Starting phenix.real_space_refine on Sun Mar 17 06:45:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onj_12996/03_2024/7onj_12996_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onj_12996/03_2024/7onj_12996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onj_12996/03_2024/7onj_12996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onj_12996/03_2024/7onj_12996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onj_12996/03_2024/7onj_12996_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onj_12996/03_2024/7onj_12996_updated.pdb" } resolution = 2.3 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 42 5.16 5 C 10955 2.51 5 N 2450 2.21 5 O 3493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16947 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "G" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "B" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "C" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "D" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "E" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "F" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "A" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 50 Chain: "G" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 50 Chain: "B" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 50 Chain: "C" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 50 Chain: "D" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 50 Chain: "E" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 50 Chain: "F" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 50 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "F" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Time building chain proxies: 9.27, per 1000 atoms: 0.55 Number of scatterers: 16947 At special positions: 0 Unit cell: (98.9055, 98.9055, 137.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 7 15.00 O 3493 8.00 N 2450 7.00 C 10955 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.55 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: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 21 through 58 removed outlier: 3.588A pdb=" N SER A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 88 Processing helix chain 'A' and resid 93 through 127 removed outlier: 5.306A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 198 through 211 Processing helix chain 'A' and resid 243 through 264 removed outlier: 3.614A pdb=" N LEU A 246 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLN A 247 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 253 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 58 removed outlier: 3.587A pdb=" N SER G 26 " --> pdb=" O ALA G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 88 Processing helix chain 'G' and resid 93 through 127 removed outlier: 5.306A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 171 Processing helix chain 'G' and resid 198 through 211 Processing helix chain 'G' and resid 243 through 264 removed outlier: 3.615A pdb=" N LEU G 246 " --> pdb=" O SER G 243 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLN G 247 " --> pdb=" O GLY G 244 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL G 253 " --> pdb=" O TYR G 250 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE G 261 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 58 removed outlier: 3.588A pdb=" N SER B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 88 Processing helix chain 'B' and resid 93 through 127 removed outlier: 5.305A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 198 through 211 Processing helix chain 'B' and resid 243 through 264 removed outlier: 3.615A pdb=" N LEU B 246 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLN B 247 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 253 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 261 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 58 removed outlier: 3.587A pdb=" N SER C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 88 Processing helix chain 'C' and resid 93 through 127 removed outlier: 5.306A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 198 through 211 Processing helix chain 'C' and resid 243 through 264 removed outlier: 3.614A pdb=" N LEU C 246 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLN C 247 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 253 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 261 " --> pdb=" O LYS C 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 58 removed outlier: 3.587A pdb=" N SER D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 88 Processing helix chain 'D' and resid 93 through 127 removed outlier: 5.306A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N SER D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 198 through 211 Processing helix chain 'D' and resid 243 through 264 removed outlier: 3.614A pdb=" N LEU D 246 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLN D 247 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 253 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE D 261 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 