Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 6 14:16:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nb6_12256/10_2023/7nb6_12256.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nb6_12256/10_2023/7nb6_12256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nb6_12256/10_2023/7nb6_12256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nb6_12256/10_2023/7nb6_12256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nb6_12256/10_2023/7nb6_12256.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nb6_12256/10_2023/7nb6_12256.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 85 5.16 5 C 8700 2.51 5 N 2085 2.21 5 O 2150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 92": "NH1" <-> "NH2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ARG 56": "NH1" <-> "NH2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B GLU 326": "OE1" <-> "OE2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C ARG 56": "NH1" <-> "NH2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "C ARG 114": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C GLU 326": "OE1" <-> "OE2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D ARG 56": "NH1" <-> "NH2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D GLU 326": "OE1" <-> "OE2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E ARG 188": "NH1" <-> "NH2" Residue "E ARG 221": "NH1" <-> "NH2" Residue "E GLU 326": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 13020 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2604 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain: "B" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2604 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain: "C" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2604 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain: "D" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2604 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain: "E" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2604 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 17, 'TRANS': 322} Time building chain proxies: 6.94, per 1000 atoms: 0.53 Number of scatterers: 13020 At special positions: 0 Unit cell: (129.735, 126.387, 77.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 85 16.00 O 2150 8.00 N 2085 7.00 C 8700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.76 Conformation dependent library (CDL) restraints added in 1.9 seconds 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 88.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 7 through 30 Processing helix chain 'A' and resid 30 through 57 Proline residue: A 36 - end of helix Proline residue: A 49 - end of helix Processing helix chain 'A' and resid 60 through 94 Processing helix chain 'A' and resid 94 through 109 removed outlier: 3.546A pdb=" N ARG A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Proline residue: A 104 - end of helix Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 129 through 147 removed outlier: 3.526A pdb=" N ALA A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 165 removed outlier: 3.825A pdb=" N PHE A 152 " --> pdb=" O MET A 148 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 177 through 184 removed outlier: 3.629A pdb=" N GLU A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 218 Processing helix chain 'A' and resid 222 through 234 Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.836A pdb=" N VAL A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 256 removed outlier: 3.653A pdb=" N ILE A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 275 Processing helix chain 'A' and resid 278 through 283 removed outlier: 4.405A pdb=" N ILE A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 306 Processing helix chain 'A' and resid 307 through 328 removed outlier: 3.550A pdb=" N MET A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL A 315 " --> pdb=" O MET A 311 " (cutoff:3.500A) Proline residue: A 316 - end of helix removed outlier: 3.879A pdb=" N GLN A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'B' and resid 7 through 30 Processing helix chain 'B' and resid 30 through 57 Proline residue: B 36 - end of helix Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 60 through 94 Processing helix chain 'B' and resid 94 through 109 removed outlier: 3.545A pdb=" N ARG B 98 " --> pdb=" O LEU B 94 " (cutoff:3.500A) Proline residue: B 104 - end of helix Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 129 through 147 removed outlier: 3.526A pdb=" N ALA B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 165 removed outlier: 3.825A pdb=" N PHE B 152 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 177 through 184 removed outlier: 3.629A pdb=" N GLU B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 218 Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 238 through 245 removed outlier: 3.836A pdb=" N VAL B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 256 removed outlier: 3.653A pdb=" N ILE B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 Processing helix chain 'B' and resid 278 through 283 removed outlier: 4.405A pdb=" N ILE B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 306 Processing helix chain 'B' and