Starting phenix.real_space_refine on Wed Jun 11 13:07:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vvn_43563/06_2025/8vvn_43563.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vvn_43563/06_2025/8vvn_43563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vvn_43563/06_2025/8vvn_43563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vvn_43563/06_2025/8vvn_43563.map" model { file = "/net/cci-nas-00/data/ceres_data/8vvn_43563/06_2025/8vvn_43563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vvn_43563/06_2025/8vvn_43563.cif" } resolution = 2.2 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= 1.061 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: 5 Type Number sf(0) Gaussians S 24 5.16 5 Na 2 4.78 5 C 8308 2.51 5 N 2111 2.21 5 O 2490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12935 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 1821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1821 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 4, 'TRANS': 220} Chain: "A" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1831 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 5, 'TRANS': 220} Chain: "C" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1830 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 5, 'TRANS': 226} Chain: "D" Number of atoms: 1821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1821 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain: "E" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1830 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 5, 'TRANS': 226} Chain: "F" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1830 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 5, 'TRANS': 226} Chain: "G" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1830 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 5, 'TRANS': 226} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "F" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "G" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Time building chain proxies: 10.38, per 1000 atoms: 0.80 Number of scatterers: 12935 At special positions: 0 Unit cell: (89.652, 86.037, 182.919, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 Na 2 11.00 O 2490 8.00 N 2111 7.00 C 8308 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.8 seconds 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3010 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 6 sheets defined 70.4% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'B' and resid 19 through 59 removed outlier: 3.733A pdb=" N LYS B 59 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 78 Processing helix chain 'B' and resid 113 through 131 removed outlier: 3.555A pdb=" N LEU B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 removed outlier: 5.869A pdb=" N TRP B 135 " --> pdb=" O ASN B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 177 Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 233 through 241 removed outlier: 3.546A pdb=" N LYS B 241 " --> pdb=" O TYR B 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 19 through 78 removed outlier: 3.817A pdb=" N SER A 23 " --> pdb=" O TRP A 19 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 131 Processing helix chain 'A' and resid 132 through 136 removed outlier: 5.867A pdb=" N TRP A 135 " --> pdb=" O ASN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 177 Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'C' and resid 8 through 13 removed outlier: 3.505A pdb=" N TRP C 11 " --> pdb=" O GLU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 67 removed outlier: 4.174A pdb=" N VAL C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU C 62 " --> pdb=" O LYS C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 89 removed outlier: 4.600A pdb=" N ALA C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLU C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL C 80 " --> pdb=" O GLN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 105 removed outlier: 4.080A pdb=" N GLU C 105 " --> pdb=" O MET C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 removed outlier: 4.013A pdb=" N PHE C 127 " --> pdb=" O ASP C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 134 through 139 removed outlier: 3.704A pdb=" N THR C 138 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU C 139 " --> pdb=" O ASN C 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 134 through 139' Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 145 through 168 removed outlier: 4.753A pdb=" N ASP C 168 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 190 Processing helix chain 'C' and resid 190 through 234 removed outlier: 4.644A pdb=" N THR C 197 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 13 Processing helix chain 'D' and resid 25 through 65 removed outlier: 3.734A pdb=" N ASP D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU D 62 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN D 63 " --> pdb=" O ILE D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 89 removed