Starting phenix.real_space_refine on Thu Sep 18 01:09:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vvn_43563/09_2025/8vvn_43563.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vvn_43563/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vvn_43563/09_2025/8vvn_43563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vvn_43563/09_2025/8vvn_43563.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vvn_43563/09_2025/8vvn_43563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vvn_43563/09_2025/8vvn_43563.map" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.08, per 1000 atoms: 0.24 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: 1.07 Conformation dependent library (CDL) restraints added in 630.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.33 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: 2.02 Time building geometry restraints manager: 1.42 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: 0.010 Normalize map: mean=0, sd=1: 9.900 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.930 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 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:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.780 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG B 65 TYR 0.009 0.001 TYR G 47 PHE 0.020 0.002 PHE E 208 TRP 0.036 0.002 TRP B 153 HIS 0.004 0.001 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00396 (13037) covalent geometry : angle 0.60026 (17641) hydrogen bonds : bond 0.20933 ( 853) hydrogen bonds : angle 6.70164 ( 2469) *********************** 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 : 0.491 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: 0.8300 time to fit residues: 153.6777 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 : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.4302 r_free = 0.4302 target = 0.199416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.128436 restraints weight = 11836.039| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.62 r_work: 0.3379 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1205 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= 0.188 Angle : 0.613 6.225 17641 Z= 0.328 Chirality : 0.043 0.202 2067 Planarity : 0.004 0.050 2199 Dihedral : 4.547 21.239 1696 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.88 % Favored : 97.06 % Rotamer: Outliers : 1.01 % Allowed : 5.96 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.21), residues: 1596 helix: 1.51 (0.16), residues: 1017 sheet: 0.33 (0.74), residues: 47 loop : -1.09 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 65 TYR 0.016 0.002 TYR G 47 PHE 0.022 0.002 PHE D 98 TRP 0.016 0.002 TRP B 153 HIS 0.004 0.001 HIS E 22 Details of bonding type rmsd covalent geometry : bond 0.00425 (13037) covalent geometry : angle 0.61306 (17641) hydrogen bonds : bond 0.05787 ( 853) hydrogen bonds : angle 4.41077 ( 2469) *********************** 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 158 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.467 Fit side-chains REVERT: B 75 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: B 133 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7661 (mt-10) outliers start: 14 outliers final: 1 residues processed: 151 average time/residue: 0.7604 time to fit residues: 122.5176 Evaluate side-chains 143 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 111 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 126 optimal weight: 0.0010 chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 0.0870 chunk 132 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 64 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 overall best weight: 0.4164 ------------------------------------------------------------------------------- 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 D 24 GLN D 181 GLN E 181 GLN G 22 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.201348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.131235 restraints weight = 12047.605| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.62 r_work: 0.3418 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13037 Z= 0.123 Angle : 0.505 6.353 17641 Z= 0.273 Chirality : 0.039 0.159 2067 Planarity : 0.003 0.044 2199 Dihedral : 4.239 20.320 1696 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.63 % Favored : 97.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.21), residues: 1596 helix: 1.91 (0.16), residues: 1020 sheet: 0.31 (0.76), residues: 47 loop : -1.04 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 119 TYR 0.015 0.001 TYR G 47 PHE 0.016 0.001 PHE D 98 TRP 0.013 0.001 TRP F 200 HIS 0.002 0.000 HIS E 22 Details of bonding type rmsd covalent geometry : bond 0.00256 (13037) covalent geometry : angle 0.50525 (17641) hydrogen bonds : bond 0.04813 ( 853) hydrogen bonds : angle 4.06479 ( 2469) *********************** 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 162 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.519 Fit side-chains REVERT: B 133 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: G 22 HIS cc_start: 0.7788 (t70) cc_final: 0.6653 (m-70) outliers start: 12 outliers final: 2 residues processed: 154 average time/residue: 0.7012 time to fit residues: 116.0486 Evaluate side-chains 141 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 138 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain G residue 151 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 62 optimal weight: 0.5980 chunk 90 optimal weight: 0.0980 chunk 105 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 68 optimal weight: 0.0470 chunk 147 optimal weight: 5.9990 chunk 119 optimal weight: 0.0170 overall best weight: 0.3116 ------------------------------------------------------------------------------- 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 E 6 GLN E 60 ASN E 181 GLN F 24 GLN G 24 GLN G 181 GLN G 209 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.202612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132982 restraints weight = 11963.437| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.61 r_work: 0.3439 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13037 Z= 0.112 Angle : 0.472 6.488 17641 Z= 0.255 Chirality : 0.038 0.144 2067 Planarity : 0.003 0.046 2199 Dihedral : 4.052 20.225 1696 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.38 % Favored : 97.56 % Rotamer: Outliers : 0.72 % Allowed : 9.48 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.21), residues: 1596 helix: 2.09 (0.16), residues: 1022 sheet: 0.40 (0.76), residues: 53 loop : -1.05 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 119 TYR 0.014 0.001 TYR G 47 PHE 0.014 0.001 PHE D 232 TRP 0.013 0.001 TRP D 200 HIS 0.002 0.000 HIS G 22 Details of bonding type rmsd covalent geometry : bond 0.00229 (13037) covalent geometry : angle 0.47163 (17641) hydrogen bonds : bond 0.04329 ( 853) hydrogen bonds : angle 3.85406 ( 2469) *********************** 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 168 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 0.518 Fit side-chains REVERT: B 78 LYS cc_start: 0.7497 (mtmt) cc_final: 0.7201 (mttp) REVERT: B 133 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: A 60 LYS cc_start: 0.8265 (tptp) cc_final: 0.7949 (ttmt) REVERT: A 214 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6685 (tp30) REVERT: C 102 GLU cc_start: 0.6079 (tp30) cc_final: 0.5878 (tp30) REVERT: G 22 HIS cc_start: 0.7486 (t70) cc_final: 0.6480 (m-70) outliers start: 10 outliers final: 0 residues processed: 163 average time/residue: 0.6721 time to fit residues: 118.1344 Evaluate side-chains 146 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 77 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 24 GLN G 181 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.199979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128992 restraints weight = 11963.877| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.61 r_work: 0.3386 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1779 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= 0.152 Angle : 0.513 6.524 17641 Z= 0.276 Chirality : 0.040 0.140 2067 Planarity : 0.003 0.049 2199 Dihedral : 4.162 20.755 1696 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.51 % Favored : 97.43 % Rotamer: Outliers : 1.08 % Allowed : 10.55 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.21), residues: 1596 helix: 2.03 (0.16), residues: 1020 sheet: 0.30 (0.73), residues: 53 loop : -1.00 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 119 TYR 0.016 0.001 TYR D 47 PHE 0.014 0.002 PHE C 33 TRP 0.011 0.001 TRP F 200 HIS 0.004 0.001 HIS G 22 Details of bonding type rmsd covalent geometry : bond 0.00337 (13037) covalent geometry : angle 0.51345 (17641) hydrogen bonds : bond 0.04859 ( 853) hydrogen bonds : angle 3.93734 ( 2469) *********************** 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 167 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.458 Fit side-chains REVERT: B 75 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: B 78 LYS cc_start: 0.7474 (mtmt) cc_final: 0.7154 (mttp) REVERT: B 133 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7638 (mt-10) REVERT: B 214 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7039 (mm-30) REVERT: C 102 GLU cc_start: 0.6189 (tp30) cc_final: 0.5981 (tp30) REVERT: G 22 HIS cc_start: 0.7695 (t70) cc_final: 0.7338 (t-170) REVERT: G 24 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7874 (mp-120) outliers start: 15 outliers final: 4 residues processed: 159 average time/residue: 0.7285 time to fit residues: 124.1553 Evaluate side-chains 149 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 155 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain G residue 24 GLN 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 9 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 GLN A 150 ASN E 181 GLN F 24 GLN G 24 GLN G 181 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.200162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.129363 restraints weight = 11785.220| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.62 r_work: 0.3387 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13037 Z= 0.140 Angle : 0.499 6.594 17641 Z= 0.269 Chirality : 0.039 0.141 2067 Planarity : 0.003 0.051 2199 Dihedral : 4.122 20.915 1696 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.37 % Rotamer: Outliers : 1.01 % Allowed : 11.56 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.21), residues: 1596 helix: 2.06 (0.16), residues: 1020 sheet: 0.27 (0.73), residues: 53 loop : -0.97 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 119 TYR 0.014 0.001 TYR D 47 PHE 0.013 0.001 PHE C 33 TRP 0.013 0.001 TRP D 200 HIS 0.004 