Starting phenix.real_space_refine on Mon Jul 28 10:45:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ntm_12591/07_2025/7ntm_12591.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ntm_12591/07_2025/7ntm_12591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ntm_12591/07_2025/7ntm_12591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ntm_12591/07_2025/7ntm_12591.map" model { file = "/net/cci-nas-00/data/ceres_data/7ntm_12591/07_2025/7ntm_12591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ntm_12591/07_2025/7ntm_12591.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 Zn 8 6.06 5 S 56 5.16 5 C 6556 2.51 5 N 1760 2.21 5 O 1956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10336 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2582 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "B" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2582 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "D" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2582 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "C" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2582 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 340 SG CYS A 43 38.557 22.324 26.956 1.00 61.37 S ATOM 1159 SG CYS A 153 39.151 27.004 28.663 1.00 52.86 S ATOM 766 SG CYS A 100 35.384 34.553 48.913 1.00 63.83 S ATOM 793 SG CYS A 103 35.197 35.182 45.606 1.00 58.40 S ATOM 851 SG CYS A 111 33.407 32.254 46.328 1.00 56.85 S ATOM 2922 SG CYS B 43 75.521 22.601 58.159 1.00 59.45 S ATOM 3741 SG CYS B 153 75.027 26.886 56.389 1.00 52.44 S ATOM 3348 SG CYS B 100 78.374 35.166 36.250 1.00 64.62 S ATOM 3375 SG CYS B 103 79.375 34.932 39.507 1.00 56.68 S ATOM 3433 SG CYS B 111 80.669 32.247 38.640 1.00 56.55 S ATOM 5504 SG CYS D 43 75.607 62.548 27.015 1.00 59.46 S ATOM 6323 SG CYS D 153 75.027 58.119 28.612 1.00 51.08 S ATOM 5911 SG CYS D 97 81.654 50.042 47.764 1.00 61.19 S ATOM 5930 SG CYS D 100 78.101 50.395 48.840 1.00 65.41 S ATOM 5957 SG CYS D 103 79.309 49.924 45.663 1.00 57.83 S ATOM 6015 SG CYS D 111 80.737 52.740 46.512 1.00 55.09 S ATOM 8086 SG CYS C 43 38.698 62.436 58.188 1.00 59.60 S ATOM 8905 SG CYS C 153 39.118 58.117 56.393 1.00 51.26 S ATOM 8512 SG CYS C 100 35.947 50.617 36.389 1.00 74.89 S ATOM 8539 SG CYS C 103 34.816 49.669 39.226 1.00 55.83 S ATOM 8597 SG CYS C 111 33.383 52.792 38.450 1.00 55.10 S Time building chain proxies: 8.20, per 1000 atoms: 0.79 Number of scatterers: 10336 At special positions: 0 Unit cell: (114.761, 85.6152, 85.6152, 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) Zn 8 29.99 S 56 16.00 O 1956 8.00 N 1760 7.00 C 6556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS D 277 " - pdb=" SG CYS C 277 " distance=2.59 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: 2.70 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 153 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 66 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 111 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 100 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 103 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 66 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 153 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 43 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 103 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 100 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 111 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 66 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 43 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 153 " pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 103 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 100 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 111 " pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" NE2 HIS D 66 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 43 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 153 " pdb=" ZN D 402 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 97 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 103 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 111 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 100 " Number of angles added : 6 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 15 sheets defined 33.1% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 43 through 52 removed outlier: 3.993A pdb=" N LEU A 47 " --> pdb=" O CYS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 149 through 152 Processing helix chain 'A' and resid 153 through 166 Processing helix chain 'A' and resid 180 through 193 removed outlier: 3.970A pdb=" N LEU A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.580A pdb=" N ALA