outlier: 3.972A pdb=" N GLU D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL D 80 " --> pdb=" O GLN D 76 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR D 82 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 84 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 removed outlier: 3.707A pdb=" N PHE D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 127 removed outlier: 3.893A pdb=" N HIS D 126 " --> pdb=" O ASP D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 140 through 168 Proline residue: D 147 - end of helix removed outlier: 4.069A pdb=" N ASP D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 234 removed outlier: 3.798A pdb=" N PHE D 232 " --> pdb=" O ASP D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 13 Processing helix chain 'E' and resid 25 through 67 removed outlier: 3.810A pdb=" N VAL E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU E 62 " --> pdb=" O LYS E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 90 removed outlier: 3.837A pdb=" N VAL E 80 " --> pdb=" O GLN E 76 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR E 82 " --> pdb=" O LYS E 78 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU E 84 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER E 87 " --> pdb=" O GLN E 83 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS E 88 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS E 90 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 105 removed outlier: 3.600A pdb=" N PHE E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU E 105 " --> pdb=" O MET E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 removed outlier: 4.383A pdb=" N HIS E 126 " --> pdb=" O ASP E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 145 through 168 removed outlier: 3.642A pdb=" N ASP E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 195 removed outlier: 3.660A pdb=" N LYS E 192 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE E 193 " --> pdb=" O ASN E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 234 removed outlier: 3.655A pdb=" N LYS E 229 " --> pdb=" O GLU E 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 13 Processing helix chain 'F' and resid 25 through 65 removed outlier: 3.587A pdb=" N LEU F 62 " --> pdb=" O LYS F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 73 Processing helix chain 'F' and resid 74 through 89 removed outlier: 4.745A pdb=" N GLU F 79 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL F 80 " --> pdb=" O GLN F 76 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 106 removed outlier: 3.614A pdb=" N GLU F 105 " --> pdb=" O MET F 101 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 134 through 139 removed outlier: 4.015A pdb=" N GLU F 139 " --> pdb=" O ASN F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 145 Processing helix chain 'F' and resid 145 through 168 removed outlier: 3.678A pdb=" N ASP F 168 " --> pdb=" O LEU F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 234 removed outlier: 3.572A pdb=" N LYS F 229 " --> pdb=" O GLU F 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 13 Processing helix chain 'G' and resid 25 through 66 removed outlier: 4.463A pdb=" N LEU G 62 " --> pdb=" O LYS G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 77 Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.515A pdb=" N GLN G 83 " --> pdb=" O GLU G 79 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU G 84 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS G 88 " --> pdb=" O LEU G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 105 removed outlier: 4.001A pdb=" N GLU G 105 " --> pdb=" O MET G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 127 Processing helix chain 'G' and resid 129 through 134 Processing helix chain 'G' and resid 134 through 139 removed outlier: 4.019A pdb=" N GLU G 139 " --> pdb=" O ASN G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 145 Processing helix chain 'G' and resid 145 through 169 removed outlier: 3.521A pdb=" N LEU G 169 " --> pdb=" O GLY G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 234 Processing sheet with id=AA1, first strand: chain 'B' and resid 84 through 86 removed outlier: 7.041A pdb=" N ARG B 222 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLY B 145 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASP B 224 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL B 143 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG B 226 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL B 141 " --> pdb=" O ARG B 226 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR B 228 " --> pdb=" O ASP B 139 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N SER B 197 " --> pdb=" O ASP B 139 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL B 141 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N SER B 199 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL B 143 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 86 removed outlier: 7.062A pdb=" N ARG A 222 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLY A 145 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP A 224 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL A 143 " --> pdb=" O ASP A 224 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ARG A 226 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL A 141 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR A 228 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 109 through 112 removed outlier: 3.567A pdb=" N VAL C 110 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU C 117 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS C 112 " --> pdb=" O GLN C 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 108 through 111 Processing sheet with id=AA5, first strand: chain 'F' and resid 109 through 112 removed outlier: 3.738A pdb=" N VAL F 110 " --> pdb=" O GLU F 117 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU F 117 " --> pdb=" O VAL F 110 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS F 112 " --> pdb=" O GLN F 115 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN F 115 " --> pdb=" O LYS F 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 107 through 109 853 hydrogen bonds defined for protein. 2469 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: 3.80 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4023 1.34 - 1.45: 1682 1.45 - 1.57: 7289 1.57 - 1.69: 0 1.69 - 1.81: 43 Bond restraints: 13037 Sorted by residual: bond pdb=" C GLU F 67 " pdb=" N PRO F 68 " ideal model delta sigma weight residual 1.337 1.361 -0.025 1.11e-02 8.12e+03 4.87e+00 bond pdb=" CB VAL G 206 " pdb=" CG2 VAL G 206 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.73e+00 bond pdb=" CG PRO C 14 " pdb=" CD PRO C 14 " ideal model delta sigma weight residual 1.503 1.546 -0.043 3.40e-02 8.65e+02 1.62e+00 bond pdb=" CB VAL D 206 " pdb=" CG2 VAL D 206 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.44e+00 bond pdb=" CA ILE E 116 " pdb=" CB ILE E 116 " ideal model delta sigma weight residual 1.533 1.547 -0.014 1.20e-02 6.94e+03 1.38e+00 ... (remaining 13032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 16924 1.33 - 2.65: 569 2.65 - 3.98: 108 3.98 - 5.30: 37 5.30 - 6.63: 3 Bond angle restraints: 17641 Sorted by residual: angle pdb=" N VAL D 137 " pdb=" CA VAL D 137 " pdb=" C VAL D 137 " ideal model delta sigma weight residual 113.53 110.62 2.91 9.80e-01 1.04e+00 8.82e+00 angle pdb=" C ASN B 111 " pdb=" N THR B 112 " pdb=" CA THR B 112 " ideal model delta sigma weight residual 122.61 127.22 -4.61 1.56e+00 4.11e-01 8.74e+00 angle pdb=" CA PRO C 14 " pdb=" N PRO C 14 " pdb=" CD PRO C 14 " ideal model delta sigma weight residual 112.00 108.60 3.40 1.40e+00 5.10e-01 5.89e+00 angle pdb=" N GLU B 49 " pdb=" CA GLU B 49 " pdb=" CB GLU B 49 " ideal model delta sigma weight residual 110.28 113.99 -3.71 1.55e+00 4.16e-01 5.74e+00 angle pdb=" CB GLU B 74 " pdb=" CG GLU B 74 " pdb=" CD GLU B 74 " ideal model delta sigma weight residual 112.60 116.63 -4.03 1.70e+00 3.46e-01 5.62e+00 ... (remaining 17636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 6952 17.12 - 34.25: 656 34.25 - 51.37: 91 51.37 - 68.49: 21 68.49 - 85.61: 21 Dihedral angle restraints: 7741 sinusoidal: 3098 harmonic: 4643 Sorted by residual: dihedral pdb=" CA VAL A 143 " pdb=" C VAL A 143 " pdb=" N GLU A 144 " pdb=" CA GLU A 144 " ideal model delta harmonic sigma weight residual -180.00 -158.23 -21.77 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA ASN D 129 " pdb=" C ASN D 129 " pdb=" N THR D 130 " pdb=" CA THR D 130 " ideal model delta harmonic sigma weight residual 180.00 -160.34 -19.66 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LEU B 194 " pdb=" C LEU B 194 " pdb=" N LEU B 195 " pdb=" CA LEU B 195 " ideal model delta harmonic sigma weight residual 180.00 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 7738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1401 0.041 - 0.082: 551 0.082 - 0.123: 105 0.123 - 0.164: 7 0.164 - 0.205: 3 Chirality restraints: 2067 Sorted by residual: chirality pdb=" CB ILE E 116 " pdb=" CA ILE E 116 " pdb=" CG1 ILE E 116 " pdb=" CG2 ILE E 116 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL C 155 " pdb=" CA VAL C 155 " pdb=" CG1 VAL C 155 " pdb=" CG2 VAL C 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CG LEU D 107 " pdb=" CB LEU D 107 " pdb=" CD1 LEU D 107 " pdb=" CD2 LEU D 107 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 2064 not shown) Planarity restraints: 2199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 13 " 0.051 5.00e-02 4.00e+02 7.60e-02 9.25e+00 pdb=" N PRO C 14 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 153 " 0.013 2.00e-02 2.50e+03 1.38e-02 4.73e+00 pdb=" CG TRP B 153 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP B 153 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 153 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 153 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 153 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 153 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 153 