0.001 HIS G 22 Details of bonding type rmsd covalent geometry : bond 0.00307 (13037) covalent geometry : angle 0.49950 (17641) hydrogen bonds : bond 0.04703 ( 853) hydrogen bonds : angle 3.89521 ( 2469) *********************** 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 166 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.493 Fit side-chains REVERT: B 75 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: B 133 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7626 (mt-10) REVERT: B 214 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6984 (mm-30) REVERT: A 214 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6667 (tp30) REVERT: D 24 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8555 (mp10) outliers start: 14 outliers final: 5 residues processed: 161 average time/residue: 0.6729 time to fit residues: 116.8180 Evaluate side-chains 150 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 143 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 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 77 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 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 A 150 ASN A 159 ASN E 181 GLN G 22 HIS G 209 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.200002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.129327 restraints weight = 11844.273| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.62 r_work: 0.3392 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13037 Z= 0.138 Angle : 0.500 6.632 17641 Z= 0.268 Chirality : 0.039 0.140 2067 Planarity : 0.003 0.054 2199 Dihedral : 4.106 20.913 1696 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.69 % Favored : 97.24 % Rotamer: Outliers : 1.29 % Allowed : 12.06 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.21), residues: 1596 helix: 2.07 (0.16), residues: 1023 sheet: 0.28 (0.73), residues: 53 loop : -0.96 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 119 TYR 0.014 0.001 TYR D 47 PHE 0.013 0.001 PHE C 33 TRP 0.012 0.001 TRP D 200 HIS 0.003 0.001 HIS E 22 Details of bonding type rmsd covalent geometry : bond 0.00302 (13037) covalent geometry : angle 0.49966 (17641) hydrogen bonds : bond 0.04656 ( 853) hydrogen bonds : angle 3.87447 ( 2469) *********************** 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 169 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.471 Fit side-chains REVERT: B 75 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: B 133 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: B 214 GLU cc_start: 0.7259 (mm-30) cc_final: 0.7004 (mm-30) REVERT: D 24 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8581 (mp10) outliers start: 18 outliers final: 6 residues processed: 163 average time/residue: 0.7176 time to fit residues: 125.5513 Evaluate side-chains 155 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 68 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 126 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 133 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 45 optimal weight: 0.0470 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.4320 r_free = 0.4320 target = 0.201101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.130810 restraints weight = 11803.116| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.61 r_work: 0.3411 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13037 Z= 0.119 Angle : 0.482 6.655 17641 Z= 0.258 Chirality : 0.038 0.142 2067 Planarity : 0.003 0.057 2199 Dihedral : 4.013 20.693 1696 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.38 % Favored : 97.56 % Rotamer: Outliers : 0.79 % Allowed : 12.63 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.21), residues: 1596 helix: 2.14 (0.16), residues: 1030 sheet: 0.32 (0.74), residues: 53 loop : -0.98 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 119 TYR 0.013 0.001 TYR G 47 PHE 0.012 0.001 PHE D 232 TRP 0.013 0.001 TRP D 200 HIS 0.003 0.000 HIS E 22 Details of bonding type rmsd covalent geometry : bond 0.00253 (13037) covalent geometry : angle 0.48162 (17641) hydrogen bonds : bond 0.04382 ( 853) hydrogen bonds : angle 3.79853 ( 2469) *********************** 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 168 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.438 Fit side-chains REVERT: B 75 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: B 133 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7624 (mt-10) REVERT: B 214 GLU cc_start: 0.7290 (mm-30) cc_final: 0.7049 (mm-30) REVERT: B 217 ARG cc_start: 0.7588 (mtm180) cc_final: 0.7293 (mtm180) REVERT: A 24 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7311 (t0) REVERT: A 214 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7099 (tm-30) REVERT: D 24 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8587 (mp10) outliers start: 11 outliers final: 5 residues processed: 165 average time/residue: 0.6880 time to fit residues: 122.0856 Evaluate side-chains 159 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 112 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 212 GLU 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 115 optimal weight: 0.2980 chunk 29 optimal weight: 0.0980 chunk 76 optimal weight: 8.9990 chunk 45 optimal weight: 0.0470 chunk 33 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 0.2980 chunk 12 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 