 0.113 - 0.151: 53 0.151 - 0.188: 21 Chirality restraints: 2856 Sorted by residual: chirality pdb=" C2 PEE G 404 " pdb=" C1 PEE G 404 " pdb=" C3 PEE G 404 " pdb=" O2 PEE G 404 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" C2 PEE D 302 " pdb=" C1 PEE D 302 " pdb=" C3 PEE D 302 " pdb=" O2 PEE D 302 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" C2 PEE F 302 " pdb=" C1 PEE F 302 " pdb=" C3 PEE F 302 " pdb=" O2 PEE F 302 " both_signs ideal model delta sigma weight residual False -2.33 -2.51 0.19 2.00e-01 2.50e+01 8.73e-01 ... (remaining 2853 not shown) Planarity restraints: 2450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 83 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C ILE F 83 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE F 83 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA F 84 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 83 " 0.009 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C ILE C 83 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE C 83 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA C 84 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 83 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C ILE A 83 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE A 83 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA A 84 " -0.010 2.00e-02 2.50e+03 ... (remaining 2447 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 311 2.68 - 3.24: 15515 3.24 - 3.79: 24045 3.79 - 4.35: 32989 4.35 - 4.90: 56757 Nonbonded interactions: 129617 Sorted by model distance: nonbonded pdb=" O3' LMT B 308 " pdb=" O2B LMT C 308 " model vdw 2.131 2.440 nonbonded pdb=" OH TYR F 27 " pdb=" O2B LMT F 305 " model vdw 2.240 2.440 nonbonded pdb=" OH TYR C 27 " pdb=" O2B LMT C 305 " model vdw 2.241 2.440 nonbonded pdb=" OH TYR D 27 " pdb=" O2B LMT D 305 " model vdw 2.241 2.440 nonbonded pdb=" OH TYR E 27 " pdb=" O2B LMT E 305 " model vdw 2.241 2.440 ... (remaining 129612 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 303 or resid 305 through 307)) selection = (chain 'B' and (resid 19 through 280 or resid 303 or resid 305 through 307)) selection = (chain 'C' and (resid 19 through 280 or resid 303 or resid 305 through 307)) selection = (chain 'D' and (resid 19 through 280 or resid 303 or resid 305 through 307)) selection = (chain 'E' and (resid 19 through 280 or resid 303 or resid 305 through 307)) selection = (chain 'F' and (resid 19 through 280 or resid 303 or resid 305 through 307)) selection = (chain 'G' and (resid 19 through 280 or resid 403 or resid 405 through 407)) } 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: 1.190 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: 4.560 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 43.030 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.110 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 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 : 0.009 0.041 16233 Z= 0.554 Angle : 0.864 11.360 21847 Z= 0.397 Chirality : 0.049 0.188 2856 Planarity : 0.005 0.030 2450 Dihedral : 28.475 153.060 8407 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % 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 (0.16), residues: 1820 helix: -1.29 (0.10), residues: 1036 sheet: -1.80 (0.25), residues: 273 loop : 0.04 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 240 PHE 0.012 0.002 PHE B 277 TYR 0.010 0.002 TYR E 75 ARG 0.004 0.001 ARG D 219 *********************** 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 137 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.587 Fit side-chains REVERT: A 128 ARG cc_start: 0.7767 (mmt180) cc_final: 0.7423 (mmt180) REVERT: A 227 GLU cc_start: 0.8357 (tt0) cc_final: 0.7968 (tt0) REVERT: B 128 ARG cc_start: 0.7635 (mmt180) cc_final: 0.7155 (mmt180) REVERT: C 128 ARG cc_start: 0.7845 (mmt180) cc_final: 0.7520 (mmt180) REVERT: C 255 GLU cc_start: 0.7821 (tt0) cc_final: 0.7560 (tt0) REVERT: D 128 ARG cc_start: 0.7634 (mmt180) cc_final: 0.7315 (mmt180) REVERT: D 202 LYS cc_start: 0.7942 (mtpt) cc_final: 0.7667 (mtpt) REVERT: D 227 GLU