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 153 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 153 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 231 " 0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO B 232 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 232 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 232 " 0.027 5.00e-02 4.00e+02 ... (remaining 2196 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 204 2.66 - 3.22: 12838 3.22 - 3.78: 21232 3.78 - 4.34: 29364 4.34 - 4.90: 46227 Nonbonded interactions: 109865 Sorted by model distance: nonbonded pdb=" NH1 ARG C 141 " pdb=" OE1 GLU F 216 " model vdw 2.098 3.120 nonbonded pdb=" O SER F 87 " pdb=" NZ LYS F 90 " model vdw 2.150 3.120 nonbonded pdb=" ND2 ASN C 120 " pdb=" O PHE C 234 " model vdw 2.176 3.120 nonbonded pdb=" OG SER C 20 " pdb=" O HOH C 701 " model vdw 2.190 3.040 nonbonded pdb=" OG1 THR G 158 " pdb=" OG SER G 198 " model vdw 2.199 3.040 ... (remaining 109860 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 19 through 236) selection = (chain 'B' and resid 19 through 236) } ncs_group { reference = (chain 'C' and resid 5 through 235) selection = (chain 'D' and resid 5 through 235) selection = (chain 'E' and resid 5 through 235) selection = (chain 'F' and resid 5 through 235) selection = (chain 'G' and resid 5 through 235) } 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: 8.420 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: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.660 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 0.052 13037 Z= 0.164 Angle : 0.600 6.631 17641 Z= 0.315 Chirality : 0.042 0.205 2067 Planarity : 0.004 0.076 2199 Dihedral : 13.900 85.614 4731 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.21), residues: 1596 helix: 0.86 (0.16), residues: 1007 sheet: 0.54 (0.73), residues: 51 loop : -1.13 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 153 HIS 0.004 0.001 HIS B 126 PHE 0.020 0.002 PHE E 208 TYR 0.009 0.001 TYR G 47 ARG 0.011 0.001 ARG B 65 Details of bonding type rmsd hydrogen bonds : bond 0.20933 ( 853) hydrogen bonds : angle 6.70164 ( 2469) covalent geometry : bond 0.00396 (13037) covalent geometry : angle 0.60026 (17641) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.583 Fit side-chains REVERT: G 22 HIS cc_start: 0.7473 (t70) cc_final: 0.6864 (m-70) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 1.6954 time to fit residues: 314.9961 Evaluate side-chains 139 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.5980 chunk 120 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 75 optimal weight: 0.3980 chunk 92 optimal weight: 0.5980 chunk 144 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 GLN D 189 ASN D 209 ASN E 83 GLN E 163 GLN E 181 GLN F 181 GLN G 120 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.201120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.130606 restraints weight = 11863.393| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.63 r_work: 0.3403 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13037 Z= 0.150 Angle : 0.575 6.154 17641 Z= 0.308 Chirality : 0.041 0.188 2067 Planarity : 0.004 0.050 2199 Dihedral : 4.407 20.163 1696 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.88 % Favored : 97.06 % Rotamer: Outliers : 0.93 % Allowed : 5.46 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1596 helix: 1.58 (0.16), residues: 1029 sheet: 0.34 (0.75), residues: 47 loop : -1.01 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 153 HIS 0.003 0.001 HIS E 22 PHE 0.021 0.002 PHE D 98 TYR 0.017 0.002 TYR G 47 ARG 0.007 0.001 ARG G 220 Details of bonding type rmsd hydrogen bonds : bond 0.05546 ( 853) hydrogen bonds : angle 4.37682 ( 2469) covalent geometry : bond 0.00324 (13037) covalent geometry : angle 0.57460 (17641) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 1.379 Fit side-chains REVERT: B 75 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: B 133 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: A 60 LYS cc_start: 0.8297 (tptp) cc_final: 0.8010 (tttp) outliers start: 13 outliers final: 1 residues processed: 156 average time/residue: 1.5591 time to fit residues: 261.0224 Evaluate side-chains 145 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain C residue 212 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 GLN A 150 ASN C 209 ASN E 181 GLN G 22 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.199720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.129026 restraints weight = 11961.929| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.61 r_work: 0.3387 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13037 Z= 0.155 Angle : 0.541 6.317 17641 Z= 0.291 Chirality : 0.041 0.158 2067 Planarity : 0.003 0.044 2199 Dihedral : 4.331 20.507 1696 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.51 % Favored : 97.43 % Rotamer: Outliers : 0.86 % Allowed : 8.26 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1596 helix: 1.82 (0.16), residues: 1021 sheet: 0.33 (0.74), residues: 47 loop : -1.06 