Starting phenix.real_space_refine (version: dev) on Mon Dec 12 20:53:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyf_30499/12_2022/7cyf_30499_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyf_30499/12_2022/7cyf_30499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyf_30499/12_2022/7cyf_30499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyf_30499/12_2022/7cyf_30499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyf_30499/12_2022/7cyf_30499_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyf_30499/12_2022/7cyf_30499_neut_updated.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2124 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 162": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "B ARG 162": "NH1" <-> "NH2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 333": "NH1" <-> "NH2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C ARG 333": "NH1" <-> "NH2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 9996 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2474 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 1 Chain: "B" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2474 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 1 Chain: "C" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2474 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 834 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Conformer: "B" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} bond proxies already assigned to first conformer: 838 Chain: "E" Number of atoms: 834 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Conformer: "B" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} bond proxies already assigned to first conformer: 838 Chain: "F" Number of atoms: 834 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Conformer: "B" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} bond proxies already assigned to first conformer: 838 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 7.68, per 1000 atoms: 0.77 Number of scatterers: 9996 At special positions: 0 Unit cell: (104, 95.68, 85.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 3 15.00 Na 3 11.00 O 1815 8.00 N 1617 7.00 C 6504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 105 " - pdb=" SG CYS D 110 " distance=2.02 Simple disulfide: pdb=" SG CYS E 105 " - pdb=" SG CYS E 110 " distance=2.02 Simple disulfide: pdb=" SG CYS F 105 " - pdb=" SG CYS F 110 " distance=2.02 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: 4.46 Conformation dependent library (CDL) restraints added in 2.0 seconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 3 sheets defined 53.8% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 removed outlier: 3.775A pdb=" N THR A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASP A 10 " --> pdb=" O ASN A 6 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 32 removed outlier: 5.119A pdb=" N LEU A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 29 " --> pdb=" O GLY A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 47 removed outlier: 3.625A pdb=" N ILE A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 70 through 90 removed outlier: 3.908A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 80 " --> pdb=" O PHE A 76 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 111 Processing helix chain 'A' and resid 115 through 127 removed outlier: 3.853A pdb=" N ALA A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.769A pdb=" N GLY A 137 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 163 removed outlier: 3.549A pdb=" N ALA A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 162 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 215 removed outlier: 3.923A pdb=" N ILE A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 211 through 215' Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 243 No H-bonds generated for 'chain 'A' and resid 240 through 243' Processing helix chain 'A' and resid 249 through 267 removed outlier: 4.230A pdb=" N ARG A 252 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY A 253 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 254 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET A 259 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A 262 " --> pdb=" O MET A 259 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 265 " --> pdb=" O MET A 262 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP A 267 " --> pdb=" O MET A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 300 Proline residue: A 288 - end of helix removed outlier: 3.663A pdb=" N GLY A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 321 removed outlier: 3.615A pdb=" N ALA A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 330 No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'A' and resid 341 through 348 removed outlier: 3.688A pdb=" N GLY A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.554A pdb=" N LEU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 16 removed outlier: 3.774A pdb=" N THR B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASP B 10 " --> pdb=" O ASN B 6 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 12 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY B 13 " --> pdb=" O THR B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 32 removed outlier: 5.119A pdb=" N LEU B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 29 " --> pdb=" O GLY