58 removed outlier: 3.587A pdb=" N SER E 26 " --> pdb=" O ALA E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 88 Processing helix chain 'E' and resid 93 through 127 removed outlier: 5.305A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'E' and resid 198 through 211 Processing helix chain 'E' and resid 243 through 264 removed outlier: 3.614A pdb=" N LEU E 246 " --> pdb=" O SER E 243 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLN E 247 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 253 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE E 261 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 58 removed outlier: 3.589A pdb=" N SER F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 88 Processing helix chain 'F' and resid 93 through 127 removed outlier: 5.305A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 171 Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 243 through 264 removed outlier: 3.615A pdb=" N LEU F 246 " --> pdb=" O SER F 243 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLN F 247 " --> pdb=" O GLY F 244 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL F 253 " --> pdb=" O TYR F 250 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE F 261 " --> pdb=" O LYS F 258 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.536A pdb=" N VAL A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 183 through 192 removed outlier: 5.896A pdb=" N VAL A 236 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU A 225 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ARG A 238 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL A 223 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N TRP A 240 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N MET A 221 " --> pdb=" O TRP A 240 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 175 through 177 removed outlier: 3.535A pdb=" N VAL G 141 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 183 through 192 removed outlier: 5.896A pdb=" N VAL G 236 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU G 225 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ARG G 238 " --> pdb=" O VAL G 223 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL G 223 " --> pdb=" O ARG G 238 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N TRP G 240 " --> pdb=" O MET G 221 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N MET G 221 " --> pdb=" O TRP G 240 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 175 through 177 removed outlier: 3.535A pdb=" N VAL B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 183 through 192 removed outlier: 5.895A pdb=" N VAL B 236 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU B 225 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ARG B 238 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL B 223 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N TRP B 240 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N MET B 221 " --> pdb=" O TRP B 240 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 175 through 177 removed outlier: 3.536A pdb=" N VAL C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 183 through 192 removed outlier: 5.897A pdb=" N VAL C 236 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU C 225 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ARG C 238 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL C 223 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N TRP C 240 " --> pdb=" O MET C 221 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N MET C 221 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 175 through 177 removed outlier: 3.535A pdb=" N VAL D 141 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 183 through 192 removed outlier: 5.895A pdb=" N VAL D 236 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU D 225 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ARG D 238 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL D 223 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N TRP D 240 " --> pdb=" O MET D 221 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N MET D 221 " --> pdb=" O TRP D 240 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 175 through 177 removed outlier: 3.536A pdb=" N VAL E 141 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 183 through 192 removed outlier: 5.896A pdb=" N VAL E 236 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU E 225 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ARG E 238 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL E 223 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N TRP E 240 " --> pdb=" O MET E 221 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N MET E 221 " --> pdb=" O TRP E 240 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 175 through 177 removed outlier: 3.536A pdb=" N VAL F 141 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 183 through 192 removed outlier: 5.896A pdb=" N VAL F 236 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU F 225 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ARG F 238 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL F 223 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N TRP F 240 " --> pdb=" O MET F 221 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N MET F 221 " --> pdb=" O TRP F 240 " (cutoff:3.500A) 938 hydrogen bonds defined for protein. 