resid 307 through 328 removed outlier: 3.551A pdb=" N MET B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL B 315 " --> pdb=" O MET B 311 " (cutoff:3.500A) Proline residue: B 316 - end of helix removed outlier: 3.879A pdb=" N GLN B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'C' and resid 7 through 30 Processing helix chain 'C' and resid 30 through 57 Proline residue: C 36 - end of helix Proline residue: C 49 - end of helix Processing helix chain 'C' and resid 60 through 94 Processing helix chain 'C' and resid 94 through 109 removed outlier: 3.546A pdb=" N ARG C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 118 through 129 Processing helix chain 'C' and resid 129 through 147 removed outlier: 3.527A pdb=" N ALA C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 165 removed outlier: 3.825A pdb=" N PHE C 152 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 177 through 184 removed outlier: 3.628A pdb=" N GLU C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 218 Processing helix chain 'C' and resid 222 through 234 Processing helix chain 'C' and resid 238 through 245 removed outlier: 3.837A pdb=" N VAL C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 256 removed outlier: 3.654A pdb=" N ILE C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 275 Processing helix chain 'C' and resid 278 through 283 removed outlier: 4.406A pdb=" N ILE C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 306 Processing helix chain 'C' and resid 307 through 328 removed outlier: 3.550A pdb=" N MET C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 312 " --> pdb=" O PRO C 308 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL C 315 " --> pdb=" O MET C 311 " (cutoff:3.500A) Proline residue: C 316 - end of helix removed outlier: 3.878A pdb=" N GLN C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 339 Processing helix chain 'D' and resid 7 through 30 Processing helix chain 'D' and resid 30 through 57 Proline residue: D 36 - end of helix Proline residue: D 49 - end of helix Processing helix chain 'D' and resid 60 through 94 Processing helix chain 'D' and resid 94 through 109 removed outlier: 3.546A pdb=" N ARG D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 118 through 129 Processing helix chain 'D' and resid 129 through 147 removed outlier: 3.527A pdb=" N ALA D 133 " --> pdb=" O ASP D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 165 removed outlier: 3.825A pdb=" N PHE D 152 " --> pdb=" O MET D 148 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 177 through 184 removed outlier: 3.629A pdb=" N GLU D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 218 Processing helix chain 'D' and resid 222 through 234 Processing helix chain 'D' and resid 238 through 245 removed outlier: 3.836A pdb=" N VAL D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 256 removed outlier: 3.654A pdb=" N ILE D 249 " --> pdb=" O ALA D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 275 Processing helix chain 'D' and resid 278 through 283 removed outlier: 4.405A pdb=" N ILE D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 307 through 328 removed outlier: 3.550A pdb=" N MET D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 312 " --> pdb=" O PRO D 308 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL D 315 " --> pdb=" O MET D 311 " (cutoff:3.500A) Proline residue: D 316 - end of helix removed outlier: 3.878A pdb=" N GLN D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR D 328 " --> pdb=" O ALA D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 339 Processing helix chain 'E' and resid 7 through 30 Processing helix chain 'E' and resid 30 through 57 Proline residue: E 36 - end of helix Proline residue: E 49 - end of helix Processing helix chain 'E' and resid 60 through 94 Processing helix chain 'E' and resid 94 through 109 removed outlier: 3.545A pdb=" N ARG E 98 " --> pdb=" O LEU E 94 " (cutoff:3.500A) Proline residue: E 104 - end of helix Processing helix chain 'E' and resid 118 through 129 Processing helix chain 'E' and resid 129 through 147 removed outlier: 3.525A pdb=" N ALA E 133 " --> pdb=" O ASP E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 165 removed outlier: 3.825A pdb=" N PHE E 152 " --> pdb=" O MET E 148 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU E 153 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 174 Processing helix chain 'E' and resid 177 through 184 removed outlier: 3.628A pdb=" N GLU E 181 " --> pdb=" O ALA E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 218 Processing helix chain 'E' and resid 222 through 234 Processing helix chain 'E' and resid 238 through 245 removed outlier: 3.836A pdb=" N VAL E 242 " --> pdb=" O ASN E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 256 removed outlier: 3.653A pdb=" N ILE E 249 " --> pdb=" O ALA E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 275 Processing helix chain 'E' and resid 278 through 283 removed outlier: 4.405A pdb=" N ILE E 283 " --> pdb=" O LEU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 306 Processing helix chain 'E' and resid 307 through 328 removed outlier: 3.551A pdb=" N MET E 311 " --> pdb=" O GLY E 307 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU E 312 " --> pdb=" O PRO E 308 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL E 315 " --> pdb=" O MET E 311 " (cutoff:3.500A) Proline residue: E 316 - end of helix removed outlier: 3.878A pdb=" N GLN E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR E 328 " --> pdb=" O ALA E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 339 1025 hydrogen bonds defined for protein. 