B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 removed outlier: 3.625A pdb=" N ILE B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 59 Processing helix chain 'B' and resid 70 through 90 removed outlier: 3.908A pdb=" N VAL B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 111 Processing helix chain 'B' and resid 115 through 127 removed outlier: 3.745A pdb=" N ALA B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 139 removed outlier: 3.770A pdb=" N GLY B 137 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 163 removed outlier: 3.549A pdb=" N ALA B 151 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL B 154 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS B 161 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG B 162 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 removed outlier: 3.922A pdb=" N ILE B 215 " --> pdb=" O ILE B 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 211 through 215' Processing helix chain 'B' and resid 225 through 235 Processing helix chain 'B' and resid 240 through 243 No H-bonds generated for 'chain 'B' and resid 240 through 243' Processing helix chain 'B' and resid 249 through 267 removed outlier: 4.231A pdb=" N ARG B 252 " --> pdb=" O PRO B 249 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLY B 253 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 254 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU B 255 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET B 259 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 262 " --> pdb=" O MET B 259 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B 265 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP B 267 " --> pdb=" O MET B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 300 Proline residue: B 288 - end of helix removed outlier: 3.663A pdb=" N GLY B 292 " --> pdb=" O PRO B 288 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 321 removed outlier: 3.577A pdb=" N ALA B 320 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 348 removed outlier: 3.688A pdb=" N GLY B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 358 Processing helix chain 'B' and resid 361 through 370 removed outlier: 3.554A pdb=" N LEU B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 16 removed outlier: 3.774A pdb=" N THR C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASP C 10 " --> pdb=" O ASN C 6 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C 12 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY C 13 " --> pdb=" O THR C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 32 removed outlier: 5.120A pdb=" N LEU C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 29 " --> pdb=" O GLY C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 47 removed outlier: 3.625A pdb=" N ILE C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 59 Processing helix chain 'C' and resid 70 through 90 removed outlier: 3.907A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 80 " --> pdb=" O PHE C 76 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 86 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 111 Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.745A pdb=" N ALA C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 139 removed outlier: 3.770A pdb=" N GLY C 137 " --> pdb=" O ALA C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 163 removed outlier: 3.550A pdb=" N ALA C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL C 154 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS C 161 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG C 162 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.922A pdb=" N ILE C 215 " --> pdb=" O ILE C 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 211 through 215' Processing helix chain 'C' and resid 225 through 235 Processing helix chain 'C' and resid 240 through 243 No H-bonds generated for 'chain 'C' and resid 240 through 243' Processing helix chain 'C' and resid 249 through 267 removed outlier: 4.230A pdb=" N ARG C 252 " --> pdb=" O PRO C 249 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY C 253 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 254 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 255 " --> pdb=" O ARG C 252 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET C 259 " --> pdb=" O SER C 256 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET C 262 " --> pdb=" O MET C 259 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU C 265 " --> pdb=" O MET C 262 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP C 267 " --> pdb=" O MET C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 300 Proline residue: C 288 - end of helix removed outlier: 3.664A pdb=" N GLY C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 321 removed outlier: 3.538A pdb=" N ALA C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 348 removed outlier: 3.688A pdb=" N GLY C 346 " --> pdb=" O SER C 342 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER C 347 " --> pdb=" O ALA C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 358 Processing helix chain 'C' and resid 361 through 370 removed outlier: 3.555A pdb=" N LEU C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 27 removed outlier: 5.129A pdb=" N LYS D 18 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS D 19 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE D 20 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA D 21 " --> pdb=" O LYS D 18 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE D 24 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU D 26 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 80 Processing helix chain 'E' and resid 14 through 27 removed outlier: 5.129A pdb=" N LYS E 18 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS E 19 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE E 20 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA E 21 " --> pdb=" O LYS E 18 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE E 24 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU E 26 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 80 Processing helix chain 'F' and resid 14 through 27 removed outlier: 5.128A pdb=" N LYS F 18 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS F 19 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE F 20 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA F 21 " --> pdb=" O LYS F 18 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE F 24 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU F 26 " --> pdb=" O ILE F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 80 Processing sheet with id= A, first strand: chain 'D' and resid 89 through 98 Processing sheet with id= B, first strand: chain 'E' and resid 89 through 98 Processing sheet with id= C, first strand: chain 'F' and resid 89 through 98 422 hydrogen bonds defined for protein. 1104 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: 2.44 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2636 1.33 - 1.45: 1741 1.45 - 1.57: 5712 1.57 - 1.69: 3 1.69 - 1.81: 96 Bond restraints: 10188 Sorted by residual: bond pdb=" N ALA B 320 " pdb=" CA ALA B 320 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.30e-02 5.92e+03 1.38e+01 bond pdb=" N VAL B 113 " pdb=" CA VAL B 113 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.11e-02 8.12e+03 1.21e+01 bond pdb=" N ILE A 326 " pdb=" CA ILE A 326 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.48e+00 bond pdb=" N TYR A 140 " pdb=" CA TYR A 140 " ideal model delta sigma weight residual 1.462 1.486 -0.024 8.50e-03 1.38e+04 7.94e+00 bond pdb=" N VAL A 113 " pdb=" CA VAL A 113 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.65e+00 ... (remaining 10183 not shown) Histogram of bond angle deviations from ideal: 97.43 - 105.12: 251 105.12 - 112.82: 5353 112.82 - 120.51: 4650 120.51 - 128.21: 3505 128.21 - 135.90: 89 Bond angle restraints: 13848 Sorted by residual: angle pdb=" N LEU A 50 " pdb=" CA LEU A 50 " pdb=" C LEU A 50 " ideal model delta sigma weight residual 113.18 104.56 8.62 1.33e+00 5.65e-01 4.20e+01 angle pdb=" N LEU B 50 " pdb=" CA LEU B 50 " pdb=" C LEU B 50 " ideal model delta sigma weight residual 113.18 104.59 8.59 1.33e+00 5.65e-01 4.17e+01 angle pdb=" N ALA B 320 " pdb=" CA ALA B 320 " pdb=" C ALA B 320 " ideal model delta sigma weight residual 112.23 105.15 7.08 1.26e+00 6.30e-01 3.15e+01 angle pdb=" C ALA B 112 " pdb=" CA ALA B 112 " pdb=" CB ALA B 112 " ideal model delta sigma weight residual 110.42 121.19 -10.77 1.99e+00 2.53e-01 2.93e+01 angle pdb=" CA THR A 34 " pdb=" CB THR A 34 " pdb=" CG2 THR A 34 " ideal model delta sigma weight residual 110.50 119.21 -8.71 1.70e+00 3.46e-01 2.63e+01 ... (remaining 13843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 5632 15.87 - 31.74: 300 31.74 - 47.61: 103 47.61 - 63.48: 7 63.48 - 79.35: 6 Dihedral angle restraints: 6048 sinusoidal: 2280 harmonic: 3768 Sorted by residual: dihedral pdb=" CA PHE A 308 " pdb=" C PHE A 308 " pdb=" N SER A 309 " pdb=" CA SER A 309 " ideal model delta harmonic sigma weight residual -180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA PHE C 308 " pdb=" C PHE C 308 " pdb=" N SER C 309 " pdb=" CA SER C 309 " ideal model delta harmonic sigma weight residual -180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA PHE B 308 " pdb=" C PHE B 308 " pdb=" N SER B 309 " pdb=" CA SER B 309 " ideal model delta harmonic sigma weight residual -180.00 -154.80 -25.20 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 6045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1268 0.071 - 0.143: 354 0.143 - 0.214: 37 0.214 - 0.285: 13 0.285 - 0.356: 5 Chirality restraints: 1677 Sorted by residual: chirality pdb=" CA THR C 34 " pdb=" N THR C 34 " pdb=" C THR C 34 " pdb=" CB THR C 34 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CA THR A 34 " pdb=" N THR A 34 " pdb=" C THR A 34 " pdb=" CB THR A 34 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA THR B 34 " pdb=" N THR B 34 " pdb=" C THR B 34 " pdb=" CB THR B 34 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 1674 not shown) Planarity restraints: 1704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 329 " -0.055 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO B 330 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 329 " 0.055 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO C 330 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 22 " -0.010 2.00e-02 2.50e+03 1.87e-02 6.14e+00 pdb=" CG PHE B 22 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 22 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE B 22 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 22 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE B 22 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 22 " 0.002 2.00e-02 2.50e+03 ... (remaining 1701 