cc_start: 0.8124 (tt0) cc_final: 0.7904 (tt0) REVERT: E 128 ARG cc_start: 0.7848 (mmt180) cc_final: 0.7514 (mmt180) REVERT: E 187 GLU cc_start: 0.7938 (tt0) cc_final: 0.7664 (tt0) REVERT: E 221 MET cc_start: 0.8756 (mtm) cc_final: 0.8313 (mtm) REVERT: F 128 ARG cc_start: 0.7686 (mmt180) cc_final: 0.7264 (mmt180) REVERT: G 128 ARG cc_start: 0.7786 (mmt180) cc_final: 0.7421 (mmt180) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.3430 time to fit residues: 66.5486 Evaluate side-chains 125 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 142 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 16233 Z= 0.182 Angle : 0.719 7.143 21847 Z= 0.310 Chirality : 0.055 0.316 2856 Planarity : 0.005 0.029 2450 Dihedral : 25.354 140.074 5278 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.61 % Allowed : 5.80 % Favored : 93.60 % 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: 0.66 (0.18), residues: 1820 helix: 1.40 (0.14), residues: 1029 sheet: -1.14 (0.28), residues: 273 loop : -0.43 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 251 PHE 0.007 0.001 PHE A 188 TYR 0.004 0.001 TYR F 75 ARG 0.003 0.000 ARG G 259 *********************** 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 148 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 139 time to evaluate : 1.620 Fit side-chains REVERT: A 128 ARG cc_start: 0.7628 (mmt180) cc_final: 0.7207 (mmt180) REVERT: A 227 GLU cc_start: 0.8062 (tt0) cc_final: 0.7774 (tt0) REVERT: B 128 ARG cc_start: 0.7628 (mmt180) cc_final: 0.7061 (mmt180) REVERT: C 128 ARG cc_start: 0.7759 (mmt180) cc_final: 0.7426 (mmt180) REVERT: D 128 ARG cc_start: 0.7572 (mmt180) cc_final: 0.7190 (mmt180) REVERT: D 221 MET cc_start: 0.8268 (mtm) cc_final: 0.8058 (mtm) REVERT: E 128 ARG cc_start: 0.7744 (mmt180) cc_final: 0.7359 (mmt180) REVERT: E 187 GLU cc_start: 0.7968 (tt0) cc_final: 0.7732 (tt0) REVERT: E 221 MET cc_start: 0.8631 (mtm) cc_final: 0.8273 (mtm) REVERT: F 128 ARG cc_start: 0.7499 (mmt180) cc_final: 0.7070 (mmt180) REVERT: G 187 GLU cc_start: 0.7979 (tt0) cc_final: 0.7702 (tt0) outliers start: 9 outliers final: 6 residues processed: 147 average time/residue: 0.3115 time to fit residues: 66.7513 Evaluate side-chains 135 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 178 optimal weight: 0.4980 chunk 147 optimal weight: 0.7980 chunk 164 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 132 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 112 GLN C 112 GLN D 112 GLN E 112 GLN F 112 GLN F 149 GLN G 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16233 Z= 0.181 Angle : 0.730 8.641 21847 Z= 0.301 Chirality : 0.053 0.368 2856 Planarity : 0.004 0.027 2450 Dihedral : 18.573 127.685 5278 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.54 % Allowed : 7.55 % Favored : 91.91 % 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: 1.25 (0.18), residues: 1820 helix: 2.06 (0.15), residues: 1029 sheet: -0.84 (0.27), residues: 308 loop : -0.66 (0.24), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 251 PHE 0.006 0.001 PHE G 277 TYR 0.004 0.001 TYR F 75 ARG 0.009 0.000 ARG B 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 155 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 147 time to evaluate : 1.703 Fit side-chains REVERT: A 128 ARG cc_start: 0.7602 (mmt180) cc_final: 0.7071 (mmt180) REVERT: A 227 GLU cc_start: 0.8031 (tt0) cc_final: 0.7703 (tt0) REVERT: A 260 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6945 (mm-30) REVERT: B 128 ARG cc_start: 0.7407 (mmt180) cc_final: 0.7077 (mmt180) REVERT: C 128 ARG cc_start: 0.7642 (mmt180) cc_final: 0.7320 (mmt180) REVERT: D 128 ARG cc_start: 0.7494 (mmt180) cc_final: 0.6988 (mmt180) REVERT: D 137 ASP cc_start: 0.8029 (t0) cc_final: 0.7785 (t70) REVERT: E 187 GLU cc_start: 0.7977 (tt0) cc_final: 0.7731 (tt0) REVERT: E 221 MET cc_start: 0.8575 (mtm) cc_final: 0.8229 (mtm) REVERT: G 187 GLU cc_start: 0.8006 (tt0) cc_final: 0.7736 (tt0) outliers start: 8 outliers final: 4 residues processed: 155 average time/residue: 0.2845 time to fit residues: 65.6116 Evaluate side-chains 146 