Starting phenix.real_space_refine on Sun Apr 7 15:05:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5j_26352/04_2024/7u5j_26352.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5j_26352/04_2024/7u5j_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_26352/04_2024/7u5j_26352.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5j_26352/04_2024/7u5j_26352.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5j_26352/04_2024/7u5j_26352.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5j_26352/04_2024/7u5j_26352.pdb" } resolution = 2.96 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= 0.069 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 6.35, per 1000 atoms: 0.59 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: 4.32 Conformation dependent library (CDL) restraints added in 2.1 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: 1.15 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: 3.27 Time building geometry restraints manager: 4.71 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 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: 0.880 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: 4.040 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.700 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 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 % Allowed : 4.30 % Favored : 93.55 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 148 HIS 0.004 0.001 HIS D 21 PHE 0.034 0.003 PHE C 58 TYR 0.017 0.002 TYR D 214 ARG 0.003 0.000 ARG B 134 *********************** 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 : 0.999 Fit side-chains revert: symmetry clash REVERT: A 86 GLN cc_start: 0.7589 (mt0) cc_final: 0.7186 (mt0) REVERT: A 174 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8527 (t80) REVERT: A 232 ASN cc_start: 0.8152 (p0) cc_final: 0.7818 (p0) REVERT: A 251 MET cc_start: 0.7485 (mmm) cc_final: 0.6677 (mmp) REVERT: B 11 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6541 (mm-30) REVERT: B 86 GLN cc_start: 0.7605 (mt0) cc_final: 0.7203 (mt0) REVERT: B 174 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.8527 (t80) REVERT: B 251 MET cc_start: 0.7541 (mmm) cc_final: 0.6715 (mmp) REVERT: C 11 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6600 (mm-30) REVERT: C 86 GLN cc_start: 0.7546 (mt0) cc_final: 0.7202 (mt0) REVERT: C 251 MET cc_start: 0.7478 (mmm) cc_final: 0.7129 (mmp) REVERT: D 11 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6583 (mm-30) REVERT: D 86 GLN cc_start: 0.7636 (mt0) cc_final: 0.7265 (mt0) REVERT: D 174 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8521 (t80) REVERT: D 251 MET cc_start: 0.7483 (mmm) cc_final: 0.7119 (mmp) outliers start: 24 outliers final: 16 residues processed: 205 average time/residue: 1.1188 time to fit residues: 249.4092 Evaluate side-chains 174 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 155 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 296 TRP Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP 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: 1.9990 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: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 A 275 GLN 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 D 275 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10724 Z= 0.285 Angle : 0.538 4.812 14536 Z= 0.287 Chirality : 0.042 0.159 1644 Planarity : 0.005 0.037 1892 Dihedral : 6.529 59.497 1510 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.96 % Allowed : 9.77 % Favored : 87.28 % 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: 0.60 (0.22), residues: 1368 helix: 1.48 (0.19), residues: 716 sheet: -2.07 (0.37), residues: 160 loop : -0.19 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 148 HIS 0.005 0.001 HIS A 21 PHE 0.032 0.003 PHE C 58 TYR 0.012 0.002 TYR D 214 ARG 0.006 0.001 ARG D 22 *********************** 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 209 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 176 time to evaluate : 1.166 Fit side-chains REVERT: A 174 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.8509 (t80) REVERT: A 232 ASN cc_start: 0.8191 (p0) cc_final: 0.7907 (p0) REVERT: A 247 GLU cc_start: 0.6858 (mp0) cc_final: 0.6517 (mm-30) REVERT: A 251 MET cc_start: 