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 200 HIS 0.003 0.001 HIS E 22 PHE 0.017 0.002 PHE D 98 TYR 0.016 0.001 TYR D 47 ARG 0.008 0.001 ARG B 119 Details of bonding type rmsd hydrogen bonds : bond 0.05196 ( 853) hydrogen bonds : angle 4.13528 ( 2469) covalent geometry : bond 0.00343 (13037) covalent geometry : angle 0.54052 (17641) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 1.491 Fit side-chains REVERT: B 133 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: A 65 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.7256 (ttm170) REVERT: C 102 GLU cc_start: 0.6242 (tp30) cc_final: 0.6023 (tp30) outliers start: 12 outliers final: 1 residues processed: 155 average time/residue: 1.7142 time to fit residues: 286.3379 Evaluate side-chains 138 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain C residue 212 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 58 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 GLN D 24 GLN E 60 ASN E 181 GLN G 22 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.200936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130277 restraints weight = 11753.590| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.62 r_work: 0.3404 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13037 Z= 0.131 Angle : 0.503 6.445 17641 Z= 0.271 Chirality : 0.039 0.148 2067 Planarity : 0.003 0.047 2199 Dihedral : 4.193 20.477 1696 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.38 % Favored : 97.56 % Rotamer: Outliers : 1.08 % Allowed : 9.26 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.21), residues: 1596 helix: 1.96 (0.16), residues: 1020 sheet: 0.32 (0.75), residues: 47 loop : -1.01 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 200 HIS 0.003 0.001 HIS E 22 PHE 0.013 0.001 PHE D 98 TYR 0.015 0.001 TYR G 47 ARG 0.009 0.000 ARG B 119 Details of bonding type rmsd hydrogen bonds : bond 0.04708 ( 853) hydrogen bonds : angle 3.96980 ( 2469) covalent geometry : bond 0.00282 (13037) covalent geometry : angle 0.50330 (17641) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 1.491 Fit side-chains REVERT: B 49 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7710 (mt-10) REVERT: B 75 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: B 133 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7640 (mt-10) REVERT: A 65 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.7231 (ttm170) REVERT: C 102 GLU cc_start: 0.6331 (tp30) cc_final: 0.6129 (tp30) outliers start: 15 outliers final: 2 residues processed: 156 average time/residue: 1.5175 time to fit residues: 255.2476 Evaluate side-chains 146 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain G residue 151 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 157 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 119 optimal weight: 0.3980 chunk 52 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 55 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 GLN E 24 GLN E 181 GLN F 24 GLN G 181 GLN G 209 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.200857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130246 restraints weight = 11881.276| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.62 r_work: 0.3403 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13037 Z= 0.128 Angle : 0.491 6.549 17641 Z= 0.264 Chirality : 0.039 0.143 2067 Planarity : 0.003 0.047 2199 Dihedral : 4.117 20.750 1696 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.51 % Favored : 97.43 % Rotamer: Outliers : 1.08 % Allowed : 10.62 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.21), residues: 1596 helix: 2.07 (0.16), residues: 1018 sheet: 0.37 (0.74), residues: 53 loop : -1.00 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 200 HIS 0.002 0.000 HIS B 146 PHE 0.014 0.001 PHE D 232 TYR 0.014 0.001 TYR D 47 ARG 0.008 0.000 ARG B 119 Details of bonding type rmsd hydrogen bonds : bond 0.04598 ( 853) hydrogen bonds : angle 3.89363 ( 2469) covalent geometry : bond 0.00275 (13037) covalent geometry : angle 0.49121 (17641) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 1.573 Fit side-chains REVERT: B 75 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: B 133 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: B 157 LYS cc_start: 0.7621 (mmmm) cc_final: 0.7089 (mmmt) REVERT: B 214 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7029 (mm-30) REVERT: A 65 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7242 (ttm170) REVERT: A 214 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6796 (tp30) outliers start: 15 outliers final: 3 residues processed: 155 average time/residue: 1.5424 time to fit residues: 257.5545 Evaluate side-chains 148 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain G residue 151 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 GLN E 181 GLN G 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.199071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.128984 restraints weight = 11943.281| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.59 r_work: 0.3384 