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16233 Z= 0.192 Angle : 0.667 8.385 21847 Z= 0.283 Chirality : 0.051 0.360 2856 Planarity : 0.004 0.053 2450 Dihedral : 16.333 125.084 5278 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.08 % Allowed : 7.95 % Favored : 90.97 % 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: 1.31 (0.19), residues: 1820 helix: 2.14 (0.15), residues: 1029 sheet: -0.63 (0.27), residues: 308 loop : -0.84 (0.24), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 240 PHE 0.008 0.001 PHE D 188 TYR 0.005 0.001 TYR C 75 ARG 0.012 0.000 ARG E 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 159 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 1.590 Fit side-chains REVERT: A 128 ARG cc_start: 0.7605 (mmt180) cc_final: 0.7312 (mmt180) REVERT: A 227 GLU cc_start: 0.7998 (tt0) cc_final: 0.7656 (tt0) REVERT: A 260 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6998 (mm-30) REVERT: B 128 ARG cc_start: 0.7418 (mmt180) cc_final: 0.7080 (mmt180) REVERT: D 128 ARG cc_start: 0.7397 (mmt180) cc_final: 0.6901 (mmt180) REVERT: E 221 MET cc_start: 0.8612 (mtm) cc_final: 0.8298 (mtm) REVERT: G 187 GLU cc_start: 0.8034 (tt0) cc_final: 0.7762 (tt0) outliers start: 16 outliers final: 9 residues processed: 155 average time/residue: 0.2939 time to fit residues: 67.4526 Evaluate side-chains 147 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 16233 Z= 0.196 Angle : 0.632 7.749 21847 Z= 0.272 Chirality : 0.049 0.344 2856 Planarity : 0.004 0.048 2450 Dihedral : 15.634 120.911 5278 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.42 % Allowed : 8.09 % Favored : 90.50 % 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: 1.39 (0.19), residues: 1820 helix: 2.20 (0.15), residues: 1029 sheet: -0.46 (0.27), residues: 308 loop : -0.91 (0.24), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 240 PHE 0.008 0.001 PHE E 188 TYR 0.004 0.001 TYR F 75 ARG 0.009 0.000 ARG E 59 *********************** 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 164 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 1.542 Fit side-chains REVERT: A 128 ARG cc_start: 0.7541 (mmt180) cc_final: 0.7161 (mmt180) REVERT: A 227 GLU cc_start: 0.7975 (tt0) cc_final: 0.7638 (tt0) REVERT: A 260 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7043 (mm-30) REVERT: B 128 ARG cc_start: 0.7419 (mmt180) cc_final: 0.6927 (mmt180) REVERT: D 128 ARG cc_start: 0.7407 (mmt180) cc_final: 0.6911 (mmt180) REVERT: E 187 GLU cc_start: 0.8013 (tt0) cc_final: 0.7765 (tt0) REVERT: E 221 MET cc_start: 0.8616 (mtm) cc_final: 0.8300 (mtm) REVERT: F 149 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7960 (mt0) REVERT: G 187 GLU cc_start: 0.8048 (tt0) cc_final: 0.7789 (tt0) outliers start: 21 outliers final: 13 residues processed: 158 average time/residue: 0.2865 time to fit residues: 67.4613 Evaluate side-chains 155 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16233 Z= 0.236 Angle : 0.641 7.683 21847 Z= 0.278 Chirality : 0.049 0.335 2856 Planarity : 0.004 0.059 2450 Dihedral : 14.931 119.958 5278 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.75 % Allowed : 8.15 % Favored : 90.09 % 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: 1.33 (0.19), residues: 1820 helix: 2.12 (0.16), residues: 1029 sheet: -0.32 (0.27), residues: 308 loop : -0.98 (0.24), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 240 PHE 0.010 0.001 PHE D 188 TYR 0.005 0.001 TYR C 75 ARG 0.010 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 172 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 1.560 Fit side-chains REVERT: A 128 ARG cc_start: 0.7512 (mmt180) cc_final: 0.7097 (mmt180) REVERT: A 227 GLU cc_start: 0.7973 (tt0) cc_final: 0.7645 (tt0) REVERT: A 260 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7057 (mm-30) REVERT: B 58 SER cc_start: 0.7586 (t) cc_final: 0.7324 (t) REVERT: B 128 ARG cc_start: 0.7446 (mmt180) cc_final: 0.7092 (mmt180) REVERT: D 128 ARG cc_start: 0.7397 (mmt180) cc_final: 0.6869 (mmt180) REVERT: D 137 ASP cc_start: 0.8070 (t0) cc_final: 0.7808 (t70) REVERT: E 187 GLU cc_start: 0.8092 (tt0) cc_final: 0.7826 (tt0) REVERT: E 221 MET cc_start: 0.8629 (mtm) cc_final: 0.8304 (mtm) REVERT: G 187 GLU cc_start: 0.8076 (tt0) cc_final: 0.7807 (tt0) REVERT: G 260 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6761 (mm-30) outliers start: 26 outliers final: 14 residues processed: 166 average time/residue: 0.2857 time to fit residues: 70.7966 Evaluate side-chains 158 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 16233 Z= 0.167 Angle : 0.599 7.554 21847 Z= 0.262 Chirality : 0.048 0.365 2856 Planarity : 0.004 0.050 2450 Dihedral : 13.866 118.342 5278 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.28 % Allowed : 8.96 % Favored : 89.76 % 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: 1.48 (0.19), residues: 1820 helix: 2.24 (0.16), residues: 1029 sheet: -0.24 (0.27), residues: 308 loop : -0.94 (0.24), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 240 PHE 0.009 0.001 PHE F 188 TYR 0.004 0.001 TYR F 75 ARG 0.013 0.000 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 166 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 1.485 Fit side-chains REVERT: A 128 ARG cc_start: 0.7556 (mmt180) cc_final: 0.7162 (mmt180) REVERT: A 227 GLU cc_start: 0.7985 (tt0) cc_final: 0.7665 (tt0) REVERT: B 58 SER cc_start: 0.7567 (t) cc_final: 0.7327 (t) REVERT: B 128 ARG cc_start: 0.7419 (mmt180) cc_final: 0.6925 (mmt180) REVERT: D 128 ARG cc_start: 0.7351 (mmt180) cc_final: 0.6868 (mmt180) REVERT: E 187 GLU cc_start: 0.8086 (tt0) cc_final: 0.7817 (tt0) REVERT: E 221 MET cc_start: 0.8578 (mtm) cc_final: 0.8249 (mtm) REVERT: G 187 GLU cc_start: 0.8156 (tt0) cc_final: 0.7891 (tt0) REVERT: G 260 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6829 (mm-30) outliers start: 19 outliers final: 15 residues processed: 162 average time/residue: 0.2825 time to fit residues: 68.0027 Evaluate side-chains 159 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 16233 Z= 0.166 Angle : 0.573 6.237 21847 Z= 0.254 Chirality : 0.045 0.316 2856 Planarity : 0.004 0.051 2450 Dihedral : 13.100 117.093 5278 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.01 % Allowed : 9.10 % Favored : 89.89 % 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: 1.55 (0.19), residues: 1820 helix: 2.29 (0.16), residues: 1029 sheet: -0.15 (0.27), residues: 308 loop : -0.96 (0.24), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 240 PHE 0.008 0.001 PHE G 188 TYR 0.004 0.001 TYR F 75 ARG 0.008 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 161 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 146 time to evaluate : 1.665 Fit side-chains REVERT: A 128 ARG cc_start: 0.7572 (mmt180) cc_final: 0.7182 (mmt180) REVERT: A 137 ASP cc_start: 0.7722 (t70) cc_final: 0.7471 (t0) REVERT: A 227 GLU cc_start: 0.7983 (tt0) cc_final: 0.7669 (tt0) REVERT: B 128 ARG cc_start: 0.7387 (mmt180) cc_final: 0.7049 (mmt180) REVERT: C 181 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8136 (mm-30) REVERT: D 128 ARG cc_start: 0.7342 (mmt180) cc_final: 0.6864 (mmt180) REVERT: E 187 GLU cc_start: 0.8085 (tt0) cc_final: 0.7819 (tt0) REVERT: E 221 MET cc_start: 0.8591 (mtm) cc_final: 0.8241 (mtm) REVERT: G 187 GLU cc_start: 0.8130 (tt0) cc_final: 0.7861 (tt0) REVERT: G 260 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6856 (mm-30) outliers start: 15 outliers final: 10 residues processed: 156 average time/residue: 0.2990 time to fit residues: 69.2224 Evaluate side-chains 154 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.9990 chunk 168 optimal weight: 0.0980 chunk 153 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 16233 Z= 0.157 Angle : 0.548 6.073 21847 Z= 0.247 Chirality : 0.044 0.313 2856 Planarity : 0.004 0.047 2450 Dihedral : 12.632 115.017 5278 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.81 % Allowed : 9.50 % Favored : 89.69 % 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: 1.62 (0.19), residues: 1820 helix: 2.35 (0.16), residues: 1029 sheet: -0.10 (0.27), residues: 308 loop : -0.95 (0.24), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 240 PHE 0.009 0.001 PHE F 188 TYR 0.003 0.001 