0.7462 (mmm) cc_final: 0.7162 (mmm) REVERT: B 11 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6592 (mm-30) REVERT: B 86 GLN cc_start: 0.7831 (mt0) cc_final: 0.7365 (mt0) REVERT: B 247 GLU cc_start: 0.6904 (mp0) cc_final: 0.6581 (mm-30) REVERT: C 11 GLU cc_start: 0.6833 (mm-30) cc_final: 0.6595 (mm-30) REVERT: C 251 MET cc_start: 0.7495 (mmm) cc_final: 0.7184 (mmm) REVERT: D 11 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6601 (mm-30) REVERT: D 174 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.8499 (t80) REVERT: D 247 GLU cc_start: 0.6815 (mp0) cc_final: 0.6495 (mm-30) REVERT: D 251 MET cc_start: 0.7502 (mmm) cc_final: 0.7204 (mmm) outliers start: 33 outliers final: 19 residues processed: 195 average time/residue: 0.9831 time to fit residues: 211.4292 Evaluate side-chains 182 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 161 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 296 TRP Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP 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: 0.9980 chunk 102 optimal weight: 0.0980 chunk 84 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 81 HIS ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.1330 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= 0.219 Angle : 0.504 5.913 14536 Z= 0.263 Chirality : 0.040 0.154 1644 Planarity : 0.005 0.036 1892 Dihedral : 6.273 59.011 1507 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.96 % Allowed : 10.93 % Favored : 86.11 % 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: 0.93 (0.22), residues: 1368 helix: 1.75 (0.19), residues: 720 sheet: -2.18 (0.37), residues: 160 loop : 0.03 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 148 HIS 0.004 0.001 HIS D 246 PHE 0.029 0.003 PHE C 58 TYR 0.011 0.002 TYR A 214 ARG 0.006 0.000 ARG D 22 *********************** 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 206 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 173 time to evaluate : 1.232 Fit side-chains REVERT: A 156 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: A 232 ASN cc_start: 0.8118 (p0) cc_final: 0.7849 (p0) REVERT: A 247 GLU cc_start: 0.6962 (mp0) cc_final: 0.6613 (mm-30) REVERT: A 251 MET cc_start: 0.7446 (mmm) cc_final: 0.7221 (mmm) REVERT: B 11 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6569 (mm-30) REVERT: B 77 VAL cc_start: 0.6049 (m) cc_final: 0.5835 (p) REVERT: B 86 GLN cc_start: 0.7939 (mt0) cc_final: 0.7464 (mt0) REVERT: C 11 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6609 (mm-30) REVERT: C 77 VAL cc_start: 0.6078 (m) cc_final: 0.5869 (p) REVERT: C 99 LYS cc_start: 0.8144 (mmtp) cc_final: 0.7941 (mmtp) REVERT: C 247 GLU cc_start: 0.6854 (mp0) cc_final: 0.6486 (mm-30) REVERT: C 251 MET cc_start: 0.7478 (mmm) cc_final: 0.7257 (mmm) REVERT: D 11 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6583 (mm-30) REVERT: D 86 GLN cc_start: 0.7943 (mt0) cc_final: 0.7421 (mt0) REVERT: D 156 GLU cc_start: 0.7636 (tt0) cc_final: 0.7403 (tp30) REVERT: D 251 MET cc_start: 0.7489 (mmm) cc_final: 0.7272 (mmm) outliers start: 33 outliers final: 21 residues processed: 197 average time/residue: 0.9672 time to fit residues: 210.1156 Evaluate side-chains 181 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 296 TRP Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 296 TRP 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: 0.5980 chunk 64 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 117 optimal weight: 0.0670 chunk 35 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.1518 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= 0.196 Angle : 0.485 5.566 14536 Z= 0.255 Chirality : 0.040 0.156 1644 Planarity : 0.005 0.037 1892 Dihedral : 5.785 59.276 1501 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.78 % Allowed : 13.08 % Favored : 84.14 % 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: 1.14 (0.22), residues: 1368 helix: 1.94 (0.18), residues: 724 sheet: -2.16 (0.37), residues: 160 loop : 0.11 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 148 HIS 0.004 0.001 HIS D 246 PHE 0.028 0.003 PHE C 58 TYR 0.012 0.002 TYR D 302 ARG 0.009 0.000 ARG A 22 *********************** 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 198 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 