Starting phenix.real_space_refine (version: dev) on Sun Feb 19 22:38:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5j_26352/02_2023/7u5j_26352.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5j_26352/02_2023/7u5j_26352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5j_26352/02_2023/7u5j_26352.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5j_26352/02_2023/7u5j_26352.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5j_26352/02_2023/7u5j_26352.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5j_26352/02_2023/7u5j_26352.pdb" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.069 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 Process input model Symmetric amino acids flipped Residue "A TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10804 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2630 Classifications: {'peptide': 344} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 324} Chain: "B" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2630 Classifications: {'peptide': 344} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 324} Chain: "C" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2630 Classifications: {'peptide': 344} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 324} Chain: "D" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2630 Classifications: {'peptide': 344} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 324} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "C" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "D" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Time building chain proxies: 6.23, per 1000 atoms: 0.58 Number of scatterers: 10804 At special positions: 0 Unit cell: (95.23, 80.25, 103.79, 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 48 16.00 O 2268 8.00 N 1860 7.00 C 6628 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: 4.61 Conformation dependent library (CDL) restraints added in 1.6 seconds 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2528 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 53.5% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 9 through 24 Processing helix chain 'A' and resid 36 through 47 Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.932A pdb=" N VAL A 70 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 86 Processing helix chain 'A' and resid 93 through 102 Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 160 through 180 Processing helix chain 'A' and resid 198 through 220 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 245 through 261 Processing helix chain 'A' and resid 276 through 289 Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 320 through 339 removed outlier: 4.097A pdb=" N ALA A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 24 Processing helix chain 'B' and resid 36 through 47 Processing helix chain 'B' and resid 52 through 64 Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.920A pdb=" N VAL B 70 " --> pdb=" O ASP B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 86 Processing helix chain 'B' and resid 93 through 102 Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 160 through 180 Processing helix chain 'B' and resid 198 through 220 Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 245 through 261 Processing helix chain 'B' and resid 276 through 289 Processing helix chain 'B' and resid 307 through 315 Processing helix chain 'B' and resid 320 through 339 removed outlier: 4.088A pdb=" N ALA B 334 " --> pdb=" O LYS B 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 36 through 47 Processing helix chain 'C' and resid 52 through 64 Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.928A pdb=" N VAL C 70 " --> pdb=" O ASP C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 86 Processing helix chain 'C' and resid 93 through 102 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 160 through 180 Processing helix chain 'C' and resid 198 through 220 Processing helix chain 'C' and resid 223 through 227 Processing helix chain 'C' and resid 245 through 261 Processing helix chain 'C' and resid 276 through 289 Processing helix chain 'C' and resid 307 through 315 Processing helix chain 'C' and resid 320 through 339 removed outlier: 4.095A pdb=" N ALA C 334 " --> pdb=" O LYS C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 36 through 47 Processing helix chain 'D' and resid 52 through 64 Processing helix chain 'D' and resid 67 through 71 removed outlier: 3.926A pdb=" N VAL D 70 " --> pdb=" O ASP D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 86 Processing helix chain 'D' and resid 93 through 102 Processing helix chain 'D' and resid 130 through 141 Processing helix chain 'D' and resid 160 through 180 Processing helix chain 'D' and resid 198 through 220 Processing helix chain 'D' and resid 223 through 227 Processing helix chain 'D' and resid 245 through 261 Processing helix chain 'D' and resid 276 through 289 Processing helix chain 'D' and resid 307 through 315 Processing helix chain 'D' and resid 320 through 339 removed outlier: 4.110A