2478 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.81 Time building geometry restraints manager: 7.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2384 1.32 - 1.44: 4260 1.44 - 1.56: 10163 1.56 - 1.68: 14 1.68 - 1.80: 84 Bond restraints: 16905 Sorted by residual: bond pdb=" O3P PEE C 303 " pdb=" P PEE C 303 " ideal model delta sigma weight residual 1.636 1.588 0.048 2.00e-02 2.50e+03 5.78e+00 bond pdb=" O3P PEE D 303 " pdb=" P PEE D 303 " ideal model delta sigma weight residual 1.636 1.588 0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" O3P PEE E 303 " pdb=" P PEE E 303 " ideal model delta sigma weight residual 1.636 1.588 0.048 2.00e-02 2.50e+03 5.69e+00 bond pdb=" O3P PEE A 301 " pdb=" P PEE A 301 " ideal model delta sigma weight residual 1.636 1.588 0.048 2.00e-02 2.50e+03 5.68e+00 bond pdb=" O3P PEE G 403 " pdb=" P PEE G 403 " ideal model delta sigma weight residual 1.636 1.589 0.047 2.00e-02 2.50e+03 5.60e+00 ... (remaining 16900 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.02: 407 107.02 - 113.77: 10994 113.77 - 120.52: 6454 120.52 - 127.27: 4783 127.27 - 134.02: 63 Bond angle restraints: 22701 Sorted by residual: angle pdb=" O3P PEE E 303 " pdb=" P PEE E 303 " pdb=" O4P PEE E 303 " ideal model delta sigma weight residual 92.91 103.93 -11.02 3.00e+00 1.11e-01 1.35e+01 angle pdb=" O3P PEE G 403 " pdb=" P PEE G 403 " pdb=" O4P PEE G 403 " ideal model delta sigma weight residual 92.91 103.90 -10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" O3P PEE A 301 " pdb=" P PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 92.91 103.90 -10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" O3P PEE B 303 " pdb=" P PEE B 303 " pdb=" O4P PEE B 303 " ideal model delta sigma weight residual 92.91 103.89 -10.98 3.00e+00 1.11e-01 1.34e+01 angle pdb=" O3P PEE F 405 " pdb=" P PEE F 405 " pdb=" O4P PEE F 405 " ideal model delta sigma weight residual 92.91 103.89 -10.98 3.00e+00 1.11e-01 1.34e+01 ... (remaining 22696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.71: 11543 28.71 - 57.42: 609 57.42 - 86.14: 175 86.14 - 114.85: 238 114.85 - 143.56: 126 Dihedral angle restraints: 12691 sinusoidal: 7434 harmonic: 5257 Sorted by residual: dihedral pdb=" C3 PEE B 303 " pdb=" C1 PEE B 303 " pdb=" C2 PEE B 303 " pdb=" O3P PEE B 303 " ideal model delta sinusoidal sigma weight residual 62.73 -80.83 143.56 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C3 PEE E 303 " pdb=" C1 PEE E 303 " pdb=" C2 PEE E 303 " pdb=" O3P PEE E 303 " ideal model delta sinusoidal sigma weight residual 62.73 -80.76 143.49 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C3 PEE A 301 " pdb=" C1 PEE A 301 " pdb=" C2 PEE A 301 " pdb=" O3P PEE A 301 " ideal model delta sinusoidal sigma weight residual 62.73 -80.75 143.48 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 12688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2286 0.054 - 0.108: 512 0.108 - 0.163: 83 0.163 - 0.217: 38 0.217 - 0.271: 7 Chirality restraints: 2926 Sorted by residual: chirality pdb=" C2 PEE B 303 " pdb=" C1 PEE B 303 " pdb=" C3 PEE B 303 " pdb=" O2 PEE B 303 " both_signs ideal model delta sigma weight residual False -2.33 -2.60 0.27 2.00e-01 2.50e+01 1.83e+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 -2.60 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C2 PEE E 303 " pdb=" C1 PEE E 303 " pdb=" C3 PEE E 303 " pdb=" O2 PEE E 303 " both_signs ideal model delta sigma weight residual False -2.33 -2.60 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2923 not shown) Planarity restraints: 2450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 83 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.54e+00 pdb=" C ILE B 83 " -0.021 2.00e-02 2.50e+03 pdb=" O ILE B 83 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA B 84 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 83 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.53e+00 pdb=" C ILE E 83 " -0.021 2.00e-02 2.50e+03 pdb=" O ILE E 83 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA E 84 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 83 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" C ILE G 83 " 0.021 2.00e-02 2.50e+03 pdb=" O ILE G 83 " -0.008 2.00e-02 2.50e+03 pdb=" N ALA G 84 " -0.007 2.00e-02 2.50e+03 ... (remaining 2447 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 612 2.70 - 3.25: 16690 3.25 - 3.80: 28542 3.80 - 4.35: 36722 4.35 - 4.90: 61048 Nonbonded interactions: 143614 Sorted by model distance: nonbonded pdb=" OAR AV0 A 307 " pdb=" OAN AV0 G 405 " model vdw 2.155 2.440 nonbonded pdb=" OAN AV0 B 305 " pdb=" OAR AV0 C 302 " model vdw 2.155 2.440 nonbonded pdb=" OAN AV0 A 303 " pdb=" OAR AV0 B 302 " model vdw 2.155 2.440 nonbonded pdb=" OAN AV0 E 305 " pdb=" OAR AV0 F 404 " model vdw 2.155 2.440 nonbonded pdb=" OAR AV0 G 409 " pdb=" OAN AV0 