1.250 Fit side-chains REVERT: A 232 ASN cc_start: 0.8106 (p0) cc_final: 0.7837 (p0) REVERT: A 247 GLU cc_start: 0.6916 (mp0) cc_final: 0.6600 (mm-30) REVERT: A 251 MET cc_start: 0.7440 (mmm) cc_final: 0.7209 (mmm) REVERT: B 11 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6552 (mm-30) REVERT: B 86 GLN cc_start: 0.7899 (mt0) cc_final: 0.7444 (mt0) REVERT: B 247 GLU cc_start: 0.6932 (mp0) cc_final: 0.6654 (mm-30) REVERT: C 11 GLU cc_start: 0.6841 (mm-30) cc_final: 0.6574 (mm-30) REVERT: C 77 VAL cc_start: 0.6272 (m) cc_final: 0.6055 (p) REVERT: C 247 GLU cc_start: 0.6817 (mp0) cc_final: 0.6486 (mm-30) REVERT: C 251 MET cc_start: 0.7479 (mmm) cc_final: 0.7244 (mmm) REVERT: D 11 GLU cc_start: 0.6841 (mm-30) cc_final: 0.6564 (mm-30) REVERT: D 86 GLN cc_start: 0.7913 (mt0) cc_final: 0.7420 (mt0) REVERT: D 99 LYS cc_start: 0.8026 (mmtp) cc_final: 0.7669 (mmtm) REVERT: D 247 GLU cc_start: 0.6849 (mp0) cc_final: 0.6520 (mm-30) REVERT: D 251 MET cc_start: 0.7491 (mmm) cc_final: 0.7257 (mmm) outliers start: 31 outliers final: 23 residues processed: 185 average time/residue: 0.9791 time to fit residues: 199.9557 Evaluate side-chains 184 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 296 TRP Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 296 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.0980 chunk 1 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 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 81 HIS ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 81 HIS ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 HIS ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.1611 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= 0.214 Angle : 0.496 5.506 14536 Z= 0.260 Chirality : 0.040 0.157 1644 Planarity : 0.005 0.036 1892 Dihedral : 5.822 59.160 1501 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.32 % Allowed : 13.26 % Favored : 83.42 % 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: 1.18 (0.22), residues: 1368 helix: 2.02 (0.18), residues: 724 sheet: -2.21 (0.37), residues: 160 loop : 0.08 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 148 HIS 0.003 0.001 HIS D 21 PHE 0.028 0.003 PHE D 58 TYR 0.014 0.002 TYR D 302 ARG 0.009 0.000 ARG B 22 *********************** 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 199 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 162 time to evaluate : 1.237 Fit side-chains REVERT: A 86 GLN cc_start: 0.7730 (mt0) cc_final: 0.7396 (mt0) REVERT: A 232 ASN cc_start: 0.8101 (p0) cc_final: 0.7809 (p0) REVERT: A 251 MET cc_start: 0.7448 (mmm) cc_final: 0.7205 (mmm) REVERT: B 11 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6560 (mm-30) REVERT: B 86 GLN cc_start: 0.7809 (mt0) cc_final: 0.7326 (mt0) REVERT: B 247 GLU cc_start: 0.6928 (mp0) cc_final: 0.6671 (mm-30) REVERT: C 11 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6600 (mm-30) REVERT: C 71 ASN cc_start: 0.7334 (m-40) cc_final: 0.7095 (m-40) REVERT: C 156 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7348 (tt0) REVERT: C 247 GLU cc_start: 0.6719 (mp0) cc_final: 0.6440 (mm-30) REVERT: C 251 MET cc_start: 0.7501 (mmm) cc_final: 0.7269 (mmm) REVERT: D 11 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6579 (mm-30) REVERT: D 31 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6947 (tp) REVERT: D 86 GLN cc_start: 0.7866 (mt0) cc_final: 0.7385 (mt0) REVERT: D 99 LYS cc_start: 0.8032 (mmtp) cc_final: 0.7699 (mmtm) REVERT: D 251 MET cc_start: 0.7508 (mmm) cc_final: 0.7274 (mmm) outliers start: 37 outliers final: 24 residues processed: 189 average time/residue: 0.9567 time to fit residues: 199.6354 Evaluate side-chains 183 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 296 TRP Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 296 TRP 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: 0.9990 chunk 32 optimal weight: 4.9990 chunk 131 optimal weight: 0.0470 chunk 109 optimal weight: 0.0010 chunk 60 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.4484 ------------------------------------------------------------------------------- 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 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 HIS ** 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: 0.6939 