pdb=" N ALA D 334 " --> pdb=" O LYS D 330 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.129A pdb=" N GLY A 29 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE A 78 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A 31 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL A 105 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ALA A 146 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE A 107 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N TRP A 148 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASP A 144 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ILE A 186 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA A 146 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLU A 188 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP A 148 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLU A 190 " --> pdb=" O TRP A 148 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N CYS A 150 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU A 192 " --> pdb=" O CYS A 150 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU A 152 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU A 229 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.127A pdb=" N GLY B 29 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE B 78 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU B 31 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL B 105 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ALA B 146 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE B 107 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TRP B 148 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP B 144 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ILE B 186 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA B 146 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLU B 188 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP B 148 " --> pdb=" O GLU B 188 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLU B 190 " --> pdb=" O TRP B 148 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N CYS B 150 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU B 192 " --> pdb=" O CYS B 150 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU B 152 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU B 229 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 115 Processing sheet with id=AA5, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.135A pdb=" N GLY C 29 " --> pdb=" O GLY C 76 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE C 78 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU C 31 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL C 105 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ALA C 146 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE C 107 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TRP C 148 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ASP C 144 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ILE C 186 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA C 146 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLU C 188 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP C 148 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLU C 190 " --> pdb=" O TRP C 148 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N CYS C 150 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU C 192 " --> pdb=" O CYS C 150 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU C 152 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU C 229 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 113 through 115 Processing sheet with id=AA7, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.134A pdb=" N GLY D 29 " --> pdb=" O GLY D 76 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE D 78 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU D 31 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL D 105 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA D 146 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE D 107 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TRP D 148 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP D 144 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ILE D 186 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA D 146 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLU D 188 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP D 148 " --> pdb=" O GLU D 188 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLU D 190 " --> pdb=" O TRP D 148 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N CYS D 150 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU D 192 " --> pdb=" O CYS D 150 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU D 152 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU D 229 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 113 through 115 568 hydrogen bonds defined for protein. 