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13037 Z= 0.149 Angle : 0.513 6.551 17641 Z= 0.275 Chirality : 0.040 0.140 2067 Planarity : 0.003 0.051 2199 Dihedral : 4.175 20.939 1696 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 1.01 % Allowed : 10.98 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.21), residues: 1596 helix: 2.00 (0.16), residues: 1021 sheet: 0.36 (0.73), residues: 53 loop : -0.98 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 200 HIS 0.003 0.001 HIS E 22 PHE 0.014 0.001 PHE C 33 TYR 0.015 0.001 TYR D 47 ARG 0.009 0.001 ARG B 119 Details of bonding type rmsd hydrogen bonds : bond 0.04818 ( 853) hydrogen bonds : angle 3.93332 ( 2469) covalent geometry : bond 0.00330 (13037) covalent geometry : angle 0.51307 (17641) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 1.485 Fit side-chains REVERT: B 75 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7345 (tm-30) REVERT: B 133 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: A 65 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.7303 (ttm170) REVERT: D 24 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8537 (mp10) outliers start: 14 outliers final: 6 residues processed: 160 average time/residue: 1.4790 time to fit residues: 255.0509 Evaluate side-chains 158 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain G residue 151 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 41 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 137 optimal weight: 0.3980 chunk 136 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 GLN E 24 GLN E 181 GLN G 22 HIS G 181 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.200137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.129544 restraints weight = 11881.697| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.60 r_work: 0.3394 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13037 Z= 0.136 Angle : 0.498 6.619 17641 Z= 0.268 Chirality : 0.039 0.141 2067 Planarity : 0.003 0.054 2199 Dihedral : 4.125 20.933 1696 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.37 % Rotamer: Outliers : 1.36 % Allowed : 11.49 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.21), residues: 1596 helix: 2.06 (0.16), residues: 1023 sheet: 0.34 (0.73), residues: 53 loop : -0.98 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 200 HIS 0.002 0.000 HIS B 82 PHE 0.013 0.001 PHE C 33 TYR 0.015 0.001 TYR A 190 ARG 0.010 0.000 ARG B 119 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 853) hydrogen bonds : angle 3.88743 ( 2469) covalent geometry : bond 0.00298 (13037) covalent geometry : angle 0.49826 (17641) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 1.418 Fit side-chains REVERT: B 75 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: B 133 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7650 (mt-10) REVERT: A 65 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7257 (ttm170) REVERT: D 24 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8558 (mp10) outliers start: 19 outliers final: 6 residues processed: 165 average time/residue: 1.6052 time to fit residues: 288.9755 Evaluate side-chains 161 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain G residue 151 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 GLN E 181 GLN G 22 HIS G 209 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.199606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.128882 restraints weight = 11915.326| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.62 r_work: 0.3386 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13037 Z= 0.146 Angle : 0.517 6.627 17641 Z= 0.277 Chirality : 0.039 0.139 2067 Planarity : 0.003 0.057 2199 Dihedral : 4.156 21.001 1696 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.69 % Favored : 97.24 % Rotamer: Outliers : 0.86 % Allowed : 12.63 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.21), residues: 1596 helix: 2.04 (0.16), residues: 1023 sheet: 0.35 (0.73), residues: 53 loop : -0.98 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 200 HIS 0.003 0.001 HIS E 22 PHE 0.014 0.001 PHE C 33 TYR 0.014 0.001 TYR D 47 ARG 0.011 0.001 ARG B 119 Details of bonding type rmsd hydrogen bonds : bond 0.04733 ( 853) hydrogen bonds : angle 3.90499 ( 2469) covalent geometry : bond 0.00323 (13037) covalent geometry : angle 0.51681 (17641) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 1.537 Fit side-chains REVERT: B 75 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7322 (tm-30) REVERT: B 133 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7650 (mt-10) REVERT: B 217 ARG cc_start: 0.7648 (mtm180) cc_final: 0.7382 (mtm180) REVERT: A 65 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7286 (ttm170) REVERT: D 24 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8585 (mp10) outliers start: 12 outliers final: 7 residues processed: 163 average time/residue: 1.5563 time to fit residues: 273.2682 Evaluate side-chains 163 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain G residue 151 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 