moved from start: 0.1758 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= 0.183 Angle : 0.494 6.576 14536 Z= 0.259 Chirality : 0.040 0.157 1644 Planarity : 0.004 0.041 1892 Dihedral : 5.723 59.920 1501 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.49 % Allowed : 13.53 % Favored : 82.97 % 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: 1.49 (0.23), residues: 1368 helix: 2.22 (0.19), residues: 720 sheet: -1.83 (0.52), residues: 96 loop : -0.09 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 148 HIS 0.002 0.001 HIS A 81 PHE 0.027 0.002 PHE D 58 TYR 0.028 0.002 TYR A 138 ARG 0.011 0.001 ARG D 22 *********************** 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 211 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 172 time to evaluate : 1.306 Fit side-chains REVERT: A 31 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6995 (tp) REVERT: A 86 GLN cc_start: 0.7739 (mt0) cc_final: 0.7400 (mt0) REVERT: A 101 LYS cc_start: 0.7998 (tptm) cc_final: 0.7757 (tptp) REVERT: A 232 ASN cc_start: 0.7984 (p0) cc_final: 0.7692 (p0) REVERT: A 247 GLU cc_start: 0.6890 (mp0) cc_final: 0.6522 (mm-30) REVERT: A 251 MET cc_start: 0.7406 (mmm) cc_final: 0.6659 (mmp) REVERT: B 11 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6560 (mm-30) REVERT: B 31 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6895 (tp) REVERT: B 86 GLN cc_start: 0.7810 (mt0) cc_final: 0.7359 (mt0) REVERT: B 247 GLU cc_start: 0.6864 (mp0) cc_final: 0.6647 (mm-30) REVERT: C 11 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6557 (mm-30) REVERT: C 71 ASN cc_start: 0.7307 (m-40) cc_final: 0.7088 (m-40) REVERT: C 156 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7389 (tt0) REVERT: C 174 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8499 (t80) REVERT: C 247 GLU cc_start: 0.6671 (mp0) cc_final: 0.6374 (mm-30) REVERT: D 11 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6556 (mm-30) REVERT: D 31 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7073 (tp) REVERT: D 86 GLN cc_start: 0.7979 (mt0) cc_final: 0.7488 (mt0) REVERT: D 99 LYS cc_start: 0.8137 (mmtp) cc_final: 0.7878 (mmtm) REVERT: D 174 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.8409 (t80) REVERT: D 247 GLU cc_start: 0.6796 (mp0) cc_final: 0.6471 (mm-30) outliers start: 39 outliers final: 25 residues processed: 198 average time/residue: 0.9150 time to fit residues: 200.6418 Evaluate side-chains 191 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 296 TRP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS D 71 ASN ** 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: 0.6961 moved from start: 0.1821 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= 0.224 Angle : 0.522 6.982 14536 Z= 0.272 Chirality : 0.040 0.158 1644 Planarity : 0.005 0.040 1892 Dihedral : 5.806 59.636 1501 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.23 % Allowed : 14.70 % Favored : 82.08 % 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: 1.39 (0.23), residues: 1368 helix: 2.14 (0.18), residues: 720 sheet: -1.91 (0.52), residues: 96 loop : -0.12 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.005 0.001 HIS C 246 PHE 0.027 0.003 PHE D 58 TYR 0.019 0.002 TYR C 302 ARG 0.012 0.001 ARG D 22 *********************** 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 205 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 169 time to evaluate : 1.399 Fit side-chains REVERT: A 31 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7002 (tp) REVERT: A 232 ASN cc_start: 0.8096 (p0) cc_final: 0.7796 (p0) REVERT: A 247 GLU cc_start: 0.6911 (mp0) cc_final: 0.6602 (mm-30) REVERT: A 251 MET cc_start: 0.7430 (mmm) cc_final: 0.7186 (mmm) REVERT: B 11 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6569 (mm-30) REVERT: B 86 GLN cc_start: 0.7871 (mt0) cc_final: 0.7391 (mt0) REVERT: B 247 GLU cc_start: 0.6960 (mp0) cc_final: 0.6708 (mm-30) REVERT: C 11 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6594 (mm-30) REVERT: C 71 ASN cc_start: 0.7324 (m-40) cc_final: 0.7097 (m-40) REVERT: C 156 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: C 174 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.8526 (t80) REVERT: C 247 GLU cc_start: 0.6801 (mp0) cc_final: 0.6561 (mp0) REVERT: D 11 