F 407 " model vdw 2.155 2.440 ... (remaining 143609 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'B' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'C' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'D' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'E' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'F' and (resid 19 through 280 or resid 407 or (resid 409 and (name CAA or \ name CAB or name CAW or name CAX or name CAY or name CAZ or name CBA or name CB \ B or name CBC or name CBD or name CBE or name CBF or name CBG or name CBH or nam \ e CBI or name CBJ or name CBK or name CBL or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCF or name CCH or name CCJ or name CCL or name CC \ M or name CCQ or name O1 or name OAL or name OAN or name OAP or name OBV or name \ OBX or name OCB)))) selection = (chain 'G' and (resid 19 through 280 or (resid 407 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or (resid 409 and (nam \ e CAA or name CAB or name CAW or name CAX or name CAY or name CAZ or name CBA or \ name CBB or name CBC or name CBD or name CBE or name CBF or name CBG or name CB \ H or name CBI or name CBJ or name CBK or name CBL or name CBP or name CBQ or nam \ e CBR or name CBS or name CBT or name CCF or name CCH or name CCJ or name CCL or \ name CCM or name CCQ or name O1 or name OAL or name OAN or name OAP or name OBV \ or name OBX or name OCB)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.810 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 44.790 Find NCS groups from input model: 1.260 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: 0.000 Load rotamer database and sin/cos tables:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 0.048 16905 Z= 0.587 Angle : 0.857 11.017 22701 Z= 0.378 Chirality : 0.052 0.271 2926 Planarity : 0.004 0.021 2450 Dihedral : 27.956 143.559 9303 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.47 % Allowed : 3.77 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 1820 helix: -0.33 (0.11), residues: 1043 sheet: 0.31 (0.29), residues: 294 loop : 0.43 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 240 PHE 0.013 0.002 PHE E 127 TYR 0.010 0.002 TYR G 75 ARG 0.004 0.001 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 315 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 308 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7672 (ttp-170) cc_final: 0.7397 (ttm170) REVERT: A 47 MET cc_start: 0.7933 (mtt) cc_final: 0.7720 (mtm) REVERT: G 197 ASP cc_start: 0.8513 (t0) cc_final: 0.8266 (t70) REVERT: G 247 GLN cc_start: 0.9006 (tp-100) cc_final: 0.8762 (tp-100) REVERT: G 278 LYS cc_start: 0.8230 (mttt) cc_final: 0.7831 (mttt) REVERT: B 46 ARG cc_start: 0.7686 (ttp-170) cc_final: 0.7478 (ttp80) REVERT: B 54 ARG cc_start: 0.8111 (mtm110) cc_final: 0.7793 (mtm-85) REVERT: C 278 LYS cc_start: 0.8112 (mttt) cc_final: 0.7857 (mttt) REVERT: D 46 ARG cc_start: 0.7571 (ttp-170) cc_final: 0.7321 (ttp-170) REVERT: D 59 ARG cc_start: 0.8014 (mmt90) cc_final: 0.7755 (mmt90) REVERT: D 220 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8459 (pt0) REVERT: D 221 MET cc_start: 0.9153 (mtp) cc_final: 0.8904 (mtp) REVERT: F 54 ARG cc_start: 0.8026 (mtm110) cc_final: 0.7817 (mtm-85) REVERT: F 221 MET cc_start: 0.9128 (mtp) cc_final: 0.8807 (mtp) outliers start: 7 outliers final: 1 residues processed: 310 average time/residue: 1.6053 time to fit residues: 541.0007 Evaluate side-chains 248 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 246 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain D residue 220 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 142 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN G 92 GLN B 149 GLN B 210 GLN C 92 GLN C 210 GLN D 210 GLN E 210 GLN F 92 GLN F 203 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16905 Z= 0.174 Angle : 0.641 7.590 22701 Z= 0.288 Chirality : 0.050 0.390 2926 Planarity : 0.004 0.029 2450 Dihedral : 25.711 146.080 6180 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.55 % Allowed : 8.76 % 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: 1.63 (0.18), residues: 1820 helix: 1.78 (0.15), residues: 1043 sheet: 0.55 (0.29), residues: 280 loop : 0.02 (0.23), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 251 PHE 0.011 0.001 PHE G 188 TYR 0.006 0.001 TYR C 250 ARG 0.005 0.000 ARG E 46 *********************** 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 285 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 262 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8464 (mp10) REVERT: G 88 ARG cc_start: 0.8507 (mmm160) cc_final: 0.8039 (mmt-90) REVERT: G 247 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8665 (tp-100) REVERT: B 46 ARG cc_start: 0.7668 (ttp-170) cc_final: 0.7458 (ttp80) REVERT: B 54 ARG cc_start: 0.8075 (mtm110) cc_final: 0.7866 (mtm-85) REVERT: B 62 ASP cc_start: 0.8321 (t70) cc_final: 0.8041 (t70) REVERT: C 54 ARG cc_start: 0.8269 (mtm-85) cc_final: 0.7994 (mtp180) REVERT: D 59 ARG cc_start: 0.8036 (mmt90) cc_final: 0.7801 (mmt90) REVERT: E 47 MET cc_start: 0.7906 (mtm) cc_final: 0.7682 (mtm) REVERT: F 