1656 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: 3.45 Time building geometry restraints manager: 4.94 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: 3516 1.34 - 1.46: 1636 1.46 - 1.57: 5512 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 10724 Sorted by residual: bond pdb=" C ASN A 71 " pdb=" N PRO A 72 " ideal model delta sigma weight residual 1.337 1.354 -0.017 1.24e-02 6.50e+03 1.93e+00 bond pdb=" C ASN D 71 " pdb=" N PRO D 72 " ideal model delta sigma weight residual 1.337 1.354 -0.017 1.24e-02 6.50e+03 1.79e+00 bond pdb=" C ASN B 71 " pdb=" N PRO B 72 " ideal model delta sigma weight residual 1.337 1.354 -0.016 1.24e-02 6.50e+03 1.76e+00 bond pdb=" C ASN C 71 " pdb=" N PRO C 72 " ideal model delta sigma weight residual 1.337 1.353 -0.016 1.24e-02 6.50e+03 1.67e+00 bond pdb=" CA PHE A 58 " pdb=" CB PHE A 58 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.68e-02 3.54e+03 9.90e-01 ... (remaining 10719 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.85: 368 106.85 - 113.62: 5997 113.62 - 120.39: 3920 120.39 - 127.17: 4129 127.17 - 133.94: 122 Bond angle restraints: 14536 Sorted by residual: angle pdb=" CA PHE D 58 " pdb=" CB PHE D 58 " pdb=" CG PHE D 58 " ideal model delta sigma weight residual 113.80 116.26 -2.46 1.00e+00 1.00e+00 6.03e+00 angle pdb=" CA PHE B 58 " pdb=" CB PHE B 58 " pdb=" CG PHE B 58 " ideal model delta sigma weight residual 113.80 116.25 -2.45 1.00e+00 1.00e+00 6.01e+00 angle pdb=" CA PHE A 58 " pdb=" CB PHE A 58 " pdb=" CG PHE A 58 " ideal model delta sigma weight residual 113.80 116.23 -2.43 1.00e+00 1.00e+00 5.91e+00 angle pdb=" CA PHE C 58 " pdb=" CB PHE C 58 " pdb=" CG PHE C 58 " ideal model delta sigma weight residual 113.80 116.14 -2.34 1.00e+00 1.00e+00 5.50e+00 angle pdb=" C ARG D 57 " pdb=" N PHE D 58 " pdb=" CA PHE D 58 " ideal model delta sigma weight residual 121.14 117.09 4.05 1.75e+00 3.27e-01 5.35e+00 ... (remaining 14531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.97: 5826 11.97 - 23.94: 526 23.94 - 35.91: 153 35.91 - 47.88: 34 47.88 - 59.85: 5 Dihedral angle restraints: 6544 sinusoidal: 2596 harmonic: 3948 Sorted by residual: dihedral pdb=" CA THR A 260 " pdb=" C THR A 260 " pdb=" N VAL A 261 " pdb=" CA VAL A 261 " ideal model delta harmonic sigma weight residual 180.00 -164.23 -15.77 0 5.00e+00 4.00e-02 9.94e+00 dihedral pdb=" CA THR C 260 " pdb=" C THR C 260 " pdb=" N VAL C 261 " pdb=" CA VAL C 261 " ideal model delta harmonic sigma weight residual -180.00 -164.32 -15.68 0 5.00e+00 4.00e-02 9.84e+00 dihedral pdb=" CA THR B 260 " pdb=" C THR B 260 " pdb=" N VAL B 261 " pdb=" CA VAL B 261 " ideal model delta harmonic sigma weight residual -180.00 -164.32 -15.68 0 5.00e+00 4.00e-02 9.84e+00 ... (remaining 6541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1108 0.033 - 0.065: 338 0.065 - 0.098: 141 0.098 - 0.131: 53 0.131 - 0.164: 4 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CA PHE C 58 " pdb=" N PHE C 58 " pdb=" C PHE C 58 " pdb=" CB PHE C 58 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CA PHE B 58 " pdb=" N PHE B 58 " pdb=" C PHE B 58 " pdb=" CB PHE B 58 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA PHE A 58 " pdb=" N PHE A 58 " pdb=" C PHE A 58 " pdb=" CB PHE A 58 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 1641 not shown) Planarity restraints: 1892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 58 " -0.017 2.00e-02 2.50e+03 1.49e-02 3.87e+00 pdb=" CG PHE C 58 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE C 58 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 58 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 58 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 58 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 58 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 58 " 0.017 2.00e-02 2.50e+03 1.48e-02 3.83e+00 pdb=" CG PHE D 58 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE D 58 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE D 58 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 58 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 58 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE D 58 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 58 " -0.016 2.00e-02 2.50e+03 1.47e-02 3.77e+00 pdb=" CG PHE B 58 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 58 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 58 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 58 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 58 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 58 " -0.002 2.00e-02 2.50e+03 ... (remaining 1889 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1480 2.75 - 3.29: 10766 3.29 - 3.83: 19952 3.83 - 4.36: 23880 4.36 - 4.90: 39095 Nonbonded interactions: 95173 Sorted by model distance: nonbonded pdb=" O GLN B 61 " pdb=" OG1 THR B 65 " model vdw 2.215 2.440 nonbonded pdb=" O GLN C 61 " pdb=" OG1 THR C 65 " model vdw 2.216 2.440 nonbonded pdb=" O GLN A 61 " pdb=" OG1 THR A 65 " model vdw 2.219 2.440 nonbonded pdb=" O GLN D 61 " pdb=" OG1 THR D 65 " model vdw 2.219 2.440 nonbonded pdb=" O LYS C 289 " pdb=" O HOH C 401 " model vdw 2.260 2.440 ... (remaining 95168 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6628 