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6579 (mm-30) REVERT: D 31 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6981 (tp) REVERT: D 86 GLN cc_start: 0.7915 (mt0) cc_final: 0.7448 (mt0) REVERT: D 99 LYS cc_start: 0.8147 (mmtp) cc_final: 0.7882 (mmtm) REVERT: D 174 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.8490 (t80) REVERT: D 247 GLU cc_start: 0.6793 (mp0) cc_final: 0.6514 (mm-30) outliers start: 36 outliers final: 19 residues processed: 194 average time/residue: 0.9646 time to fit residues: 206.7574 Evaluate side-chains 187 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 296 TRP Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 125 optimal weight: 0.4980 chunk 114 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1886 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= 0.234 Angle : 0.529 7.757 14536 Z= 0.276 Chirality : 0.041 0.160 1644 Planarity : 0.005 0.049 1892 Dihedral : 5.794 59.861 1500 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.14 % Allowed : 15.14 % Favored : 81.72 % 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 (0.23), residues: 1368 helix: 2.15 (0.19), residues: 716 sheet: -2.55 (0.40), residues: 148 loop : -0.00 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 148 HIS 0.004 0.001 HIS C 246 PHE 0.028 0.003 PHE D 58 TYR 0.022 0.002 TYR D 302 ARG 0.014 0.001 ARG B 22 *********************** 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 200 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 165 time to evaluate : 1.038 Fit side-chains REVERT: A 31 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7029 (tp) REVERT: A 101 LYS cc_start: 0.7978 (tptm) cc_final: 0.7769 (tptp) REVERT: A 232 ASN cc_start: 0.8102 (p0) cc_final: 0.7821 (p0) REVERT: A 247 GLU cc_start: 0.6895 (mp0) cc_final: 0.6584 (mm-30) REVERT: A 251 MET cc_start: 0.7437 (mmm) cc_final: 0.7201 (mmm) REVERT: B 11 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6583 (mm-30) REVERT: B 31 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6911 (tp) REVERT: B 86 GLN cc_start: 0.7871 (mt0) cc_final: 0.7380 (mt0) REVERT: B 247 GLU cc_start: 0.6971 (mp0) cc_final: 0.6714 (mm-30) REVERT: C 11 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6622 (mm-30) REVERT: C 71 ASN cc_start: 0.7313 (m-40) cc_final: 0.7083 (m-40) REVERT: C 156 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7411 (tt0) REVERT: C 174 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.8552 (t80) REVERT: D 11 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6588 (mm-30) REVERT: D 31 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6961 (tp) REVERT: D 86 GLN cc_start: 0.8012 (mt0) cc_final: 0.7525 (mt0) REVERT: D 99 LYS cc_start: 0.7988 (mmtp) cc_final: 0.7668 (mmtm) REVERT: D 174 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8453 (t80) outliers start: 35 outliers final: 20 residues processed: 189 average time/residue: 0.9623 time to fit residues: 200.6596 Evaluate side-chains 188 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 296 TRP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10724 Z= 0.259 Angle : 0.551 7.676 14536 Z= 0.288 Chirality : 0.041 0.161 1644 Planarity : 0.005 0.052 1892 Dihedral : 5.865 59.821 1500 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.69 % Allowed : 15.95 % Favored : 81.36 % 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: 2.12 (0.19), residues: 712 sheet: -2.74 (0.34), residues: 188 loop : 0.02 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 148 HIS 0.005 0.001 HIS C 246 PHE 0.028 0.003 PHE D 58 TYR 0.024 0.002 TYR C 302 ARG 0.014 0.001 ARG C 22 *********************** 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 191 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 1.253 Fit side-chains REVERT: A 31 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7108 (tp) REVERT: A 140 LYS cc_start: 0.7823 (ttpt) cc_final: 0.7597 (tptm) REVERT: A 232 ASN cc_start: 0.8105 (p0) cc_final: 0.7832 (p0) REVERT: A 247 GLU cc_start: 0.6950 (mp0) cc_final: 0.6636 (mm-30) REVERT: A 251 MET cc_start: 0.7437 (mmm) cc_final: 0.7094 (mmm) REVERT: B 11 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6596 (mm-30) REVERT: B 31 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7073 (tp) REVERT: B 86 GLN cc_start: 