A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 258 Processing helix chain 'A' and resid 279 through 287 removed outlier: 3.700A pdb=" N GLN A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 311 Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.613A pdb=" N CYS B 111 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 152 Processing helix chain 'B' and resid 153 through 164 Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.913A pdb=" N LEU B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 226 through 235 removed outlier: 3.600A pdb=" N ALA B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 279 through 287 removed outlier: 3.852A pdb=" N GLN B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 324 through 335 removed outlier: 4.090A pdb=" N GLU B 330 " --> pdb=" O PRO B 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 52 Processing helix chain 'D' and resid 107 through 111 removed outlier: 3.553A pdb=" N CYS D 111 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 152 Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 180 through 193 removed outlier: 4.061A pdb=" N LEU D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 226 through 235 removed outlier: 3.549A pdb=" N ALA D 230 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 258 Processing helix chain 'D' and resid 279 through 287 removed outlier: 3.699A pdb=" N GLN D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 311 Processing helix chain 'D' and resid 324 through 335 removed outlier: 4.102A pdb=" N GLU D 330 " --> pdb=" O PRO D 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 52 removed outlier: 4.126A pdb=" N LEU C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 105 removed outlier: 3.721A pdb=" N LEU C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.828A pdb=" N CYS C 111 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 152 Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'C' and resid 180 through 193 removed outlier: 4.044A pdb=" N LEU C 185 " --> pdb=" O GLY C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 214 Processing helix chain 'C' and resid 226 through 235 removed outlier: 3.636A pdb=" N ALA C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 258 removed outlier: 3.570A pdb=" N ILE C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 287 removed outlier: 3.828A pdb=" N GLN C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 311 Processing helix chain 'C' and resid 324 through 335 removed outlier: 4.081A pdb=" N GLU C 330 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 24 removed outlier: 3.637A pdb=" N LEU A 62 " --> pdb=" O PHE A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 132 removed outlier: 6.542A pdb=" N LEU A 33 " --> pdb=" O MET A 75 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N MET A 75 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE A 35 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL A 73 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL A 37 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A 71 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU A 67 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR A 87 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 132 removed outlier: 5.921A pdb=" N LYS A 318 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASP A 344 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 320 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 220 removed outlier: 6.814A pdb=" N VAL A 197 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ILE A 219 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY A 199 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP A 172 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS A 240 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL A 266 " --> pdb=" O HIS A 240 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A 242 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS B 240 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N VAL B 266 " --> pdb=" O HIS B 240 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 242 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP B 172 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 197 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ILE B 219 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY B 199 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 24 removed outlier: 3.525A pdb=" N LYS B 21 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 8 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 11 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B 62 " --> pdb=" O PHE B 11 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.381A pdb=" N ASN B 36 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 