2.51 5 N 1860 2.21 5 O 2268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 4.330 Check model and map are aligned: 0.170 Process input model: 30.570 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 : 0.004 0.038 10724 Z= 0.240 Angle : 0.543 5.247 14536 Z= 0.301 Chirality : 0.041 0.164 1644 Planarity : 0.005 0.039 1892 Dihedral : 10.541 59.847 4016 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.21 (0.22), residues: 1368 helix: 1.07 (0.19), residues: 708 sheet: -1.58 (0.35), residues: 192 loop : -0.34 (0.26), residues: 468 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 1.324 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 205 average time/residue: 1.0845 time to fit residues: 242.4591 Evaluate side-chains 171 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 1.7761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 169 ASN ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS B 55 ASN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS B 275 GLN C 55 ASN C 169 ASN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS C 275 GLN D 55 ASN D 169 ASN ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 10724 Z= 0.238 Angle : 0.517 4.722 14536 Z= 0.276 Chirality : 0.041 0.159 1644 Planarity : 0.005 0.035 1892 Dihedral : 4.379 15.145 1480 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.73 (0.22), residues: 1368 helix: 1.54 (0.19), residues: 716 sheet: -1.99 (0.37), residues: 160 loop : -0.09 (0.27), residues: 492 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 1.287 Fit side-chains outliers start: 33 outliers final: 16 residues processed: 190 average time/residue: 0.9555 time to fit residues: 200.3036 Evaluate side-chains 174 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 0.2228 time to fit residues: 3.2902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 0.0170 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 133 optimal weight: 10.0000 chunk 110 optimal weight: 0.3980 chunk 122 optimal weight: 0.5980 chunk 42 optimal weight: 0.0970 chunk 99 optimal weight: 9.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 10724 Z= 0.170 Angle : 0.488 6.625 14536 Z= 0.251 Chirality : 0.039 0.154 1644 Planarity : 0.004 0.031 1892 Dihedral : 4.116 14.750 1480 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.17 (0.23), residues: 1368 helix: 1.88 (0.19), residues: 724 sheet: -2.00 (0.37), residues: 160 loop : 0.23 (0.29), residues: 484 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 182 time to evaluate : 1.288 Fit side-chains outliers start: 29 outliers final: 21 residues processed: 203 average time/residue: 0.9542 time to fit residues: 215.0618 Evaluate side-chains 187 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 15 residues processed: 6 average time/residue: 0.4878 time to fit residues: 5.2891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.6980 chunk 93 optimal weight: 0.4980 chunk 64 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 109 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 81 HIS B 86 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN C 81 HIS ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 HIS ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 10724 Z= 0.200 Angle : 0.501 8.344 14536 Z= 0.260 Chirality : 0.040 0.156 1644 Planarity : 0.004 0.030 1892 Dihedral : 4.119 14.690 1480 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 3.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.21 (0.22), residues: 1368 helix: 2.01 (0.18), residues: 720 sheet: -2.12 (0.36), residues: 160 loop : 0.15 (0.28), residues: 488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 165 time to evaluate : 1.378 Fit side-chains outliers start: 36 outliers final: 24 residues processed: 196 average time/residue: 0.8888 time to fit residues: 193.5336 Evaluate side-chains 185 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 19 residues processed: 5 average time/residue: 0.2035 time to fit residues: 2.9367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.0370 chunk 1 optimal weight: 0.0770 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 81 HIS B 86 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 HIS ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS D 81 HIS ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 10724 Z= 0.195 Angle : 0.493 5.138 14536 Z= 0.258 Chirality : 0.040 0.157 1644 Planarity : 0.004 0.035 1892 Dihedral : 4.118 14.639 1480 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 3.