0.7777 (mt0) cc_final: 0.7475 (mt0) REVERT: B 247 GLU cc_start: 0.6975 (mp0) cc_final: 0.6716 (mm-30) REVERT: C 11 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6638 (mm-30) REVERT: C 71 ASN cc_start: 0.7271 (m-40) cc_final: 0.7046 (m-40) REVERT: C 174 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.8523 (t80) REVERT: D 11 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6598 (mm-30) REVERT: D 31 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7019 (tp) REVERT: D 86 GLN cc_start: 0.7998 (mt0) cc_final: 0.7510 (mt0) REVERT: D 99 LYS cc_start: 0.7965 (mmtp) cc_final: 0.7621 (mmtm) REVERT: D 174 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.8494 (t80) REVERT: D 247 GLU cc_start: 0.6873 (mp0) cc_final: 0.6556 (mm-30) outliers start: 30 outliers final: 17 residues processed: 185 average time/residue: 0.9761 time to fit residues: 199.0953 Evaluate side-chains 187 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 296 TRP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 135 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 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 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN D 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10724 Z= 0.233 Angle : 0.540 8.004 14536 Z= 0.282 Chirality : 0.041 0.160 1644 Planarity : 0.005 0.051 1892 Dihedral : 5.801 59.948 1500 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.15 % Allowed : 16.31 % Favored : 81.54 % 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: 2.13 (0.19), residues: 712 sheet: -2.65 (0.40), residues: 148 loop : -0.13 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 148 HIS 0.004 0.001 HIS C 246 PHE 0.027 0.003 PHE D 58 TYR 0.030 0.002 TYR A 302 ARG 0.013 0.001 ARG C 22 ********************** 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 192 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 1.252 Fit side-chains REVERT: A 31 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7113 (tp) REVERT: A 232 ASN cc_start: 0.8090 (p0) cc_final: 0.7810 (p0) REVERT: A 247 GLU cc_start: 0.6954 (mp0) cc_final: 0.6642 (mm-30) REVERT: A 251 MET cc_start: 0.7424 (mmm) cc_final: 0.7083 (mmm) REVERT: B 11 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6588 (mm-30) REVERT: B 31 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7049 (tp) REVERT: B 86 GLN cc_start: 0.7744 (mt0) cc_final: 0.7440 (mt0) REVERT: B 247 GLU cc_start: 0.6978 (mp0) cc_final: 0.6724 (mm-30) REVERT: C 11 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6627 (mm-30) REVERT: C 174 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8502 (t80) REVERT: D 11 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6587 (mm-30) REVERT: D 31 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6949 (tp) REVERT: D 99 LYS cc_start: 0.7953 (mmtp) cc_final: 0.7607 (mmtm) REVERT: D 174 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.8473 (t80) REVERT: D 247 GLU cc_start: 0.6891 (mp0) cc_final: 0.6564 (mm-30) outliers start: 24 outliers final: 17 residues processed: 187 average time/residue: 0.9817 time to fit residues: 202.1416 Evaluate side-chains 188 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 296 TRP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 108 optimal weight: 9.9990 chunk 45 optimal weight: 0.2980 chunk 110 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.208657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.157572 restraints weight = 11689.718| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.26 r_work: 0.3557 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10724 Z= 0.263 Angle : 0.556 7.796 14536 Z= 0.291 Chirality : 0.041 0.170 1644 Planarity : 0.005 0.048 1892 Dihedral : 5.876 59.983 1500 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.33 % Allowed : 16.49 % Favored : 81.18 % 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: 1.03 (0.23), residues: 1368 helix: 2.06 (0.19), residues: 712 sheet: -2.68 (0.40), residues: 148 loop : -0.15 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.005 0.001 HIS A 21 PHE 0.028 0.003 PHE B 58 TYR 0.033 0.003 TYR C 302 ARG 0.014 0.001 ARG C 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3790.58 seconds wall clock time: 69 minutes 18.93 seconds (4158.93 seconds total)