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 29 2.49 - 3.09: 6534 3.09 - 3.70: 15428 3.70 - 4.30: 22712 4.30 - 4.90: 37097 Nonbonded interactions: 81800 Sorted by model distance: nonbonded pdb=" O PRO A 329 " pdb=" O THR A 331 " model vdw 1.890 3.040 nonbonded pdb=" CE MET A 118 " pdb=" CD1 ILE A 319 " model vdw 1.909 3.880 nonbonded pdb=" O PHE C 110 " pdb="NA NA C 401 " model vdw 2.010 2.470 nonbonded pdb=" O PHE B 110 " pdb="NA NA B 401 " model vdw 2.061 2.470 nonbonded pdb=" O PHE A 110 " pdb="NA NA A 401 " model vdw 2.207 2.470 ... (remaining 81795 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 94 or resid 96 through 110 or resid 201)) selection = (chain 'E' and (resid 2 through 94 or resid 96 through 110 or resid 201)) selection = (chain 'F' and (resid 2 through 94 or resid 96 through 110 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 54 5.16 5 Na 3 4.78 5 C 6504 2.51 5 N 1617 2.21 5 O 1815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 2.750 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.080 Process input model: 31.630 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 0.073 10188 Z= 0.597 Angle : 1.284 11.455 13848 Z= 0.672 Chirality : 0.066 0.356 1677 Planarity : 0.008 0.082 1704 Dihedral : 11.567 79.350 3639 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.42 % 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: -6.27 (0.15), residues: 1314 helix: -4.50 (0.08), residues: 813 sheet: -2.16 (0.48), residues: 102 loop : -3.29 (0.24), residues: 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 286 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 301 average time/residue: 0.2349 time to fit residues: 95.4696 Evaluate side-chains 214 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 207 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0871 time to fit residues: 2.6392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 75 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN A 14 GLN A 291 HIS A 340 ASN B 6 ASN B 14 GLN B 291 HIS B 340 ASN C 6 ASN C 14 GLN C 340 ASN D 44 ASN D 59 ASN E 6 ASN E 44 ASN E 59 ASN F 44 ASN F 59 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 10188 Z= 0.254 Angle : 0.754 6.554 13848 Z= 0.372 Chirality : 0.046 0.219 1677 Planarity : 0.006 0.070 1704 Dihedral : 6.742 52.689 1437 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.18), residues: 1314 helix: -2.86 (0.14), residues: 795 sheet: -1.63 (0.44), residues: 102 loop : -2.79 (0.27), residues: 417 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 217 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 15 residues processed: 229 average time/residue: 0.2172 time to fit residues: 69.5451 Evaluate side-chains 200 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 185 time to evaluate : 1.212 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0851 time to fit residues: 3.8233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 ASN C 291 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 10188 Z= 0.179 Angle : 0.679 9.030 13848 Z= 0.328 Chirality : 0.044 0.209 1677 Planarity : 0.005 0.058 1704 Dihedral : 6.149 49.222 1437 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 2.57 % 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: -3.00 (0.21), residues: 1314 helix: -1.73 (0.16), residues: 807 sheet: -1.24 (0.43), residues: 102 loop : -2.35 (0.28), residues: 405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 202 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 221 average time/residue: 0.2129 time to fit residues: 66.1779 Evaluate side-chains 199 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 187 time to evaluate : 1.118 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0897 time to fit residues: 3.4955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 60 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN E 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 10188 Z= 0.255 Angle : 0.699 7.962 13848 Z= 0.338 Chirality : 0.045 0.219 1677 Planarity : 0.004 0.054 1704 Dihedral : 6.152 50.023 1437 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer Outliers : 3.71 % 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: -2.35 (0.22), residues: 1314 helix: -1.14 (0.18), residues: 801 sheet: -0.92 (0.43), residues: 102 loop : -2.30 (0.28), residues: 411 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 180 time to evaluate : 1.224 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 26 residues processed: 205 average time/residue: 0.2207 time to fit residues: 63.5438 Evaluate side-chains 201 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 175 time to evaluate : 1.769 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1199 time to fit residues: 7.5261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 106 optimal weight: 0.0770 chunk 86 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 14 GLN C 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10188 Z= 0.212 Angle : 0.671 9.187 13848 Z= 0.323 Chirality : 0.044 0.214 1677 Planarity : 0.004 0.050 1704 Dihedral : 6.030 49.194 1437 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.22), residues: 1314 helix: -0.71 (0.18), residues: 801 sheet: -0.59 (0.43), residues: 102 loop : -2.24 (0.28), residues: 411 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 1.036 Fit side-chains outliers start: 22 outliers final: 13 residues processed: 199 average time/residue: 