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.28 (0.23), residues: 1368 helix: 2.11 (0.18), residues: 720 sheet: -2.17 (0.36), residues: 160 loop : 0.13 (0.28), residues: 488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 166 time to evaluate : 1.225 Fit side-chains outliers start: 44 outliers final: 27 residues processed: 196 average time/residue: 0.8400 time to fit residues: 184.2644 Evaluate side-chains 188 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 1.127 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 19 residues processed: 8 average time/residue: 0.1890 time to fit residues: 3.9451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10724 Z= 0.223 Angle : 0.520 6.054 14536 Z= 0.271 Chirality : 0.041 0.159 1644 Planarity : 0.005 0.034 1892 Dihedral : 4.194 14.680 1480 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.22 (0.23), residues: 1368 helix: 2.11 (0.18), residues: 716 sheet: -2.20 (0.37), residues: 160 loop : 0.03 (0.28), residues: 492 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 171 time to evaluate : 1.327 Fit side-chains outliers start: 37 outliers final: 24 residues processed: 194 average time/residue: 0.8836 time to fit residues: 191.0457 Evaluate side-chains 188 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 16 residues processed: 8 average time/residue: 0.2411 time to fit residues: 4.6145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 10724 Z= 0.229 Angle : 0.527 6.116 14536 Z= 0.275 Chirality : 0.041 0.159 1644 Planarity : 0.005 0.045 1892 Dihedral : 4.269 14.809 1480 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.22), residues: 1368 helix: 2.07 (0.18), residues: 716 sheet: -1.93 (0.52), residues: 96 loop : -0.14 (0.26), residues: 556 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 176 time to evaluate : 1.240 Fit side-chains outliers start: 35 outliers final: 23 residues processed: 197 average time/residue: 0.8964 time to fit residues: 196.5231 Evaluate side-chains 194 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 1.241 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 15 residues processed: 8 average time/residue: 0.1526 time to fit residues: 3.7329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 10724 Z= 0.242 Angle : 0.547 7.072 14536 Z= 0.286 Chirality : 0.042 0.159 1644 Planarity : 0.005 0.050 1892 Dihedral : 4.324 14.890 1480 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.10 (0.23), residues: 1368 helix: 2.04 (0.19), residues: 716 sheet: -2.62 (0.38), residues: 148 loop : 0.01 (0.27), residues: 504 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 171 time to evaluate : 1.310 Fit side-chains outliers start: 35 outliers final: 24 residues processed: 192 average time/residue: 0.9399 time to fit residues: 199.7869 Evaluate side-chains 195 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 15 residues processed: 9 average time/residue: 0.1626 time to fit residues: 3.9444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.5980 chunk 125 optimal weight: 0.3980 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 HIS ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 HIS ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 10724 Z= 0.230 Angle : 0.551 12.460 14536 Z= 0.283 Chirality : 0.042 0.159 1644 Planarity : 0.005 0.045 1892 Dihedral : 4.323 14.894 1480 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.01 (0.23), residues: 1368 helix: 2.05 (0.19), residues: 712 sheet: -2.70 (0.33), residues: 188 loop : 0.11 (0.29), residues: 468 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 1.391 Fit side-chains outliers start: 29 outliers final: 21 residues processed: 189 average time/residue: 0.8619 time to fit residues: 181.4040 Evaluate side-chains 191 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 1.236 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 14 residues processed: 7 average time/residue: 0.1832 time to fit residues: 3.6653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 0.0980 chunk 89 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 124 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10724 Z= 0.213 Angle : 0.542 7.939 14536 Z= 0.280 Chirality : 0.041 0.159 1644 Planarity : 0.005 0.044 1892 Dihedral : 4.283 16.079 1480 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.08 (0.23), residues: 1368 helix: 2.11 (0.19), residues: 712 sheet: -2.70 (0.32), residues: 188 loop : 0.17 (0.29), residues: 468 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 1.662 Fit side-chains outliers start: 21 outliers final: 14 residues processed: 182 average time/residue: 0.9402 time to fit residues: 191.0310 Evaluate side-chains 180 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 166 time to evaluate : 1.494 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.1568 time to fit residues: 2.0038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.211043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.160036 restraints weight = 11677.088| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.26 r_work: 0.3570 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10724 Z= 0.229 Angle : 0.547 7.997 14536 Z= 0.284 Chirality : 0.042 0.159 1644 Planarity : 0.005 0.041 1892 Dihedral : 4.318 16.482 1480 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.00 (0.23), residues: 1368 helix: 2.04 (0.19), residues: 712 sheet: -2.73 (0.33), residues: 188 loop : 0.15 (0.29), residues: 468 =============================================================================== Job complete usr+sys time: 3646.51 seconds wall clock time: 66 minutes 44.90 seconds (4004.90 seconds total)