Starting phenix.real_space_refine on Fri Mar 15 16:08:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyf_30499/03_2024/7cyf_30499_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyf_30499/03_2024/7cyf_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_30499/03_2024/7cyf_30499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyf_30499/03_2024/7cyf_30499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyf_30499/03_2024/7cyf_30499_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyf_30499/03_2024/7cyf_30499_neut_updated.pdb" } resolution = 3.15 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= 0.008 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 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. 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-5265/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: 6.82, per 1000 atoms: 0.68 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: 3.62 Conformation dependent library (CDL) restraints added in 2.3 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: 1.76 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: 2.40 Time building geometry restraints manager: 3.96 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 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 2.300 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.560 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 % Allowed : 6.86 % Favored : 91.24 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C 135 HIS 0.021 0.006 HIS B 303 PHE 0.039 0.004 PHE B 22 TYR 0.028 0.003 TYR E 87 ARG 0.018 0.002 ARG A 269 *********************** 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 : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PHE cc_start: 0.8296 (t80) cc_final: 0.7964 (t80) REVERT: A 17 SER cc_start: 0.9023 (t) cc_final: 0.8491 (p) REVERT: A 35 GLN cc_start: 0.7669 (mp10) cc_final: 0.7278 (mm110) REVERT: A 129 LYS cc_start: 0.7685 (mmtt) cc_final: 0.7461 (mttp) REVERT: A 238 LYS cc_start: 0.8660 (mtmt) cc_final: 0.8164 (mttt) REVERT: A 250 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8519 (pp) REVERT: A 252 ARG cc_start: 0.8341 (ttm110) cc_final: 0.7411 (mtt180) REVERT: A 275 LYS cc_start: 0.8583 (ttmp) cc_final: 0.8003 (mtmt) REVERT: A 278 GLN cc_start: 0.7508 (pt0) cc_final: 0.7242 (mt0) REVERT: A 319 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7934 (mt) REVERT: B 3 PHE cc_start: 0.7914 (t80) cc_final: 0.7707 (t80) REVERT: B 16 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8223 (mm-40) REVERT: B 17 SER cc_start: 0.9006 (t) cc_final: 0.8380 (p) REVERT: B 35 GLN cc_start: 0.7659 (mp10) cc_final: 0.7400 (mm110) REVERT: B 70 MET cc_start: 0.7609 (mtp) cc_final: 0.7393 (mtm) REVERT: B 79 ILE cc_start: 0.7905 (mm) cc_final: 0.7677 (mt) REVERT: B 238 LYS cc_start: 0.8686 (mtmt) cc_final: 0.8344 (mtmt) REVERT: B 250 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8290 (pp) REVERT: B 252 ARG cc_start: 0.8077 (ttm110) cc_final: 0.7085 (mtt180) REVERT: B 259 MET cc_start: 0.8700 (mmm) cc_final: 0.8453 (mmt) REVERT: B 275 LYS cc_start: 0.8412 (ttmp) cc_final: 0.7909 (mtmt) REVERT: B 278 GLN cc_start: 0.7306 (pt0) cc_final: 0.7012 (mt0) REVERT: B 298 LEU cc_start: 0.8956 (tm) cc_final: 0.8738 (tp) REVERT: B 300 MET cc_start: 0.8412 (mmm) cc_final: 0.7881 (mmt) REVERT: C 3 PHE cc_start: 0.7845 (t80) cc_final: 0.7577 (t80) REVERT: C 17 SER cc_start: 0.9120 (t) cc_final: 0.8532 (p) REVERT: C 79 ILE cc_start: 0.7954 (mm) cc_final: 0.7750 (mt) REVERT: C 129 LYS cc_start: 0.7794 (mmtt) cc_final: 0.7462 (mttp) REVERT: C 132 TYR cc_start: 0.8616 (p90) cc_final: 0.8253 (p90) REVERT: C 238 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8231 (mttt) REVERT: C 250 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8561 (pp) REVERT: C 252 ARG cc_start: 0.8121 (ttm110) cc_final: 0.7674 (ttm170) REVERT: C 275 LYS cc_start: 0.8552 (ttmp) cc_final: 0.7994 (mtmt) REVERT: C 278 GLN cc_start: 0.7541 (pt0) cc_final: 0.7140 (mt0) REVERT: C 300 MET cc_start: 0.8483 (mmm) cc_final: 0.7977 (mmt) REVERT: D 57 GLU cc_start: 0.7177 (pm20) cc_final: 0.6898 (mp0) REVERT: D 67 GLU cc_start: 0.7815 (tt0) cc_final: 0.7567 (mt-10) REVERT: E 53 THR cc_start: 0.8830 (p) cc_final: 0.8622 (m) REVERT: E 57 GLU cc_start: 0.7081 (pm20) cc_final: 0.6859 (pm20) REVERT: F 69 ARG cc_start: 0.8473 (tpt-90) cc_final: 0.8128 (tpt-90) outliers start: 20 outliers final: 7 residues processed: 301 average time/residue: 0.2454 time to fit residues: 98.9638 Evaluate side-chains 224 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 213 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 319 ILE 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: 0.