TYR F 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 159 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 147 time to evaluate : 1.570 Fit side-chains REVERT: A 128 ARG cc_start: 0.7559 (mmt180) cc_final: 0.7173 (mmt180) REVERT: A 137 ASP cc_start: 0.7720 (t70) cc_final: 0.7469 (t0) REVERT: A 227 GLU cc_start: 0.7961 (tt0) cc_final: 0.7628 (tt0) REVERT: B 58 SER cc_start: 0.7594 (t) cc_final: 0.7365 (t) REVERT: B 128 ARG cc_start: 0.7376 (mmt180) cc_final: 0.6874 (mmt180) REVERT: D 128 ARG cc_start: 0.7323 (mmt180) cc_final: 0.6853 (mmt180) REVERT: E 128 ARG cc_start: 0.7495 (mmt180) cc_final: 0.6886 (mmt180) REVERT: E 187 GLU cc_start: 0.8150 (tt0) cc_final: 0.7894 (tt0) REVERT: E 221 MET cc_start: 0.8569 (mtm) cc_final: 0.8226 (mtm) REVERT: F 149 GLN cc_start: 0.8375 (mt0) cc_final: 0.7750 (mm-40) REVERT: G 187 GLU cc_start: 0.8144 (tt0) cc_final: 0.7885 (tt0) REVERT: G 260 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6918 (mm-30) outliers start: 12 outliers final: 10 residues processed: 155 average time/residue: 0.2968 time to fit residues: 68.2601 Evaluate side-chains 156 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.5980 chunk 172 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 16233 Z= 0.168 Angle : 0.544 6.045 21847 Z= 0.246 Chirality : 0.043 0.314 2856 Planarity : 0.004 0.042 2450 Dihedral : 12.403 112.553 5278 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.81 % Allowed : 9.43 % Favored : 89.76 % 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: 1.62 (0.19), residues: 1820 helix: 2.34 (0.16), residues: 1029 sheet: -0.02 (0.27), residues: 308 loop : -0.98 (0.24), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 240 PHE 0.010 0.001 PHE E 188 TYR 0.003 0.001 TYR F 75 ARG 0.007 0.000 ARG B 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 158 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 1.579 Fit side-chains REVERT: A 128 ARG cc_start: 0.7561 (mmt180) cc_final: 0.7176 (mmt180) REVERT: A 137 ASP cc_start: 0.7754 (t70) cc_final: 0.7510 (t0) REVERT: A 227 GLU cc_start: 0.7961 (tt0) cc_final: 0.7650 (tt0) REVERT: B 58 SER cc_start: 0.7603 (t) cc_final: 0.7374 (t) REVERT: B 128 ARG cc_start: 0.7373 (mmt180) cc_final: 0.6869 (mmt180) REVERT: B 181 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8116 (mm-30) REVERT: C 181 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8144 (mm-30) REVERT: D 128 ARG cc_start: 0.7270 (mmt180) cc_final: 0.6817 (mmt180) REVERT: E 128 ARG cc_start: 0.7488 (mmt180) cc_final: 0.6996 (mtp85) REVERT: E 187 GLU cc_start: 0.8160 (tt0) cc_final: 0.7903 (tt0) REVERT: E 221 MET cc_start: 0.8585 (mtm) cc_final: 0.8228 (mtm) REVERT: F 149 GLN cc_start: 0.8322 (mt0) cc_final: 0.7754 (mm-40) REVERT: G 187 GLU cc_start: 0.8157 (tt0) cc_final: 0.7878 (tt0) REVERT: G 260 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6933 (mm-30) outliers start: 12 outliers final: 11 residues processed: 155 average time/residue: 0.3018 time to fit residues: 70.8362 Evaluate side-chains 156 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 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: 0.4980 chunk 26 optimal weight: 20.0000 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.142702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.115173 restraints weight = 16980.014| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.68 r_work: 0.3054 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16233 Z= 0.155 Angle : 0.532 6.041 21847 Z= 0.243 Chirality : 0.043 0.312 2856 Planarity : 0.004 0.035 2450 Dihedral : 12.273 110.671 5278 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.08 % Allowed : 9.30 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.19), residues: 1820 helix: 2.38 (0.16), residues: 1029 sheet: 0.00 (0.27), residues: 308 loop : -0.95 (0.24), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 240 PHE 0.010 0.001 PHE E 188 TYR 0.003 0.001 TYR F 75 ARG 0.007 0.000 ARG B 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2830.57 seconds wall clock time: 53 minutes 17.15 seconds (3197.15 seconds total)