3075 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: 3.62 Time building geometry restraints manager: 6.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3985 1.34 - 1.46: 2394 1.46 - 1.57: 6726 1.57 - 1.69: 0 1.69 - 1.81: 165 Bond restraints: 13270 Sorted by residual: bond pdb=" C ALA A 31 " pdb=" N GLU A 32 " ideal model delta sigma weight residual 1.334 1.301 0.033 1.38e-02 5.25e+03 5.73e+00 bond pdb=" CB VAL E 14 " pdb=" CG1 VAL E 14 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.88e+00 bond pdb=" CB VAL A 14 " pdb=" CG1 VAL A 14 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.87e+00 bond pdb=" CB VAL D 14 " pdb=" CG1 VAL D 14 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.79e+00 bond pdb=" CB VAL C 14 " pdb=" CG1 VAL C 14 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.73e+00 ... (remaining 13265 not shown) Histogram of bond angle deviations from ideal: 98.67 - 105.79: 358 105.79 - 112.91: 7771 112.91 - 120.03: 4791 120.03 - 127.15: 5060 127.15 - 134.26: 150 Bond angle restraints: 18130 Sorted by residual: angle pdb=" N ILE A 283 " pdb=" CA ILE A 283 " pdb=" C ILE A 283 " ideal model delta sigma weight residual 108.53 103.77 4.76 1.22e+00 6.72e-01 1.53e+01 angle pdb=" N ILE D 283 " pdb=" CA ILE D 283 " pdb=" C ILE D 283 " ideal model delta sigma weight residual 108.53 103.80 4.73 1.22e+00 6.72e-01 1.50e+01 angle pdb=" N ILE C 283 " pdb=" CA ILE C 283 " pdb=" C ILE C 283 " ideal model delta sigma weight residual 108.53 103.81 4.72 1.22e+00 6.72e-01 1.49e+01 angle pdb=" N ILE E 283 " pdb=" CA ILE E 283 " pdb=" C ILE E 283 " ideal model delta sigma weight residual 108.53 103.82 4.71 1.22e+00 6.72e-01 1.49e+01 angle pdb=" N ILE B 283 " pdb=" CA ILE B 283 " pdb=" C ILE B 283 " ideal model delta sigma weight residual 108.53 103.84 4.69 1.22e+00 6.72e-01 1.48e+01 ... (remaining 18125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 7039 15.46 - 30.92: 708 30.92 - 46.38: 173 46.38 - 61.83: 18 61.83 - 77.29: 12 Dihedral angle restraints: 7950 sinusoidal: 3030 harmonic: 4920 Sorted by residual: dihedral pdb=" CA PHE C 275 " pdb=" C PHE C 275 " pdb=" N GLY C 276 " pdb=" CA GLY C 276 " ideal model delta harmonic sigma weight residual 180.00 151.37 28.63 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA PHE B 275 " pdb=" C PHE B 275 " pdb=" N GLY B 276 " pdb=" CA GLY B 276 " ideal model delta harmonic sigma weight residual 180.00 151.40 28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA PHE E 275 " pdb=" C PHE E 275 " pdb=" N GLY E 276 " pdb=" CA GLY E 276 " ideal model delta harmonic sigma weight residual 180.00 151.40 28.60 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 7947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1268 0.035 - 0.070: 716 0.070 - 0.105: 264 0.105 - 0.141: 79 0.141 - 0.176: 18 Chirality restraints: 2345 Sorted by residual: chirality pdb=" CB ILE C 283 " pdb=" CA ILE C 283 " pdb=" CG1 ILE C 283 " pdb=" CG2 ILE C 283 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CB ILE D 283 " pdb=" CA ILE D 283 " pdb=" CG1 ILE D 283 " pdb=" CG2 ILE D 283 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CB ILE B 283 " pdb=" CA ILE B 283 " pdb=" CG1 ILE B 283 " pdb=" CG2 ILE B 283 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 2342 not shown) Planarity restraints: 2180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 178 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO B 179 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 179 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 179 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 178 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO C 179 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 178 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO E 179 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 179 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 179 " 0.028 5.00e-02 4.00e+02 ... (remaining 2177 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3205 2.79 - 3.32: 14859 3.32 - 3.84: 22037 3.84 - 4.37: 23352 4.37 - 4.90: 40652 Nonbonded interactions: 104105 Sorted by model distance: nonbonded pdb=" OG1 THR A 201 " pdb=" OH TYR A 235 " model vdw 2.261 2.440 nonbonded pdb=" OG1 THR C 201 " pdb=" OH TYR C 235 " model vdw 2.261 2.440 nonbonded pdb=" OG1 THR B 201 " pdb=" OH TYR B 235 " model vdw 2.262 2.440 nonbonded pdb=" OG1 THR E 201 " pdb=" OH TYR E 235 " model vdw 2.262 2.440 nonbonded pdb=" OG1 THR D 201 " pdb=" OH TYR D 235 " model vdw 2.263 2.440 ... (remaining 104100 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' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.250 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 35.200 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.010 0.074 13270 Z= 0.615 