203 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7979 (tm-30) outliers start: 23 outliers final: 4 residues processed: 266 average time/residue: 1.8775 time to fit residues: 538.2588 Evaluate side-chains 253 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 247 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 203 GLN 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: 0.8980 chunk 112 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 chunk 147 optimal weight: 0.0070 chunk 164 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 GLN B 112 GLN B 210 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN D 112 GLN ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16905 Z= 0.158 Angle : 0.623 9.389 22701 Z= 0.276 Chirality : 0.044 0.293 2926 Planarity : 0.004 0.031 2450 Dihedral : 20.799 137.946 6174 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.62 % Allowed : 9.10 % Favored : 89.29 % 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: 1.96 (0.18), residues: 1820 helix: 2.09 (0.15), residues: 1043 sheet: 0.75 (0.27), residues: 294 loop : -0.02 (0.24), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 251 PHE 0.012 0.001 PHE E 277 TYR 0.009 0.001 TYR E 250 ARG 0.006 0.000 ARG E 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 295 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 271 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7936 (mmt90) cc_final: 0.7369 (mmt90) REVERT: G 88 ARG cc_start: 0.8513 (mmm160) cc_final: 0.8083 (mmt-90) REVERT: B 54 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7835 (mtm-85) REVERT: B 149 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: C 88 ARG cc_start: 0.8547 (mmm160) cc_final: 0.7940 (mmt-90) outliers start: 24 outliers final: 6 residues processed: 277 average time/residue: 1.7640 time to fit residues: 529.1030 Evaluate side-chains 264 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 257 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 210 GLN G 92 GLN G 112 GLN B 112 GLN C 92 GLN C 112 GLN C 210 GLN D 112 GLN E 112 GLN F 92 GLN F 112 GLN F 203 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16905 Z= 0.211 Angle : 0.616 7.466 22701 Z= 0.276 Chirality : 0.047 0.355 2926 Planarity : 0.004 0.034 2450 Dihedral : 18.994 137.086 6174 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.62 % Allowed : 10.38 % Favored : 88.01 % 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: 2.14 (0.19), residues: 1820 helix: 2.27 (0.16), residues: 1043 sheet: 0.78 (0.29), residues: 280 loop : 0.01 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 240 PHE 0.012 0.001 PHE G 188 TYR 0.012 0.001 TYR E 250 ARG 0.005 0.000 ARG E 46 *********************** 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 282 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 258 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 88 ARG cc_start: 0.8578 (mmm160) cc_final: 0.8065 (mmt-90) REVERT: G 149 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.7713 (mp10) REVERT: G 197 ASP cc_start: 0.8373 (t0) cc_final: 0.8153 (t70) REVERT: B 59 ARG cc_start: 0.7989 (mmt90) cc_final: 0.7590 (mtt90) REVERT: B 149 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8189 (mt0) REVERT: C 161 LYS cc_start: 0.9070 (mtmm) cc_final: 0.8706 (mttt) REVERT: D 88 ARG cc_start: 0.8553 (tpt90) cc_final: 0.8198 (tpt170) REVERT: F 59 ARG cc_start: 0.7970 (mmt90) cc_final: 0.7362 (mmt90) REVERT: F 149 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8125 (mp10) outliers start: 24 outliers final: 7 residues processed: 263 average time/residue: 1.7875 time to fit residues: 507.6064 Evaluate side-chains 253 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 243 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 149 GLN Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 213 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 0.2980 chunk 157 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 210 GLN G 30 ASN G 92 GLN B 30 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 92 GLN D 210 GLN E 30 ASN F 92 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16905 Z= 0.187 Angle : 0.574 7.672 22701 Z= 0.261 Chirality : 0.045 0.349 2926 Planarity : 0.003 0.027 2450 Dihedral : 17.834 132.317 6174 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.89 % Allowed : 10.38 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.19), residues: 1820 helix: 2.33 (0.16), residues: 1043 sheet: 0.78 (0.29), residues: 280 loop : -0.01 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 240 PHE 0.011 0.001 PHE A 188 TYR 0.011 0.001 TYR G 250 ARG 0.008 0.000 ARG E 46 *********************** 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 275 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 247 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 46 ARG cc_start: 0.7601 (ttp-110) cc_final: 0.7258 (ttp80) REVERT: B 59 ARG cc_start: 0.7964 (mmt90) cc_final: 0.7558 (mtt90) REVERT: B 149 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8199 (mt0) REVERT: C 149 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8260 (mt0) REVERT: D 88 ARG cc_start: 0.8581 (tpt90) cc_final: 0.8242 (tpt170) REVERT: E 149 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8288 (mt0) outliers start: 28 outliers final: 8 residues processed: 255 average time/residue: 1.8394 time to fit residues: 506.4770 Evaluate side-chains 250 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 239 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 213 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.0980 chunk 158 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 176 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN G 30 ASN G 92 GLN G 149 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 92 GLN C 112 GLN C 210 GLN D 112 GLN D 210 GLN E 30 ASN F 92 GLN F 210 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16905 Z= 0.146 Angle : 0.553 6.840 22701 Z= 0.251 Chirality : 0.046 0.355 2926 Planarity : 0.003 0.027 2450 Dihedral : 17.155 132.179 6174 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.35 % Allowed : 11.39 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.19), residues: 1820 helix: 2.39 (0.16), residues: 1043 sheet: 0.73 (0.28), residues: 280 loop : -0.00 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 240 PHE 0.012 0.001 PHE G 277 TYR 0.009 0.001 TYR B 250 ARG 0.005 0.000 ARG D 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 268 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 248 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 46 ARG cc_start: 0.7577 (ttp-110) cc_final: 0.7246 (ttp80) REVERT: G 169 LYS cc_start: 0.9122 (tttp) cc_final: 0.8891 (tttt) REVERT: B 59 ARG cc_start: 0.7960 (mmt90) cc_final: 0.7489 (mtt90) REVERT: B 149 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8185 (mt0) REVERT: D 59 ARG cc_start: 0.8023 (mmt90) cc_final: 0.7710 (mpt-90) REVERT: D 88 ARG cc_start: 0.8564 (tpt90) cc_final: 0.8301 (tpt170) REVERT: E 149 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8230 (mt0) REVERT: F 59 ARG cc_start: 0.7978 (mmt90) cc_final: 0.7352 (mmt90) outliers start: 20 outliers final: 5 residues processed: 254 average time/residue: 1.8314 time to fit residues: 501.7985 Evaluate side-chains 251 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 244 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 4.9990 chunk 19 optimal weight: 0.0040 chunk 100 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 99 optimal weight: 0.4980 chunk 148 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 30 ASN G 210 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN D 149 GLN D 210 GLN E 30 ASN F 92 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16905 Z= 0.142 Angle : 0.527 7.452 22701 Z= 0.242 Chirality : 0.043 0.377 2926 Planarity : 0.003 0.021 2450 Dihedral : 16.441 132.215 6174 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.62 % Allowed : 11.12 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.19), residues: 1820 helix: 2.42 (0.16), residues: 1043 sheet: 0.71 (0.28), residues: 280 loop : -0.03 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 251 PHE 0.012 0.001 PHE E 277 TYR 0.012 0.001 TYR B 250 ARG 0.005 0.000 ARG B 46 *********************** 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 274 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 250 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7658 (ttp-110) cc_final: 0.7412 (ttp80) REVERT: A 88 ARG cc_start: 0.8642 (mmm160) cc_final: 0.8207 (mmt-90) REVERT: G 278 LYS cc_start: 0.8406 (mttt) cc_final: 0.8143 (mttt) REVERT: B 59 ARG cc_start: 0.7959 (mmt90) cc_final: 0.7484 (mtt90) REVERT: B 149 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8240 (mt0) REVERT: D 88 ARG cc_start: 0.8556 (tpt90) cc_final: 0.8150 (tpp-160) REVERT: E 149 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8031 (mt0) REVERT: F 59 ARG cc_start: 0.8011 (mmt90) cc_final: 0.7371 (mmt90) outliers start: 24 outliers final: 5 residues processed: 257 average time/residue: 1.8561 time to fit residues: 514.5024 Evaluate side-chains 258 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 251 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 213 ASP 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: 0.8980 chunk 104 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 210 GLN G 30 ASN C 92 GLN C 210 GLN E 30 ASN F 92 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16905 Z= 0.202 Angle : 0.549 7.985 22701 Z= 0.257 Chirality : 0.044 0.421 2926 Planarity : 0.003 0.022 2450 Dihedral : 16.053 133.001 6174 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.15 % Allowed : 11.99 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.19), residues: 1820 helix: 2.36 (0.16), residues: 1043 sheet: 0.74 (0.29), residues: 280 loop : -0.05 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 240 PHE 0.013 0.001 PHE G 188 TYR 0.013 0.001 TYR B 250 ARG 0.004 0.000 ARG B 46 *********************** 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 268 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 251 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 197 ASP cc_start: 0.8358 (t0) cc_final: 0.8151 (t70) REVERT: G 278 LYS cc_start: 0.8389 (mttt) cc_final: 0.8171 (mttt) REVERT: B 59 ARG cc_start: 0.7963 (mmt90) cc_final: 0.7477 (mtt90) REVERT: B 149 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8262 (mt0) REVERT: D 88 ARG cc_start: 0.8601 (tpt90) cc_final: 0.8191 (tpt170) REVERT: D 149 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.7975 (mp10) REVERT: E 149 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8040 (mt0) REVERT: F 59 ARG cc_start: 0.8011 (mmt90) cc_final: 0.7360 (mmt90) outliers start: 17 outliers final: 6 residues processed: 256 average time/residue: 1.8720 time to fit residues: 516.8335 Evaluate side-chains 250 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 241 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 213 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 210 GLN G 30 ASN E 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16905 Z= 0.179 Angle : 0.532 7.880 22701 Z= 0.250 Chirality : 0.044 0.434 2926 Planarity : 0.003 0.021 2450 Dihedral : 15.784 133.122 6174 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.01 % Allowed : 11.99 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.19), residues: 1820 helix: 2.36 (0.16), residues: 1043 sheet: 0.76 (0.29), residues: 280 loop : -0.06 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 240 PHE 0.012 0.001 PHE B 277 TYR 0.013 0.001 TYR B 250 ARG 0.004 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 260 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 245 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 278 LYS cc_start: 0.8431 (mttt) cc_final: 0.8223 (mttt) REVERT: B 59 ARG cc_start: 0.7946 (mmt90) cc_final: 0.7457 (mtt90) REVERT: C 149 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8062 (mt0) REVERT: D 88 ARG cc_start: 0.8561 (tpt90) cc_final: 0.8111 (tpt170) REVERT: D 149 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.7924 (mp10) REVERT: E 149 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8038 (mt0) REVERT: F 59 ARG cc_start: 0.8003 (mmt90) cc_final: 0.7352 (mmt90) outliers start: 15 outliers final: 5 residues processed: 248 average time/residue: 1.8660 time to fit residues: 498.1949 Evaluate side-chains 248 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 240 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 213 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 105 optimal weight: 0.0870 chunk 82 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 181 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 210 GLN G 30 ASN E 30 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16905 Z= 0.155 Angle : 0.501 7.254 22701 Z= 0.238 Chirality : 0.042 0.421 2926 Planarity : 0.003 0.020 2450 Dihedral : 15.190 133.491 6174 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.74 % Allowed : 12.47 % Favored : 86.79 % 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: 2.26 (0.19), residues: 1820 helix: 2.43 (0.16), residues: 1043 sheet: 0.73 (0.28), residues: 280 loop : -0.04 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 240 PHE 0.009 0.001 PHE D 188 TYR 0.011 0.001 TYR B 250 ARG 0.004 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 256 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 245 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7617 (ttp-110) cc_final: 0.7373 (ttp80) REVERT: B 59 ARG cc_start: 0.7937 (mmt90) cc_final: 0.7439 (mtt90) REVERT: B 149 GLN cc_start: 0.8840 (mm110) cc_final: 0.8561 (mp10) REVERT: C 149 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8027 (mt0) REVERT: D 88 ARG cc_start: 0.8578 (tpt90) cc_final: 0.8145 (tpt170) REVERT: D 210 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8313 (mt0) REVERT: F 59 ARG cc_start: 0.8014 (mmt90) cc_final: 0.7353 (mmt90) outliers start: 11 outliers final: 4 residues processed: 248 average time/residue: 1.8729 time to fit residues: 500.7421 Evaluate side-chains 247 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 242 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 213 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 144 optimal weight: 0.1980 chunk 60 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 210 GLN G 30 ASN E 30 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.117795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.083019 restraints weight = 19197.071| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.47 r_work: 0.2711 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16905 Z= 0.154 Angle : 0.488 7.496 22701 Z= 0.235 Chirality : 0.041 0.309 2926 Planarity : 0.003 0.020 2450 Dihedral : 14.879 133.671 6174 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.54 % Allowed : 12.80 % Favored : 86.66 % 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: 2.26 (0.19), residues: 1820 helix: 2.45 (0.16), residues: 1043 sheet: 0.72 (0.28), residues: 280 loop : -0.08 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 251 PHE 0.009 0.001 PHE G 188 TYR 0.012 0.001 TYR B 250 ARG 0.004 0.000 ARG E 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7581.56 seconds wall clock time: 134 minutes 25.00 seconds (8065.00 seconds total)