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 59 ASN E 6 ASN E 44 ASN E 59 ASN F 59 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2193 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= 0.205 Angle : 0.725 6.624 13848 Z= 0.358 Chirality : 0.045 0.216 1677 Planarity : 0.006 0.070 1704 Dihedral : 7.143 51.419 1454 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.48 % Allowed : 13.14 % Favored : 84.38 % 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: -4.34 (0.18), residues: 1314 helix: -2.86 (0.14), residues: 792 sheet: -1.61 (0.44), residues: 102 loop : -2.79 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 212 HIS 0.011 0.003 HIS C 303 PHE 0.015 0.002 PHE B 308 TYR 0.013 0.001 TYR A 344 ARG 0.003 0.000 ARG B 269 *********************** 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 259 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 233 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7787 (m-30) REVERT: A 17 SER cc_start: 0.8859 (t) cc_final: 0.8337 (p) REVERT: A 35 GLN cc_start: 0.7694 (mp10) cc_final: 0.7432 (mm110) REVERT: A 40 GLU cc_start: 0.7172 (tt0) cc_final: 0.6819 (mt-10) REVERT: A 62 ILE cc_start: 0.8942 (tt) cc_final: 0.8575 (tt) REVERT: A 79 ILE cc_start: 0.8178 (mm) cc_final: 0.7972 (mt) REVERT: A 90 PHE cc_start: 0.8341 (m-80) cc_final: 0.8099 (m-80) REVERT: A 126 GLU cc_start: 0.7819 (pp20) cc_final: 0.6862 (pp20) REVERT: A 132 TYR cc_start: 0.8629 (p90) cc_final: 0.8314 (p90) REVERT: A 238 LYS cc_start: 0.8380 (mtmt) cc_final: 0.8041 (mttt) REVERT: A 250 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8188 (pp) REVERT: A 252 ARG cc_start: 0.8232 (ttm110) cc_final: 0.7466 (mtt180) REVERT: A 275 LYS cc_start: 0.8540 (ttmp) cc_final: 0.7942 (mtmt) REVERT: A 278 GLN cc_start: 0.7402 (pt0) cc_final: 0.7098 (mt0) REVERT: A 298 LEU cc_start: 0.8518 (tp) cc_final: 0.8307 (tp) REVERT: B 3 PHE cc_start: 0.7762 (t80) cc_final: 0.7546 (t80) REVERT: B 10 ASP cc_start: 0.8221 (t0) cc_final: 0.7980 (m-30) REVERT: B 17 SER cc_start: 0.8868 (t) cc_final: 0.8389 (p) REVERT: B 35 GLN cc_start: 0.7768 (mp10) cc_final: 0.7568 (mm110) REVERT: B 79 ILE cc_start: 0.7982 (mm) cc_final: 0.7761 (mt) REVERT: B 132 TYR cc_start: 0.8522 (p90) cc_final: 0.8281 (p90) REVERT: B 238 LYS cc_start: 0.8724 (mtmt) cc_final: 0.8386 (mtmt) REVERT: B 250 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8113 (pp) REVERT: B 252 ARG cc_start: 0.8067 (ttm110) cc_final: 0.7067 (mtt180) REVERT: B 272 GLU cc_start: 0.7744 (tt0) cc_final: 0.7493 (tt0) REVERT: B 275 LYS cc_start: 0.8379 (ttmp) cc_final: 0.7928 (mtmt) REVERT: B 278 GLN cc_start: 0.7172 (pt0) cc_final: 0.6887 (mt0) REVERT: B 298 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8467 (tp) REVERT: B 359 VAL cc_start: 0.8779 (p) cc_final: 0.8332 (t) REVERT: C 10 ASP cc_start: 0.8086 (t0) cc_final: 0.7839 (m-30) REVERT: C 17 SER cc_start: 0.8982 (t) cc_final: 0.8478 (p) REVERT: C 79 ILE cc_start: 0.8047 (mm) cc_final: 0.7831 (mt) REVERT: C 129 LYS cc_start: 0.7749 (mmtt) cc_final: 0.7379 (mttp) REVERT: C 132 TYR cc_start: 0.8608 (p90) cc_final: 0.8312 (p90) REVERT: C 250 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8363 (pp) REVERT: C 252 ARG cc_start: 0.8085 (ttm110) cc_final: 0.7718 (ttm170) REVERT: C 259 MET cc_start: 0.8844 (mmt) cc_final: 0.8460 (mmt) REVERT: C 275 LYS cc_start: 0.8582 (ttmp) cc_final: 0.8127 (mtmt) REVERT: C 278 GLN cc_start: 0.7443 (pt0) cc_final: 0.7012 (mt0) REVERT: C 300 MET cc_start: 0.8441 (mmm) cc_final: 