Angle : 0.958 10.604 18130 Z= 0.471 Chirality : 0.050 0.176 2345 Planarity : 0.005 0.050 2180 Dihedral : 13.567 77.292 4760 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 0.49 % Allowed : 0.77 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.21), residues: 1690 helix: 1.37 (0.14), residues: 1405 sheet: None (None), residues: 0 loop : -3.86 (0.32), residues: 285 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 204 time to evaluate : 1.487 Fit side-chains outliers start: 7 outliers final: 0 residues processed: 211 average time/residue: 0.1924 time to fit residues: 63.8195 Evaluate side-chains 150 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.544 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 251 GLN B 126 HIS ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 GLN E 126 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13270 Z= 0.288 Angle : 0.779 10.336 18130 Z= 0.372 Chirality : 0.045 0.191 2345 Planarity : 0.006 0.049 2180 Dihedral : 5.056 26.771 1790 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.35 % Allowed : 10.53 % Favored : 89.12 % 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: 1.37 (0.21), residues: 1690 helix: 1.76 (0.14), residues: 1410 sheet: None (None), residues: 0 loop : -3.68 (0.32), residues: 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 164 time to evaluate : 1.542 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 167 average time/residue: 0.2009 time to fit residues: 53.2719 Evaluate side-chains 146 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 1.461 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1160 time to fit residues: 2.8038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 167 optimal weight: 0.0770 chunk 137 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 GLN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 GLN E 251 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13270 Z= 0.188 Angle : 0.704 8.954 18130 Z= 0.335 Chirality : 0.042 0.171 2345 Planarity : 0.006 0.049 2180 Dihedral : 4.734 24.832 1790 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.26 % Allowed : 13.26 % Favored : 85.47 % 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: 1.85 (0.21), residues: 1690 helix: 2.09 (0.14), residues: 1410 sheet: None (None), residues: 0 loop : -3.59 (0.33), residues: 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 153 time to evaluate : 1.583 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 163 average time/residue: 0.1919 time to fit residues: 49.7817 Evaluate side-chains 152 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 1.517 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1324 time to fit residues: 3.8092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 164 optimal weight: 0.0040 chunk 81 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 GLN D 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13270 Z= 0.231 Angle : 0.696 8.834 18130 Z= 0.332 Chirality : 0.041 0.167 2345 Planarity : 0.006 0.047 2180 Dihedral : 4.552 23.748 1790 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.77 % Allowed : 17.19 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.21), residues: 1690 helix: 2.10 (0.14), residues: 1410 sheet: None (None), residues: 0 loop : -3.52 (0.35), residues: 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 163 time to evaluate : 1.370 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 172 average time/residue: 0.1859 time to fit residues: 51.1363 Evaluate side-chains 150 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 1.313 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1104 time to fit residues: 2.9637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.8235 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13270 Z= 0.206 Angle : 0.691 8.901 18130 Z= 0.327 Chirality : 0.041 0.166 2345 Planarity : 0.006 0.052 2180 Dihedral : 4.463 23.891 1790 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.77 % Allowed : 19.93 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.21), residues: 1690 helix: 2.12 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -3.57 (0.35), residues: 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 1.465 Fit side-chains outliers start: 11 outliers final: 1 residues processed: 158 average time/residue: 0.1982 time to fit residues: 49.5361 Evaluate side-chains 143 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 1.442 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1108 time to fit residues: 2.0133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 96 optimal weight: 0.0980 chunk 40 optimal weight: 0.5980 chunk 164 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.8205 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13270 Z= 0.173 Angle : 0.681 14.143 18130 Z= 0.318 Chirality : 0.040 0.162 2345 Planarity : 0.005 0.051 2180 Dihedral : 4.287 22.253 1790 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.40 % Allowed : 20.63 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.21), residues: 1690 helix: 2.27 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -3.33 (0.36), residues: 270 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 1.320 Fit side-chains