overall best weight: 0.2478 ------------------------------------------------------------------------------- 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 = 0.4338 r_free = 0.4338 target = 0.202915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.133334 restraints weight = 12009.518| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.62 r_work: 0.3443 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13037 Z= 0.105 Angle : 0.461 6.680 17641 Z= 0.248 Chirality : 0.037 0.138 2067 Planarity : 0.003 0.060 2199 Dihedral : 3.882 20.270 1696 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.49 % Rotamer: Outliers : 0.79 % Allowed : 13.07 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.21), residues: 1596 helix: 2.27 (0.16), residues: 1033 sheet: 0.41 (0.77), residues: 53 loop : -1.02 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 119 TYR 0.012 0.001 TYR G 47 PHE 0.012 0.001 PHE D 232 TRP 0.014 0.001 TRP D 200 HIS 0.002 0.000 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00215 (13037) covalent geometry : angle 0.46098 (17641) hydrogen bonds : bond 0.04055 ( 853) hydrogen bonds : angle 3.70293 ( 2469) *********************** 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 169 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 0.450 Fit side-chains REVERT: B 133 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7626 (mt-10) REVERT: D 24 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8602 (mp10) REVERT: G 22 HIS cc_start: 0.7771 (t70) cc_final: 0.6620 (m-70) outliers start: 11 outliers final: 6 residues processed: 167 average time/residue: 0.6665 time to fit residues: 120.2388 Evaluate side-chains 154 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 GLU 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 151 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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** B 210 GLN A 50 GLN A 150 ASN E 181 GLN E 209 ASN F 24 GLN G 163 GLN G 181 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.198250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.127047 restraints weight = 11792.193| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.61 r_work: 0.3364 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13037 Z= 0.205 Angle : 0.572 6.596 17641 Z= 0.305 Chirality : 0.042 0.146 2067 Planarity : 0.004 0.063 2199 Dihedral : 4.243 21.296 1696 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.37 % Rotamer: Outliers : 0.86 % Allowed : 13.78 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.21), residues: 1596 helix: 2.03 (0.16), residues: 1023 sheet: 0.60 (0.73), residues: 51 loop : -0.94 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 119 TYR 0.020 0.002 TYR A 190 PHE 0.017 0.002 PHE A 22 TRP 0.016 0.002 TRP F 200 HIS 0.005 0.001 HIS E 22 Details of bonding type rmsd covalent geometry : bond 0.00471 (13037) covalent geometry : angle 0.57204 (17641) hydrogen bonds : bond 0.05177 ( 853) hydrogen bonds : angle 3.99159 ( 2469) ********************** 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 162 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.516 Fit side-chains REVERT: B 133 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: B 210 GLN cc_start: 0.7816 (tt0) cc_final: 0.7410 (mt0) REVERT: B 217 ARG cc_start: 0.7667 (mtm180) cc_final: 0.7420 (mtm180) REVERT: D 24 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8560 (mp10) REVERT: F 101 MET cc_start: 0.4680 (OUTLIER) cc_final: 0.3132 (mpt) REVERT: F 102 GLU cc_start: 0.6581 (mt-10) cc_final: 0.6095 (mm-30) outliers start: 12 outliers final: 7 residues processed: 158 average time/residue: 0.7099 time to fit residues: 120.5954 Evaluate side-chains 148 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 179 ASN 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 F residue 101 MET 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 18 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 137 optimal weight: 0.4980 chunk 106 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 chunk 123 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 90 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 E 181 GLN E 209 ASN F 24 GLN G 22 HIS G 181 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.200386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130142 restraints weight = 11803.547| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.61 r_work: 0.3404 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13037 Z= 0.125 Angle : 0.495 6.678 17641 Z= 0.266 Chirality : 0.039 0.141 2067 Planarity : 0.003 0.063 2199 Dihedral : 4.065 21.227 1696 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.19 % Favored : 97.74 % Rotamer: Outliers : 0.65 % Allowed : 13.57 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.21), residues: 1596 helix: 2.14 (0.16), residues: 1030 sheet: 0.33 (0.73), residues: 53 loop : -0.91 (0.29), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 119 TYR 0.013 0.001 TYR D 47 PHE 0.013 0.001 PHE C 33 TRP 0.013 0.001 TRP F 200 HIS 0.003 0.000 HIS E 22 Details of bonding type rmsd covalent geometry : bond 0.00270 (13037) covalent geometry : angle 0.49460 (17641) hydrogen bonds : bond 0.04447 ( 853) hydrogen bonds : angle 3.84417 ( 2469) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7392.26 seconds wall clock time: 126 minutes 7.27 seconds (7567.27 seconds total)