0.7863 (mmt) REVERT: D 52 ASN cc_start: 0.8525 (t0) cc_final: 0.8313 (t0) REVERT: D 57 GLU cc_start: 0.7242 (pm20) cc_final: 0.6871 (mp0) REVERT: D 67 GLU cc_start: 0.7686 (tt0) cc_final: 0.7470 (tt0) REVERT: F 6 ASN cc_start: 0.8511 (m-40) cc_final: 0.8136 (m-40) outliers start: 26 outliers final: 18 residues processed: 249 average time/residue: 0.2149 time to fit residues: 74.1299 Evaluate side-chains 216 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 193 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 331 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 94 optimal weight: 0.3980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10188 Z= 0.177 Angle : 0.673 9.798 13848 Z= 0.324 Chirality : 0.043 0.208 1677 Planarity : 0.005 0.059 1704 Dihedral : 6.408 48.917 1445 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.57 % Allowed : 13.71 % Favored : 81.71 % 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: -2.93 (0.21), residues: 1314 helix: -1.66 (0.16), residues: 804 sheet: -1.22 (0.42), residues: 102 loop : -2.36 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 135 HIS 0.011 0.003 HIS C 303 PHE 0.010 0.001 PHE C 22 TYR 0.015 0.001 TYR A 140 ARG 0.006 0.001 ARG E 78 *********************** 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 243 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 195 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7736 (m-30) REVERT: A 17 SER cc_start: 0.8711 (t) cc_final: 0.8256 (p) REVERT: A 80 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8324 (tt) REVERT: A 90 PHE cc_start: 0.8351 (m-80) cc_final: 0.8146 (m-80) REVERT: A 132 TYR cc_start: 0.8620 (p90) cc_final: 0.8359 (p90) REVERT: A 238 LYS cc_start: 0.8392 (mtmt) cc_final: 0.7953 (mttt) REVERT: A 250 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8079 (pp) REVERT: A 262 MET cc_start: 0.8641 (mmp) cc_final: 0.8264 (mmt) REVERT: A 275 LYS cc_start: 0.8457 (ttmp) cc_final: 0.8018 (mtmt) REVERT: A 278 GLN cc_start: 0.7406 (pt0) cc_final: 0.7089 (mt0) REVERT: A 359 VAL cc_start: 0.8680 (p) cc_final: 0.8470 (t) REVERT: B 70 MET cc_start: 0.7754 (mtm) cc_final: 0.7356 (mtt) REVERT: B 79 ILE cc_start: 0.8041 (mm) cc_final: 0.7801 (mt) REVERT: B 132 TYR cc_start: 0.8544 (p90) cc_final: 0.8293 (p90) REVERT: B 161 LYS cc_start: 0.7997 (ptpt) cc_final: 0.7784 (ptpp) REVERT: B 238 LYS cc_start: 0.8761 (mtmt) cc_final: 0.8329 (mtmt) REVERT: B 250 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8070 (pp) REVERT: B 275 LYS cc_start: 0.8282 (ttmp) cc_final: 0.7996 (mtmt) REVERT: B 278 GLN cc_start: 0.7125 (pt0) cc_final: 0.6865 (mt0) REVERT: B 298 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8466 (tp) REVERT: C 10 ASP cc_start: 0.8049 (t0) cc_final: 0.7812 (m-30) REVERT: C 40 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7282 (mm-30) REVERT: C 79 ILE cc_start: 0.8048 (mm) cc_final: 0.7816 (mt) REVERT: C 89 ARG cc_start: 0.8263 (tmt-80) cc_final: 0.7913 (tpt-90) REVERT: C 132 TYR cc_start: 0.8632 (p90) cc_final: 0.8372 (p90) REVERT: C 250 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8337 (pp) REVERT: C 259 MET cc_start: 0.8915 (mmt) cc_final: 0.8534 (mmt) REVERT: C 275 LYS cc_start: 0.8439 (ttmp) cc_final: 0.8126 (mtmt) REVERT: D 52 ASN cc_start: 0.8570 (t0) cc_final: 0.8363 (t0) REVERT: F 6 ASN cc_start: 0.8460 (m-40) cc_final: 0.8098 (m-40) outliers start: 48 outliers final: 32 residues processed: 223 average time/residue: 0.2097 time to fit residues: 65.3712 Evaluate side-chains 224 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 185 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 291 HIS E 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10188 Z= 0.182 Angle : 0.644 8.004 13848 Z= 0.311 Chirality : 0.043 0.206 1677 Planarity : 0.004 0.055 1704 Dihedral : 6.240 49.097 1445 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.86 % Allowed : 13.71 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.22), residues: 1314 helix: -0.97 (0.18), residues: 804 sheet: -0.80 (0.42), residues: 102 loop : -2.15 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 