72 " --> pdb=" O ASN B 36 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LYS B 38 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLY B 70 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER B 40 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY B 68 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TYR B 87 " --> pdb=" O ILE B 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 132 removed outlier: 4.774A pdb=" N TYR B 341 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LYS B 318 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP B 344 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 320 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 96 removed outlier: 5.445A pdb=" N ASP B 115 " --> pdb=" O ASN B 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.506A pdb=" N LYS D 21 " --> pdb=" O GLY D 8 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY D 8 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 62 " --> pdb=" O PHE D 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 128 through 132 removed outlier: 6.428A pdb=" N ASN D 36 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL D 72 " --> pdb=" O ASN D 36 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LYS D 38 " --> pdb=" O GLY D 70 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLY D 70 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER D 40 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY D 68 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR D 87 " --> pdb=" O ILE D 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 128 through 132 removed outlier: 4.791A pdb=" N TYR D 341 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL D 320 " --> pdb=" O ASP D 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 217 through 219 removed outlier: 6.794A pdb=" N VAL D 197 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ILE D 219 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY D 199 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP D 172 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N HIS D 240 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N HIS C 240 " --> pdb=" O ASN C 262 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP C 172 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL C 197 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ILE C 219 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY C 199 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 5 through 10 removed outlier: 3.530A pdb=" N GLY C 8 " --> pdb=" O LYS C 21 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C 21 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 132 removed outlier: 6.440A pdb=" N ASN C 36 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL C 72 " --> pdb=" O ASN C 36 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LYS C 38 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLY C 70 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N SER C 40 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY C 68 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR C 87 " --> pdb=" O ILE C 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 128 through 132 removed outlier: 4.817A pdb=" N TYR C 341 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS C 318 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ASP C 344 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL C 320 " --> pdb=" O ASP C 344 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1191 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: 3.58 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1984 1.33 - 1.45: 2457 1.45 - 1.57: 6023 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 10544 Sorted by residual: bond pdb=" C TYR C 102 " pdb=" N CYS C 103 " ideal model delta sigma weight residual 1.334 1.552 -0.218 1.41e-02 5.03e+03 2.40e+02 bond pdb=" C CYS C 103 " pdb=" N GLU C 104 " ideal model delta sigma weight residual 1.335 1.507 -0.172 1.35e-02 5.49e+03 1.62e+02 bond pdb=" C ALA C 99 " pdb=" N CYS C 100 " ideal model delta sigma weight residual 1.328 1.250 0.078 8.50e-03 1.38e+04 8.41e+01 bond pdb=" C MET C 98 " pdb=" N ALA C 99 " ideal model delta sigma weight residual 1.336 1.482 -0.146 1.68e-02 3.54e+03 7.56e+01 bond pdb=" C CYS D 97 " pdb=" N MET D 98 " ideal model delta sigma weight residual 1.333 1.229 0.104 1.39e-02 5.18e+03 5.55e+01 ... (remaining 10539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.83: 14222 4.83 - 9.66: 53 9.66 - 14.50: 10 14.50 - 19.33: 3 19.33 - 24.16: 4 Bond angle restraints: 14292 Sorted by residual: angle pdb=" O CYS D 97 " pdb=" C CYS D 97 " pdb=" N MET D 98 " ideal model delta sigma weight residual 122.36 146.52 -24.16 1.42e+00 