outliers start: 20 outliers final: 3 residues processed: 166 average time/residue: 0.1856 time to fit residues: 49.1198 Evaluate side-chains 149 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 146 time to evaluate : 1.328 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1170 time to fit residues: 2.5328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 93 optimal weight: 0.0470 chunk 120 optimal weight: 0.0030 chunk 138 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 102 optimal weight: 0.0970 chunk 99 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.4088 ------------------------------------------------------------------------------- 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: 0.8195 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13270 Z= 0.167 Angle : 0.690 10.114 18130 Z= 0.320 Chirality : 0.041 0.248 2345 Planarity : 0.005 0.049 2180 Dihedral : 4.147 21.445 1790 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.05 % Allowed : 21.26 % Favored : 77.68 % 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: 2.27 (0.22), residues: 1690 helix: 2.29 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -3.41 (0.37), residues: 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 1.338 Fit side-chains outliers start: 15 outliers final: 2 residues processed: 162 average time/residue: 0.1939 time to fit residues: 49.6318 Evaluate side-chains 146 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 1.344 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1452 time to fit residues: 2.4124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.0050 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 30.0000 chunk 81 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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: 0.8221 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13270 Z= 0.192 Angle : 0.732 14.674 18130 Z= 0.334 Chirality : 0.041 0.236 2345 Planarity : 0.005 0.045 2180 Dihedral : 4.108 21.204 1790 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.68 % Allowed : 20.56 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.22), residues: 1690 helix: 2.26 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -3.51 (0.37), residues: 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 1.422 Fit side-chains outliers start: 24 outliers final: 2 residues processed: 171 average time/residue: 0.1940 time to fit residues: 52.4267 Evaluate side-chains 147 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 1.411 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1360 time to fit residues: 2.4459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 8.9990 chunk 46 optimal weight: 50.0000 chunk 137 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13270 Z= 0.187 Angle : 0.718 11.795 18130 Z= 0.332 Chirality : 0.041 0.238 2345 Planarity : 0.005 0.047 2180 Dihedral : 4.101 20.965 1790 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.35 % Allowed : 21.68 % Favored : 77.96 % 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: 2.30 (0.21), residues: 1690 helix: 2.31 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -3.43 (0.36), residues: 255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 148 time to evaluate : 1.453 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 153 average time/residue: 0.1965 time to fit residues: 47.9798 Evaluate side-chains 146 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 1.404 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1690 time to fit residues: 2.7348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8226 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13270 Z= 0.187 Angle : 0.746 15.774 18130 Z= 0.339 Chirality : 0.041 0.218 2345 Planarity : 0.005 0.049 2180 Dihedral : 4.086 20.667 1790 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.21 % Allowed : 22.04 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.21), residues: 1690 helix: 2.31 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -3.42 (0.36), residues: 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 151 time to evaluate : 1.521 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 153 average time/residue: 0.1980 time to fit residues: 47.9095 Evaluate side-chains 150 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.300 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1313 time to fit residues: 2.0784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.121372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.085147 restraints weight = 27522.180| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.46 r_work: 0.3155 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13270 Z= 0.189 Angle : 0.724 11.097 18130 Z= 0.333 Chirality : 0.041 0.210 2345 Planarity : 0.005 0.047 2180 Dihedral : 4.081 20.508 1790 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.21 % Allowed : 21.96 % Favored : 77.82 % 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: 2.28 (0.21), residues: 1690 helix: 2.29 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -3.41 (0.36), residues: 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2445.20 seconds wall clock time: 45 minutes 11.47 seconds (2711.47 seconds total)