135 HIS 0.009 0.002 HIS B 303 PHE 0.014 0.001 PHE D 62 TYR 0.015 0.001 TYR A 140 ARG 0.007 0.000 ARG E 78 *********************** 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 246 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 195 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7770 (m-30) REVERT: A 17 SER cc_start: 0.8612 (t) cc_final: 0.8118 (p) REVERT: A 80 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8306 (tt) REVERT: A 132 TYR cc_start: 0.8638 (p90) cc_final: 0.8381 (p90) REVERT: A 238 LYS cc_start: 0.8383 (mtmt) cc_final: 0.8046 (mttt) REVERT: A 250 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8119 (pp) REVERT: A 262 MET cc_start: 0.8627 (mmp) cc_final: 0.8314 (mmt) REVERT: A 275 LYS cc_start: 0.8430 (ttmp) cc_final: 0.8054 (mtmt) REVERT: A 278 GLN cc_start: 0.7457 (pt0) cc_final: 0.7098 (mt0) REVERT: B 40 GLU cc_start: 0.6533 (tt0) cc_final: 0.6068 (tt0) REVERT: B 79 ILE cc_start: 0.8091 (mm) cc_final: 0.7817 (mt) REVERT: B 161 LYS cc_start: 0.7870 (ptpt) cc_final: 0.7655 (ptpp) REVERT: B 238 LYS cc_start: 0.8729 (mtmt) cc_final: 0.8310 (mtmt) REVERT: B 250 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8067 (pp) REVERT: B 275 LYS cc_start: 0.8239 (ttmp) cc_final: 0.8021 (mtmt) REVERT: B 278 GLN cc_start: 0.7144 (pt0) cc_final: 0.6866 (mt0) REVERT: B 298 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8408 (tp) REVERT: C 10 ASP cc_start: 0.8055 (t0) cc_final: 0.7851 (m-30) REVERT: C 40 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7272 (mm-30) REVERT: C 79 ILE cc_start: 0.8085 (mm) cc_final: 0.7845 (mt) REVERT: C 118 MET cc_start: 0.8625 (ttp) cc_final: 0.8386 (ttp) REVERT: C 132 TYR cc_start: 0.8641 (p90) cc_final: 0.8395 (p90) REVERT: C 250 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8316 (pp) REVERT: C 275 LYS cc_start: 0.8419 (ttmp) cc_final: 0.8213 (mtmt) REVERT: D 35 MET cc_start: 0.7853 (ptp) cc_final: 0.7528 (ptp) REVERT: D 52 ASN cc_start: 0.8596 (t0) cc_final: 0.8330 (t0) REVERT: E 50 GLN cc_start: 0.6605 (pt0) cc_final: 0.6348 (pt0) REVERT: E 78 ARG cc_start: 0.8564 (mtp85) cc_final: 0.8212 (mtp180) REVERT: F 6 ASN cc_start: 0.8579 (m-40) cc_final: 0.8231 (m-40) outliers start: 51 outliers final: 35 residues processed: 228 average time/residue: 0.2153 time to fit residues: 69.0306 Evaluate side-chains 224 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 183 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.1980 chunk 70 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 106 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10188 Z= 0.160 Angle : 0.620 6.957 13848 Z= 0.299 Chirality : 0.042 0.202 1677 Planarity : 0.004 0.052 1704 Dihedral : 6.070 48.545 1444 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.76 % Allowed : 14.67 % Favored : 80.57 % 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: -1.54 (0.23), residues: 1314 helix: -0.37 (0.19), residues: 783 sheet: -0.39 (0.44), residues: 102 loop : -2.27 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 135 HIS 0.009 0.002 HIS C 303 PHE 0.013 0.001 PHE D 62 TYR 0.009 0.001 TYR E 92 ARG 0.007 0.000 ARG E 78 *********************** 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 245 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 195 time to evaluate : 1.059 Fit side-chains REVERT: A 10 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7797 (m-30) REVERT: A 16 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7735 (mt0) REVERT: A 40 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6884 (mt-10) REVERT: A 80 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8274 (tt) REVERT: A 97 ASN cc_start: 0.7422 (OUTLIER) cc_final: 0.7209 (p0) REVERT: A 132 TYR cc_start: 0.8606 (p90) cc_final: 0.8403 (p90) REVERT: A 158 TYR cc_start: 0.8562 (t80) cc_final: 0.8284 (t80) REVERT: A 238 LYS cc_start: 0.8328 (mtmt) cc_final: 0.7943 (mttt) REVERT: A 250 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8017 (pp) REVERT: A 262 MET cc_start: 0.8562 (mmp) cc_final: 0.8199 (mmt) REVERT: A 275 LYS cc_start: 0.8375 (ttmp) cc_final: 0.8057 (mtmt) REVERT: A 278 GLN cc_start: 0.7438 (pt0) cc_final: 0.7061 (mt0) REVERT: B 3 PHE cc_start: 0.8229 (t80) cc_final: 0.7880 (t80) REVERT: B 40 GLU cc_start: 0.6633 (tt0) cc_final: 0.6129 (tt0) REVERT: B 79 ILE cc_start: 0.8065 (mm) cc_final: 0.7813 (mt) REVERT: B 161 LYS cc_start: 0.7878 (ptpt) cc_final: 0.7663 (ptpp) REVERT: B 238 LYS cc_start: 0.8619 (mtmt) cc_final: 0.8416 (mtmt) REVERT: B 250 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8063 (pp) REVERT: B 278 GLN cc_start: 0.7156 (pt0) cc_final: 0.6866 (mt0) REVERT: B 298 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8382 (tp) REVERT: C 40 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7215 (mm-30) REVERT: C 79 ILE cc_start: 0.8064 (mm) cc_final: 0.7821 (mt) REVERT: C 132 TYR cc_start: 0.8633 (p90) cc_final: 0.8415 (p90) REVERT: C 250 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8291 (pp) REVERT: E 50 GLN cc_start: 0.6493 (pt0) cc_final: 0.5944 (pt0) REVERT: E 78 ARG cc_start: 0.8551 (mtp85) cc_final: 0.8263 (mtp180) REVERT: F 6 ASN cc_start: 0.8582 (m-40) cc_final: 0.8237 (m-40) outliers start: 50 outliers final: 38 residues processed: 228 average time/residue: 0.2132 time to fit residues: 68.5762 Evaluate side-chains 229 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 183 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 120 optimal weight: 0.2980 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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: 0.8032 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10188 Z= 0.183 Angle : 0.633 7.519 13848 Z= 0.303 Chirality : 0.043 0.202 1677 Planarity : 0.004 0.050 1704 Dihedral : 6.071 49.101 1444 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 6.00 % Allowed : 14.95 % Favored : 79.05 % 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: -1.26 (0.23), residues: 1314 helix: -0.13 (0.19), residues: 786 sheet: -0.22 (0.45), residues: 102 loop : -2.23 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 135 HIS 0.009 0.002 HIS C 303 PHE 0.011 0.001 PHE D 62 TYR 0.009 0.001 TYR B 344 ARG 0.006 0.000 ARG E 78 *********************** 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 247 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 184 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7850 (m-30) REVERT: A 16 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7843 (mt0) REVERT: A 80 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8231 (tt) REVERT: A 97 ASN cc_start: 0.7562 (OUTLIER) cc_final: 0.7345 (p0) REVERT: A 132 TYR cc_start: 0.8607 (p90) cc_final: 0.8404 (p90) REVERT: A 238 LYS cc_start: 0.8328 (mtmt) cc_final: 0.7929 (mttt) REVERT: A 250 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8030 (pp) REVERT: A 262 MET cc_start: 0.8565 (mmp) cc_final: 0.8241 (mmt) REVERT: A 275 LYS cc_start: 0.8381 (ttmp) cc_final: 0.8075 (mtmt) REVERT: A 278 GLN cc_start: 0.7510 (pt0) cc_final: 0.7142 (mt0) REVERT: B 3 PHE cc_start: 0.8180 (t80) cc_final: 0.7796 (t80) REVERT: B 10 ASP cc_start: 0.8081 (m-30) cc_final: 0.7780 (m-30) REVERT: B 40 GLU cc_start: 0.6771 (tt0) cc_final: 0.6194 (tt0) REVERT: B 49 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7373 (ptm) REVERT: B 79 ILE cc_start: 0.8089 (mm) cc_final: 0.7822 (mt) REVERT: B 161 LYS cc_start: 0.7844 (ptpt) cc_final: 0.7623 (ptpp) REVERT: B 240 GLU cc_start: 0.7650 (mp0) cc_final: 0.7364 (mp0) REVERT: B 250 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8110 (pp) REVERT: B 278 GLN cc_start: 0.7175 (pt0) cc_final: 0.6892 (mt0) REVERT: B 298 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8413 (tp) REVERT: C 40 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7067 (mm-30) REVERT: C 79 ILE cc_start: 0.8045 (mm) cc_final: 0.7810 (mt) REVERT: C 132 TYR cc_start: 0.8631 (p90) cc_final: 0.8390 (p90) REVERT: C 250 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8287 (pp) REVERT: D 6 ASN cc_start: 0.8172 (m110) cc_final: 0.7904 (m-40) REVERT: D 57 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: E 50 GLN cc_start: 0.6525 (pt0) cc_final: 0.5882 (pt0) REVERT: E 78 ARG cc_start: 0.8566 (mtp85) cc_final: 0.8315 (mtp180) REVERT: F 6 ASN cc_start: 0.8596 (m-40) cc_final: 0.8233 (m-40) outliers start: 63 outliers final: 42 residues processed: 224 average time/residue: 0.2083 time to fit residues: 66.1146 Evaluate side-chains 231 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 180 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 70 optimal weight: 0.0770 chunk 105 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- 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: 0.8112 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10188 Z= 0.294 Angle : 0.714 7.995 13848 Z= 0.344 Chirality : 0.046 0.220 1677 Planarity : 0.004 0.052 1704 Dihedral : 6.409 49.762 1444 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 6.48 % Allowed : 15.52 % Favored : 78.00 % 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: -1.36 (0.23), residues: 1314 helix: -0.42 (0.18), residues: 822 sheet: -0.10 (0.45), residues: 102 loop : -1.96 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 135 HIS 0.008 0.002 HIS C 303 PHE 0.019 0.002 PHE C 110 TYR 0.014 0.002 TYR E 100 ARG 0.004 0.001 ARG E 78 *********************** 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 243 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 175 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7987 (m-30) REVERT: A 80 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8187 (tt) REVERT: A 132 TYR cc_start: 0.8654 (p90) cc_final: 0.8338 (p90) REVERT: A 238 LYS cc_start: 0.8403 (mtmt) cc_final: 0.7987 (mttt) REVERT: A 250 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8149 (pp) REVERT: A 252 ARG cc_start: 0.8157 (ttm110) cc_final: 0.7306 (mtt180) REVERT: A 275 LYS cc_start: 0.8515 (ttmp) cc_final: 0.8082 (mtmt) REVERT: A 278 GLN cc_start: 0.7505 (pt0) cc_final: 0.7161 (mt0) REVERT: B 3 PHE cc_start: 0.8274 (t80) cc_final: 0.7866 (t80) REVERT: B 10 ASP cc_start: 0.8175 (m-30) cc_final: 0.7944 (m-30) REVERT: B 40 GLU cc_start: 0.7103 (tt0) cc_final: 0.6523 (tt0) REVERT: B 49 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7737 (ptm) REVERT: B 70 MET cc_start: 0.7835 (mtm) cc_final: 0.7398 (mtt) REVERT: B 227 MET cc_start: 0.8577 (ttp) cc_final: 0.8339 (ttm) REVERT: B 250 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8121 (pp) REVERT: B 264 MET cc_start: 0.8734 (mtm) cc_final: 0.8489 (mtp) REVERT: B 278 GLN cc_start: 0.7292 (pt0) cc_final: 0.7009 (mt0) REVERT: B 298 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8414 (tp) REVERT: B 300 MET cc_start: 0.8160 (mmt) cc_final: 0.7554 (mmt) REVERT: C 40 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6923 (mm-30) REVERT: C 79 ILE cc_start: 0.8115 (mm) cc_final: 0.7893 (mt) REVERT: C 132 TYR cc_start: 0.8677 (p90) cc_final: 0.8288 (p90) REVERT: C 250 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8330 (pp) REVERT: D 6 ASN cc_start: 0.8240 (m110) cc_final: 0.7979 (m-40) REVERT: E 50 GLN cc_start: 0.6908 (pt0) cc_final: 0.6290 (pt0) REVERT: E 78 ARG cc_start: 0.8579 (mtp85) cc_final: 0.8367 (mtp180) outliers start: 68 outliers final: 45 residues processed: 216 average time/residue: 0.2192 time to fit residues: 65.6322 Evaluate side-chains 225 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 172 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 275 LYS Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 0.0870 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 97 optimal weight: 0.2980 chunk 113 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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: 0.8020 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10188 Z= 0.153 Angle : 0.636 8.667 13848 Z= 0.300 Chirality : 0.043 0.197 1677 Planarity : 0.004 0.051 1704 Dihedral : 6.002 47.815 1444 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 5.14 % Allowed : 17.33 % Favored : 77.52 % 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: -0.90 (0.23), residues: 1314 helix: 0.11 (0.19), residues: 792 sheet: 0.33 (0.47), residues: 102 loop : -2.12 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 135 HIS 0.009 0.002 HIS