0.2115 time to fit residues: 59.2779 Evaluate side-chains 182 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 1.429 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1060 time to fit residues: 4.3787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 24 optimal weight: 0.0570 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 120 optimal weight: 0.4980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN E 6 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10188 Z= 0.163 Angle : 0.636 10.236 13848 Z= 0.305 Chirality : 0.043 0.206 1677 Planarity : 0.004 0.048 1704 Dihedral : 5.773 48.552 1437 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.23), residues: 1314 helix: -0.19 (0.19), residues: 786 sheet: -0.28 (0.43), residues: 102 loop : -2.27 (0.28), residues: 426 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 196 time to evaluate : 1.021 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 202 average time/residue: 0.2163 time to fit residues: 61.4996 Evaluate side-chains 184 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 176 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1189 time to fit residues: 2.8961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 75 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.8323 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10188 Z= 0.199 Angle : 0.657 9.160 13848 Z= 0.313 Chirality : 0.044 0.206 1677 Planarity : 0.004 0.047 1704 Dihedral : 5.787 49.257 1437 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer Outliers : 1.81 % 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: -1.16 (0.23), residues: 1314 helix: -0.03 (0.19), residues: 786 sheet: -0.02 (0.44), residues: 102 loop : -2.27 (0.28), residues: 426 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 1.197 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 181 average time/residue: 0.2218 time to fit residues: 56.1055 Evaluate side-chains 177 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 170 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0904 time to fit residues: 2.6757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 0.0670 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10188 Z= 0.186 Angle : 0.673 12.502 13848 Z= 0.316 Chirality : 0.044 0.203 1677 Planarity : 0.004 0.046 1704 Dihedral : 5.736 48.939 1437 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 1.24 % 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: -0.95 (0.23), residues: 1314 helix: 0.10 (0.19), residues: 795 sheet: 0.24 (0.45), residues: 96 loop : -2.16 (0.28), residues: 423 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 1.112 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 178 average time/residue: 0.2544 time to fit residues: 63.3069 Evaluate side-chains 174 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 168 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0863 time to fit residues: 2.4852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 0.1980 chunk 35 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.8319 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 10188 Z= 0.202 Angle : 0.686 11.894 13848 Z= 0.322 Chirality : 0.044 0.206 1677 Planarity : 0.004 0.046 1704 Dihedral : 5.753 49.082 1437 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer Outliers : 0.29 % 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: -0.89 (0.23), residues: 1314 helix: 0.15 (0.19), residues: 801 sheet: 0.35 (0.45), residues: 96 loop : -2.19 (0.28), residues: 417 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 1.100 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 173 average time/residue: 0.2281 time to fit residues: 54.9664 Evaluate side-chains 169 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0978 time to fit residues: 1.8334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10188 Z= 0.200 Angle : 0.689 11.594 13848 Z= 0.323 Chirality : 0.044 0.202 1677 Planarity : 0.004 0.046 1704 Dihedral : 5.765 49.137 1437 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.23), residues: 1314 helix: 0.18 (0.19), residues: 795 sheet: 0.31 (0.46), residues: 102 loop : -2.04 (0.28), residues: 417 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 173 time to evaluate : 1.203 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 177 average time/residue: 0.2353 time to fit residues: 58.0429 Evaluate side-chains 170 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0908 time to fit residues: 1.8642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 0.0000 chunk 5 optimal weight: 0.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.118984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.092293 restraints weight = 25983.336| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.96 r_work: 0.2749 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10188 Z= 0.172 Angle : 0.669 11.309 13848 Z= 0.313 Chirality : 0.043 0.204 1677 Planarity : 0.004 0.046 1704 Dihedral : 5.664 48.602 1437 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 0.38 % 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: -0.61 (0.23), residues: 1314 helix: 0.45 (0.19), residues: 786 sheet: 0.45 (0.46), residues: 96 loop : -2.18 (0.28), residues: 432 =============================================================================== Job complete usr+sys time: 2164.21 seconds wall clock time: 40 minutes 3.06 seconds (2403.06 seconds total)