4.96e-01 2.89e+02 angle pdb=" CA CYS D 97 " pdb=" C CYS D 97 " pdb=" N MET D 98 " ideal model delta sigma weight residual 118.14 94.95 23.19 1.56e+00 4.11e-01 2.21e+02 angle pdb=" C CYS D 97 " pdb=" N MET D 98 " pdb=" CA MET D 98 " ideal model delta sigma weight residual 122.40 101.89 20.51 1.45e+00 4.76e-01 2.00e+02 angle pdb=" C TYR C 102 " pdb=" CA TYR C 102 " pdb=" CB TYR C 102 " ideal model delta sigma weight residual 110.85 132.40 -21.55 1.70e+00 3.46e-01 1.61e+02 angle pdb=" O MET C 98 " pdb=" C MET C 98 " pdb=" N ALA C 99 " ideal model delta sigma weight residual 122.59 139.43 -16.84 1.33e+00 5.65e-01 1.60e+02 ... (remaining 14287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 5310 16.02 - 32.03: 594 32.03 - 48.05: 227 48.05 - 64.06: 45 64.06 - 80.08: 6 Dihedral angle restraints: 6182 sinusoidal: 2318 harmonic: 3864 Sorted by residual: dihedral pdb=" C TYR C 102 " pdb=" N TYR C 102 " pdb=" CA TYR C 102 " pdb=" CB TYR C 102 " ideal model delta harmonic sigma weight residual -122.60 -153.14 30.54 0 2.50e+00 1.60e-01 1.49e+02 dihedral pdb=" N TYR C 102 " pdb=" C TYR C 102 " pdb=" CA TYR C 102 " pdb=" CB TYR C 102 " ideal model delta harmonic sigma weight residual 122.80 145.00 -22.20 0 2.50e+00 1.60e-01 7.89e+01 dihedral pdb=" CB CYS D 277 " pdb=" SG CYS D 277 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual -86.00 -35.08 -50.92 1 1.00e+01 1.00e-02 3.55e+01 ... (remaining 6179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.223: 1574 0.223 - 0.446: 15 0.446 - 0.670: 2 0.670 - 0.893: 0 0.893 - 1.116: 1 Chirality restraints: 1592 Sorted by residual: chirality pdb=" CA TYR C 102 " pdb=" N TYR C 102 " pdb=" C TYR C 102 " pdb=" CB TYR C 102 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.11e+01 chirality pdb=" CA ALA D 99 " pdb=" N ALA D 99 " pdb=" C ALA D 99 " pdb=" CB ALA D 99 " both_signs ideal model delta sigma weight residual False 2.48 3.06 -0.58 2.00e-01 2.50e+01 8.27e+00 chirality pdb=" CA ALA C 99 " pdb=" N ALA C 99 " pdb=" C ALA C 99 " pdb=" CB ALA C 99 " both_signs ideal model delta sigma weight residual False 2.48 1.99 0.50 2.00e-01 2.50e+01 6.20e+00 ... (remaining 1589 not shown) Planarity restraints: 1844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 99 " -0.036 2.00e-02 2.50e+03 6.88e-02 4.73e+01 pdb=" C ALA C 99 " 0.119 2.00e-02 2.50e+03 pdb=" O ALA C 99 " -0.040 2.00e-02 2.50e+03 pdb=" N CYS C 100 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 210 " -0.021 2.00e-02 2.50e+03 4.31e-02 1.85e+01 pdb=" C PHE D 210 " 0.074 2.00e-02 2.50e+03 pdb=" O PHE D 210 " -0.028 2.00e-02 2.50e+03 pdb=" N ARG D 211 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 98 " -0.015 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C MET C 98 " 0.065 2.00e-02 2.50e+03 pdb=" O MET C 98 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA C 99 " -0.021 2.00e-02 2.50e+03 ... (remaining 1841 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 57 2.55 - 3.14: 7304 3.14 - 3.72: 15370 3.72 - 4.31: 23133 4.31 - 4.90: 37616 Nonbonded interactions: 83480 Sorted by model distance: nonbonded pdb=" OE1 GLU D 108 " pdb=" NE2 GLN D 135 " model vdw 1.962 3.120 nonbonded pdb=" OE1 GLU B 108 " pdb=" NE2 GLN B 135 " model vdw 1.974 3.120 nonbonded pdb=" O LEU B 232 " pdb=" O ASP B 236 " model vdw 1.986 3.040 nonbonded pdb=" O SER C 176 " pdb=" CG2 VAL C 245 " model vdw 2.033 3.460 nonbonded pdb=" O SER D 176 " pdb=" CG2 VAL D 245 " model vdw 2.039 3.460 ... (remaining 83475 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.520 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: 0.470 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 31.620 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9375 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 : 0.021 0.921 10571 Z= 1.145 Angle : 1.653 34.408 14302 Z= 1.218 Chirality : 0.105 1.116 1592 Planarity : 0.003 0.069 1844 Dihedral : 15.613 80.079 3752 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.77 % Allowed : 16.14 % Favored : 82.09 % Cbeta Deviations : 0.58 % Peptide Plane: Cis-proline : 7.69 % 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: -3.56 (0.17), residues: 1380 helix: -2.61 (0.17), residues: 464 sheet: -1.10 (0.28), residues: 268 loop : -2.69 (0.18), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 172 HIS 0.003 0.001 HIS D 66 PHE 0.010 0.001 PHE D 11 TYR 0.009 0.001 TYR A 329 ARG 0.001 0.000 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.18446 ( 402) hydrogen bonds : angle 7.36218 ( 1191) metal coordination : bond 0.32544 ( 25) metal coordination : angle 11.30170 ( 6) SS BOND : bond 0.39369 ( 2) SS BOND : angle 18.11518 ( 4) covalent geometry : bond 0.01286 (10544) covalent geometry : angle 1.60913 (14292) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 1.124 Fit side-chains REVERT: B 27 LYS cc_start: 0.9596 (OUTLIER) cc_final: 0.9024 (mttt) outliers start: 19 outliers final: 5 residues processed: 58 average time/residue: 1.4518 time to fit residues: 90.9474 Evaluate side-chains 32 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain C residue 182 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 ASN A 244 ASN ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN D 126 GLN C 78 ASN C 138 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2058 r_free = 0.2058 target = 0.026169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.1895 r_free = 0.1895 target = 0.022699 restraints weight = 28029.151| |-----------------------------------------------------------------------------| r_work (start): 0.1894 rms_B_bonded: 0.93 r_work: 0.1839 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.1766 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.1766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9437 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10571 Z= 0.115 Angle : 0.510 10.888 14302 Z= 0.268 Chirality : 0.044 0.132 1592 Planarity : 0.003 0.038 1844 Dihedral : 5.725 62.014 1491 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.33 % Allowed : 16.60 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.68 (0.20), residues: 1380 helix: -0.57 (0.24), residues: 464 sheet: -0.21 (0.31), residues: 264 loop : -1.90 (0.19), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 92 HIS 0.003 0.001 HIS A 66 PHE 0.014 0.002 PHE D 11 TYR 0.033 0.001 TYR A 258 ARG 0.004 0.001 ARG A 257 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 402) hydrogen bonds : angle 5.07165 ( 1191) metal coordination : bond 0.00765 ( 25) metal coordination : angle 6.81213 ( 6) SS BOND : bond 0.00903 ( 2) SS BOND : angle 2.37534 ( 4) covalent geometry : bond 0.00248 (10544) covalent geometry : angle 0.48953 (14292) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 25 time to evaluate : 1.298 Fit side-chains REVERT: B 182 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8614 (mp) REVERT: C 182 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8699 (mp) outliers start: 25 outliers final: 8 residues processed: 50 average time/residue: 1.2294 time to fit residues: 68.4521 Evaluate side-chains 35 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 1 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 213 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 126 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 ASN D 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.1974 r_free = 0.1974 target = 0.024116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.1804 r_free = 0.1804 target = 0.020668 restraints weight = 28118.869| |-----------------------------------------------------------------------------| r_work (start): 0.1802 rms_B_bonded: 0.91 r_work: 0.1746 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.1672 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.1672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9492 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10571 Z= 0.128 Angle : 0.487 9.248 14302 Z= 0.254 Chirality : 0.044 0.136 1592 Planarity : 0.003 0.041 1844 Dihedral : 4.947 54.299 1485 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.59 % Allowed : 15.67 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.75 (0.21), residues: 1380 helix: 0.28 (0.25), residues: 440 sheet: 0.16 (0.30), residues: 292 loop : -1.34 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 92 HIS 0.003 0.001 HIS D 66 PHE 0.015 0.001 PHE D 11 TYR 0.022 0.001 TYR A 258 ARG 0.002 0.000 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.04610 ( 402) hydrogen bonds : angle 4.97451 ( 1191) metal coordination : bond 0.00574 ( 25) metal coordination : angle 5.95481 ( 6) SS BOND : bond 0.00349 ( 2) SS BOND : angle 1.53839 ( 4) covalent geometry : bond 0.00298 (10544) covalent geometry : angle 0.47050 (14292) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 25 time to evaluate : 1.121 Fit side-chains outliers start: 17 outliers final: 3 residues processed: 42 average time/residue: 1.2168 time to fit residues: 56.3415 Evaluate side-chains 28 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain C residue 213 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 40 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 124 optimal weight: 0.0270 chunk 116 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.1962 r_free = 0.1962 target = 0.023939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.1793 r_free = 0.1793 target = 0.020478 restraints weight = 29443.407| |-----------------------------------------------------------------------------| r_work (start): 0.1791 rms_B_bonded: 0.93 r_work: 0.1733 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.1658 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.1658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9496 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.340 10571 Z= 0.169 Angle : 0.474 8.452 14302 Z= 0.247 Chirality : 0.044 0.134 1592 Planarity : 0.003 0.041 1844 Dihedral : 4.289 49.368 1476 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.12 % Allowed : 16.23 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.41 (0.22), residues: 1380 helix: 0.56 (0.25), residues: 440 sheet: 0.34 (0.30), residues: 292 loop : -1.13 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 92 HIS 0.003 0.001 HIS B 138 PHE 0.014 0.002 PHE D 11 TYR 0.019 0.001 TYR A 258 ARG 0.002 0.000 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.04368 ( 402) hydrogen bonds : angle 4.91623 ( 1191) metal coordination : bond 0.06822 ( 25) metal coordination : angle 5.56233 ( 6) SS BOND : bond 0.00391 ( 2) SS BOND : angle 1.41509 ( 4) covalent geometry : bond 0.00299 (10544) covalent geometry : angle 0.46011 (14292) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 25 time to evaluate : 1.159 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 37 average time/residue: 1.1967 time to fit residues: 49.2969 Evaluate side-chains 29 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain C residue 213 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 126 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.1887 r_free = 0.1887 target = 0.022332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.1712 r_free = 0.1712 target = 0.018903 restraints weight = 29949.719| |-----------------------------------------------------------------------------| r_work (start): 0.1710 rms_B_bonded: 0.91 r_work: 0.1649 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.1574 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.1574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9537 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 10571 Z= 0.231 Angle : 0.539 8.329 14302 Z= 0.281 Chirality : 0.047 0.137 1592 Planarity : 0.003 0.040 1844 Dihedral : 4.574 49.569 1476 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.12 % Allowed : 16.88 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.50 (0.21), residues: 1380 helix: 0.44 (0.25), residues: 440 sheet: 0.36 (0.30), residues: 292 loop : -1.18 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 92 HIS 0.004 0.001 HIS D 138 PHE 0.017 0.002 PHE B 221 TYR 0.016 0.001 TYR A 258 ARG 0.002 0.000 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.05762 ( 402) hydrogen bonds : angle 5.25735 ( 1191) metal coordination : bond 0.00618 ( 25) metal coordination : angle 5.63055 ( 6) SS BOND : bond 0.00731 ( 2) SS BOND : angle 1.92770 ( 4) covalent geometry : bond 0.00565 (10544) covalent geometry : angle 0.52540 (14292) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 24 time to evaluate : 1.127 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 36 average time/residue: 1.2215 time to fit residues: 48.7284 Evaluate side-chains 30 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain C residue 213 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 119 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.1931 r_free = 0.1931 target = 0.023260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.1760 r_free = 0.1760 target = 0.019812 restraints weight = 29821.338| |-----------------------------------------------------------------------------| r_work (start): 0.1757 rms_B_bonded: 0.92 r_work: 0.1697 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.1622 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.1622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9513 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10571 Z= 0.134 Angle : 0.478 8.084 14302 Z= 0.249 Chirality : 0.044 0.135 1592 Planarity : 0.003 0.041 1844 Dihedral : 4.371 46.401 1476 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.49 % Allowed : 16.88 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.34 (0.22), residues: 1380 helix: 0.47 (0.25), residues: 464 sheet: 0.40 (0.30), residues: 292 loop : -1.03 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 92 HIS 0.003 0.001 HIS B 138 PHE 0.014 0.002 PHE D 11 TYR 0.017 0.001 TYR A 258 ARG 0.002 0.000 ARG D 260 Details of bonding type rmsd hydrogen bonds : bond 0.04512 ( 402) hydrogen bonds : angle 4.99351 ( 1191) metal coordination : bond 0.00471 ( 25) metal coordination : angle 5.44792 ( 6) SS BOND : bond 0.00392 ( 2) SS BOND : angle 1.50978 ( 4) covalent geometry : bond 0.00313 (10544) covalent geometry : angle 0.46385 (14292) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 25 time to evaluate : 1.196 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 41 average time/residue: 1.1812 time to fit residues: 54.1955 Evaluate side-chains 32 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain C residue 213 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 94 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 29 optimal weight: 0.0770 chunk 14 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 110 optimal weight: 0.0270 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.1959 r_free = 0.1959 target = 0.023868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.1791 r_free = 0.1791 target = 0.020413 restraints weight = 29649.169| |-----------------------------------------------------------------------------| r_work (start): 0.1788 rms_B_bonded: 0.92 r_work: 0.1729 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.1655 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.1655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9497 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10571 Z= 0.111 Angle : 0.456 8.069 14302 Z= 0.236 Chirality : 0.044 0.134 1592 Planarity : 0.003 0.041 1844 Dihedral : 4.145 40.982 1476 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.21 % Allowed : 17.72 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.14 (0.22), residues: 1380 helix: 0.65 (0.25), residues: 464 sheet: 0.43 (0.30), residues: 292 loop : -0.87 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 92 HIS 0.003 0.001 HIS B 138 PHE 0.013 0.001 PHE D 11 TYR 0.017 0.001 TYR A 258 ARG 0.002 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 402) hydrogen bonds : angle 4.81897 ( 1191) metal coordination : bond 0.00438 ( 25) metal coordination : angle 5.39511 ( 6) SS BOND : bond 0.00305 ( 2) SS BOND : angle 1.33498 ( 4) covalent geometry : bond 0.00257 (10544) covalent geometry : angle 0.44162 (14292) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 1.123 Fit side-chains REVERT: D 317 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8919 (pt) outliers start: 13 outliers final: 6 residues processed: 38 average time/residue: 1.2130 time to fit residues: 51.1295 Evaluate side-chains 32 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain C residue 213 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 9 optimal weight: 0.4980 chunk 109 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.1949 r_free = 0.1949 target = 0.023669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.1781 r_free = 0.1781 target = 0.020217 restraints weight = 29692.836| |-----------------------------------------------------------------------------| r_work (start): 0.1779 rms_B_bonded: 0.92 r_work: 0.1720 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.1645 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.1645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9501 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10571 Z= 0.121 Angle : 0.462 8.341 14302 Z= 0.239 Chirality : 0.044 0.136 1592 Planarity : 0.003 0.040 1844 Dihedral : 4.112 38.709 1476 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.12 % Allowed : 18.10 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.06 (0.22), residues: 1380 helix: 0.69 (0.25), residues: 464 sheet: 0.45 (0.30), residues: 292 loop : -0.78 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 92 HIS 0.003 0.001 HIS B 138 PHE 0.014 0.002 PHE D 11 TYR 0.016 0.001 TYR A 258 ARG 0.002 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 402) hydrogen bonds : angle 4.84440 ( 1191) metal coordination : bond 0.00439 ( 25) metal coordination : angle 5.62097 ( 6) SS BOND : bond 0.00351 ( 2) SS BOND : angle 1.35707 ( 4) covalent geometry : bond 0.00284 (10544) covalent geometry : angle 0.44740 (14292) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 25 time to evaluate : 1.297 Fit side-chains REVERT: D 317 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8982 (pt) outliers start: 12 outliers final: 8 residues processed: 37 average time/residue: 1.5209 time to fit residues: 62.4118 Evaluate side-chains 34 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 213 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.1965 r_free = 0.1965 target = 0.024020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.1799 r_free = 0.1799 target = 0.020561 restraints weight = 29886.893| |-----------------------------------------------------------------------------| r_work (start): 0.1796 rms_B_bonded: 0.93 r_work: 0.1737 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.1663 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.1663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9492 