C 303 PHE 0.010 0.001 PHE D 62 TYR 0.012 0.001 TYR E 92 ARG 0.006 0.000 ARG E 78 *********************** 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 232 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 178 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7919 (m-30) REVERT: A 16 GLN cc_start: 0.8294 (mm-40) cc_final: 0.7943 (mt0) REVERT: A 40 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7393 (mm-30) REVERT: A 80 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8216 (tt) REVERT: A 132 TYR cc_start: 0.8625 (p90) cc_final: 0.8400 (p90) REVERT: A 238 LYS cc_start: 0.8305 (mtmt) cc_final: 0.7876 (mttt) REVERT: A 250 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8032 (pp) REVERT: A 262 MET cc_start: 0.8520 (mmp) cc_final: 0.8237 (mmt) REVERT: A 275 LYS cc_start: 0.8468 (ttmp) cc_final: 0.8154 (mtmt) REVERT: A 278 GLN cc_start: 0.7459 (pt0) cc_final: 0.7090 (mt0) REVERT: B 10 ASP cc_start: 0.8056 (m-30) cc_final: 0.7842 (m-30) REVERT: B 40 GLU cc_start: 0.7036 (tt0) cc_final: 0.6780 (tt0) REVERT: B 161 LYS cc_start: 0.7859 (ptpt) cc_final: 0.7639 (ptpp) REVERT: B 227 MET cc_start: 0.8472 (ttp) cc_final: 0.8233 (ttm) REVERT: B 250 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8050 (pp) REVERT: B 264 MET cc_start: 0.8655 (mtm) cc_final: 0.8412 (mtm) REVERT: B 300 MET cc_start: 0.7815 (mmt) cc_final: 0.7283 (mmt) REVERT: C 40 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6948 (mm-30) REVERT: C 79 ILE cc_start: 0.8006 (mm) cc_final: 0.7774 (mt) REVERT: C 132 TYR cc_start: 0.8657 (p90) cc_final: 0.8372 (p90) REVERT: C 250 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8282 (pp) REVERT: D 71 MET cc_start: 0.7935 (ttp) cc_final: 0.7710 (ttp) outliers start: 54 outliers final: 37 residues processed: 213 average time/residue: 0.2295 time to fit residues: 69.1708 Evaluate side-chains 215 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 172 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 119 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 90 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 122 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8023 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10188 Z= 0.168 Angle : 0.633 7.719 13848 Z= 0.300 Chirality : 0.043 0.196 1677 Planarity : 0.004 0.049 1704 Dihedral : 5.983 48.536 1444 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 4.67 % Allowed : 17.62 % Favored : 77.71 % 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: -0.78 (0.23), residues: 1314 helix: 0.28 (0.20), residues: 783 sheet: 0.40 (0.46), residues: 102 loop : -2.19 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 135 HIS 0.009 0.002 HIS C 303 PHE 0.011 0.001 PHE D 62 TYR 0.010 0.001 TYR E 92 ARG 0.001 0.000 ARG B 269 *********************** 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 225 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 176 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7920 (m-30) REVERT: A 16 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7982 (mt0) REVERT: A 80 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8200 (tt) REVERT: A 132 TYR cc_start: 0.8606 (p90) cc_final: 0.8402 (p90) REVERT: A 238 LYS cc_start: 0.8330 (mtmt) cc_final: 0.7907 (mttt) REVERT: A 250 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.7984 (pp) REVERT: A 262 MET cc_start: 0.8492 (mmp) cc_final: 0.8203 (mmt) REVERT: A 275 LYS cc_start: 0.8496 (ttmp) cc_final: 0.8133 (mtmt) REVERT: A 278 GLN cc_start: 0.7498 (pt0) cc_final: 0.7137 (mt0) REVERT: B 40 GLU cc_start: 0.7052 (tt0) cc_final: 0.6807 (tt0) REVERT: B 161 LYS cc_start: 0.7840 (ptpt) cc_final: 0.7620 (ptpp) REVERT: B 227 MET cc_start: 0.8472 (ttp) cc_final: 0.8239 (ttm) REVERT: B 250 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.7983 (pp) REVERT: B 264 MET cc_start: 0.8680 (mtm) cc_final: 0.8400 (mtm) REVERT: B 300 MET cc_start: 0.7930 (mmt) cc_final: 0.7285 (mmt) REVERT: C 40 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6964 (mm-30) REVERT: C 79 ILE cc_start: 0.7980 (mm) cc_final: 0.7758 (mt) REVERT: C 132 TYR cc_start: 