30 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 158 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 150 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 GLN E 181 GLN G 22 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.199823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.129386 restraints weight = 11851.343| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.60 r_work: 0.3392 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13037 Z= 0.139 Angle : 0.513 6.655 17641 Z= 0.274 Chirality : 0.039 0.139 2067 Planarity : 0.003 0.058 2199 Dihedral : 4.129 20.988 1696 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 0.93 % Allowed : 12.71 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.21), residues: 1596 helix: 2.09 (0.16), residues: 1023 sheet: 0.35 (0.73), residues: 53 loop : -0.96 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 200 HIS 0.004 0.001 HIS E 22 PHE 0.013 0.001 PHE C 33 TYR 0.020 0.001 TYR A 190 ARG 0.013 0.001 ARG B 119 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 853) hydrogen bonds : angle 3.88467 ( 2469) covalent geometry : bond 0.00307 (13037) covalent geometry : angle 0.51253 (17641) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 1.435 Fit side-chains REVERT: B 75 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7330 (tm-30) REVERT: B 133 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: A 65 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.7253 (ttm170) REVERT: A 214 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7107 (tm-30) outliers start: 13 outliers final: 7 residues processed: 164 average time/residue: 1.5247 time to fit residues: 269.3952 Evaluate side-chains 159 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain G residue 151 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 45 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 GLN E 24 GLN E 181 GLN G 22 HIS G 181 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.198832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.128324 restraints weight = 11798.592| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.60 r_work: 0.3378 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13037 Z= 0.160 Angle : 0.537 6.641 17641 Z= 0.287 Chirality : 0.040 0.139 2067 Planarity : 0.003 0.063 2199 Dihedral : 4.212 21.103 1696 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.18 % Rotamer: Outliers : 1.01 % Allowed : 12.78 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.21), residues: 1596 helix: 2.00 (0.16), residues: 1028 sheet: 0.35 (0.72), residues: 53 loop : -0.98 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 200 HIS 0.002 0.001 HIS B 82 PHE 0.014 0.001 PHE C 33 TYR 0.014 0.001 TYR D 47 ARG 0.014 0.001 ARG B 119 Details of bonding type rmsd hydrogen bonds : bond 0.04874 ( 853) hydrogen bonds : angle 3.94223 ( 2469) covalent geometry : bond 0.00359 (13037) covalent geometry : angle 0.53694 (17641) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 1.526 Fit side-chains REVERT: B 75 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: B 133 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7644 (mt-10) REVERT: A 65 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.7309 (ttm170) REVERT: D 24 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8541 (mp10) REVERT: F 102 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6141 (mm-30) outliers start: 14 outliers final: 7 residues processed: 163 average time/residue: 1.5332 time to fit residues: 268.8691 Evaluate side-chains 163 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain G residue 151 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 21 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 121 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.0060 chunk 12 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 GLN E 181 GLN G 22 HIS G 181 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.199985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.129830 restraints weight = 11851.970| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.61 r_work: 0.3400 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13037 Z= 0.129 Angle : 0.508 6.679 17641 Z= 0.272 Chirality : 0.039 0.141 2067 Planarity : 0.003 0.063 2199 Dihedral : 4.119 21.033 1696 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.37 % Rotamer: Outliers : 0.72 % Allowed : 13.21 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.21), residues: 1596 helix: 2.11 (0.16), residues: 1028 sheet: 0.34 (0.74), residues: 53 loop : -0.92 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 200 HIS 0.003 0.000 HIS E 22 PHE 0.013 0.001 PHE C 33 TYR 0.013 0.001 TYR D 47 ARG 0.014 0.001 ARG B 119 Details of bonding type rmsd hydrogen bonds : bond 0.04522 ( 853) hydrogen bonds : angle 3.86323 ( 2469) covalent geometry : bond 0.00280 (13037) covalent geometry : angle 0.50849 (17641) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15618.94 seconds wall clock time: 265 minutes 56.82 seconds (15956.82 seconds total)