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10571 Z= 0.107 Angle : 0.450 8.058 14302 Z= 0.232 Chirality : 0.044 0.134 1592 Planarity : 0.003 0.041 1844 Dihedral : 4.021 36.185 1476 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.84 % Allowed : 18.38 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.03 (0.22), residues: 1380 helix: 0.78 (0.25), residues: 464 sheet: 0.46 (0.30), residues: 292 loop : -0.71 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 92 HIS 0.003 0.000 HIS D 138 PHE 0.013 0.001 PHE A 11 TYR 0.016 0.001 TYR A 258 ARG 0.002 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 402) hydrogen bonds : angle 4.76588 ( 1191) metal coordination : bond 0.00424 ( 25) metal coordination : angle 5.44819 ( 6) SS BOND : bond 0.00290 ( 2) SS BOND : angle 1.29050 ( 4) covalent geometry : bond 0.00245 (10544) covalent geometry : angle 0.43517 (14292) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 1.135 Fit side-chains REVERT: D 317 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8965 (pt) outliers start: 9 outliers final: 7 residues processed: 34 average time/residue: 1.2605 time to fit residues: 47.4870 Evaluate side-chains 33 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 213 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 40 optimal weight: 4.9990 chunk 126 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.1953 r_free = 0.1953 target = 0.023749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.1785 r_free = 0.1785 target = 0.020296 restraints weight = 29613.276| |-----------------------------------------------------------------------------| r_work (start): 0.1782 rms_B_bonded: 0.92 r_work: 0.1723 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.1649 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.1649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9499 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10571 Z= 0.121 Angle : 0.463 9.016 14302 Z= 0.238 Chirality : 0.044 0.135 1592 Planarity : 0.003 0.040 1844 Dihedral : 4.048 35.448 1476 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.84 % Allowed : 18.10 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.03 (0.22), residues: 1380 helix: 0.76 (0.25), residues: 464 sheet: 0.45 (0.30), residues: 292 loop : -0.70 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 92 HIS 0.003 0.001 HIS B 138 PHE 0.014 0.002 PHE A 11 TYR 0.015 0.001 TYR A 258 ARG 0.002 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 402) hydrogen bonds : angle 4.81657 ( 1191) metal coordination : bond 0.00428 ( 25) metal coordination : angle 6.01516 ( 6) SS BOND : bond 0.00341 ( 2) SS BOND : angle 1.34685 ( 4) covalent geometry : bond 0.00284 (10544) covalent geometry : angle 0.44576 (14292) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 1.313 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 34 average time/residue: 1.2336 time to fit residues: 46.5610 Evaluate side-chains 33 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 213 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 128 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 118 optimal weight: 0.0870 chunk 38 optimal weight: 6.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.1884 r_free = 0.1884 target = 0.022263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.1708 r_free = 0.1708 target = 0.018838 restraints weight = 29896.940| |-----------------------------------------------------------------------------| r_work (start): 0.1706 rms_B_bonded: 0.91 r_work: 0.1645 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.1570 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.1570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9538 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 10571 Z= 0.234 Angle : 0.535 8.671 14302 Z= 0.278 Chirality : 0.047 0.136 1592 Planarity : 0.003 0.040 1844 Dihedral : 4.451 41.596 1476 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.75 % Allowed : 18.56 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.33 (0.22), residues: 1380 helix: 0.46 (0.25), residues: 464 sheet: 0.25 (0.30), residues: 300 loop : -0.93 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 92 HIS 0.003 0.001 HIS D 138 PHE 0.018 0.002 PHE B 221 TYR 0.013 0.001 TYR A 258 ARG 0.001 0.000 ARG D 260 Details of bonding type rmsd hydrogen bonds : bond 0.05686 ( 402) hydrogen bonds : angle 5.19398 ( 1191) metal coordination : bond 0.00530 ( 25) metal coordination : angle 5.92074 ( 6) SS BOND : bond 0.00714 ( 2) SS BOND : angle 1.89461 ( 4) covalent geometry : bond 0.00575 (10544) covalent geometry : angle 0.52048 (14292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4808.58 seconds wall clock time: 85 minutes 7.73 seconds (5107.73 seconds total)