0.8650 (p90) cc_final: 0.8385 (p90) REVERT: C 250 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8246 (pp) REVERT: D 71 MET cc_start: 0.7936 (ttp) cc_final: 0.7708 (ttp) REVERT: F 100 TYR cc_start: 0.8383 (m-80) cc_final: 0.8066 (m-80) outliers start: 49 outliers final: 38 residues processed: 206 average time/residue: 0.2221 time to fit residues: 64.1653 Evaluate side-chains 220 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 176 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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: 0.8071 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10188 Z= 0.225 Angle : 0.670 7.477 13848 Z= 0.319 Chirality : 0.044 0.202 1677 Planarity : 0.004 0.050 1704 Dihedral : 6.130 49.721 1443 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.57 % Allowed : 17.43 % Favored : 78.00 % 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: -0.84 (0.23), residues: 1314 helix: 0.04 (0.19), residues: 816 sheet: 0.36 (0.46), residues: 102 loop : -1.91 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 135 HIS 0.009 0.002 HIS C 303 PHE 0.013 0.002 PHE C 110 TYR 0.010 0.001 TYR E 92 ARG 0.003 0.000 ARG D 69 ********************** 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 223 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 175 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: A 16 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8043 (mt0) REVERT: A 80 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8199 (tt) REVERT: A 132 TYR cc_start: 0.8618 (p90) cc_final: 0.8386 (p90) REVERT: A 238 LYS cc_start: 0.8352 (mtmt) cc_final: 0.7923 (mttt) REVERT: A 250 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8045 (pp) REVERT: A 252 ARG cc_start: 0.8094 (ttm110) cc_final: 0.7221 (mtt-85) REVERT: A 262 MET cc_start: 0.8546 (mmp) cc_final: 0.8200 (mmt) REVERT: A 275 LYS cc_start: 0.8487 (ttmp) cc_final: 0.8119 (mtmt) REVERT: A 278 GLN cc_start: 0.7512 (pt0) cc_final: 0.7141 (mt0) REVERT: B 40 GLU cc_start: 0.7086 (tt0) cc_final: 0.6563 (tt0) REVERT: B 70 MET cc_start: 0.7725 (mtm) cc_final: 0.7322 (mtt) REVERT: B 161 LYS cc_start: 0.7850 (ptpt) cc_final: 0.7625 (ptpp) REVERT: B 227 MET cc_start: 0.8540 (ttp) cc_final: 0.8266 (ttm) REVERT: B 250 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8065 (pp) REVERT: B 264 MET cc_start: 0.8723 (mtm) cc_final: 0.8498 (mtm) REVERT: B 300 MET cc_start: 0.8023 (mmt) cc_final: 0.7344 (mmt) REVERT: C 40 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6935 (mm-30) REVERT: C 79 ILE cc_start: 0.8069 (mm) cc_final: 0.7831 (mt) REVERT: C 132 TYR cc_start: 0.8631 (p90) cc_final: 0.8317 (p90) REVERT: C 250 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8223 (pp) REVERT: D 71 MET cc_start: 0.7998 (ttp) cc_final: 0.7740 (ttp) outliers start: 48 outliers final: 38 residues processed: 206 average time/residue: 0.2313 time to fit residues: 66.0640 Evaluate side-chains 217 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 173 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 102 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 12 optimal weight: 0.0980 chunk 18 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.120954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.093693 restraints weight = 26018.111| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.96 r_work: 0.2764 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10188 Z= 0.155 Angle : 0.621 7.064 13848 Z= 0.294 Chirality : 0.043 0.194 1677 Planarity : 0.004 0.049 1704 Dihedral : 5.910 48.050 1443 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.10 % Allowed : 17.90 % Favored : 78.00 % 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: -0.70 (0.23), residues: 1314 helix: 0.38 (0.19), residues: 786 sheet: 0.46 (0.46), residues: 96 loop : -2.24 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 135 HIS 0.009 0.002 HIS C 303 PHE 0.010 0.001 PHE D 62 TYR 0.011 0.001 TYR E 92 ARG 0.001 0.000 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2272.56 seconds wall clock time: 41 minutes 32.47 seconds (2492.47 seconds total)