Starting phenix.real_space_refine on Fri Feb 14 14:06:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ntm_12591/02_2025/7ntm_12591.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ntm_12591/02_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_12591/02_2025/7ntm_12591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ntm_12591/02_2025/7ntm_12591.map" model { file = "/net/cci-nas-00/data/ceres_data/7ntm_12591/02_2025/7ntm_12591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ntm_12591/02_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 7.01, per 1000 atoms: 0.68 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: 2.49 Conformation dependent library (CDL) restraints added in 1.3 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: 1.25 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: 3.18 Time building geometry restraints manager: 2.89 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: 2.900 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.470 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.190 ------------------------------------------------------------------------------- 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 : 0.013 0.218 10544 Z= 0.856 Angle : 1.609 24.160 14292 Z= 1.209 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 *********************** 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 : 1.127 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: 1.5041 time to fit residues: 94.1290 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 : 1.208 ------------------------------------------------------------------------------- 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: 0.6980 chunk 123 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 126 GLN D 126 GLN D 138 HIS C 78 ASN C 138 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2085 r_free = 0.2085 target = 0.026832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.1925 r_free = 0.1925 target = 0.023347 restraints weight = 28050.537| |-----------------------------------------------------------------------------| r_work (start): 0.1924 rms_B_bonded: 0.94 r_work: 0.1870 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.1796 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.1796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9420 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10544 Z= 0.151 Angle : 0.484 6.180 14292 Z= 0.262 Chirality : 0.044 0.130 1592 Planarity : 0.003 0.039 1844 Dihedral : 5.723 61.768 1491 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.43 % Allowed : 16.42 % Favored : 81.16 % 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: -1.66 (0.20), residues: 1380 helix: -0.55 (0.24), residues: 464 sheet: -0.14 (0.31), residues: 260 loop : -1.91 (0.19), residues: 656 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 C 210 TYR 0.034 0.001 TYR A 258 ARG 0.004 0.001 ARG D 260 *********************** 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 51 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 25 time to evaluate : 1.015 Fit side-chains REVERT: B 182 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8590 (mp) REVERT: C 182 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8711 (mp) outliers start: 26 outliers final: 6 residues processed: 50 average time/residue: 1.1139 time to fit residues: 61.5974 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 : 1.228 ------------------------------------------------------------------------------- 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 B residue 182 LEU Chi-restraints excluded: chain D residue 71 VAL 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: 5.9990 chunk 33 optimal weight: 0.0070 chunk 20 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 107 ASN ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.1949 r_free = 0.1949 target = 0.023664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.1777 r_free = 0.1777 target = 0.020186 restraints weight = 29821.318| |-----------------------------------------------------------------------------| r_work (start): 0.1776 rms_B_bonded: 0.93 r_work: 0.1717 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.1641 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.1641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9505 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10544 Z= 0.242 Angle : 0.491 5.401 14292 Z= 0.264 Chirality : 0.045 0.138 1592 Planarity : 0.003 0.041 1844 Dihedral : 5.063 55.627 1485 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.68 % Allowed : 15.76 % Favored : 82.56 % 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: -0.83 (0.21), residues: 1380 helix: 0.21 (0.25), residues: 440 sheet: 0.13 (0.30), residues: 292 loop : -1.40 (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 B 138 PHE 0.016 0.002 PHE D 11 TYR 0.021 0.001 TYR A 258 ARG 0.003 0.000 ARG A 211 *********************** 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 43 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 25 time to evaluate : 1.292 Fit side-chains outliers start: 18 outliers final: 5 residues processed: 43 average time/residue: 1.2519 time to fit residues: 59.3110 Evaluate side-chains 30 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain D 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: 1.9990 chunk 76 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.1954 r_free = 0.1954 target = 0.023766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.1785 r_free = 0.1785 target = 0.020319 restraints weight = 29655.333| |-----------------------------------------------------------------------------| r_work (start): 0.1783 rms_B_bonded: 0.92 r_work: 0.1725 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.1650 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.1650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9500 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10544 Z= 0.208 Angle : 0.463 5.223 14292 Z= 0.247 Chirality : 0.044 0.134 1592 Planarity : 0.003 0.041 1844 Dihedral : 4.348 50.506 1476 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.40 % Allowed : 16.04 % Favored : 82.56 % 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: -0.47 (0.22), residues: 1380 helix: 0.53 (0.25), residues: 440 sheet: 0.32 (0.30), residues: 292 loop : -1.17 (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 0.001 PHE D 11 TYR 0.020 0.001 TYR A 258 ARG 0.002 0.000 ARG B 260 *********************** 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 40 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 1.039 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 40 average time/residue: 1.1943 time to fit residues: 52.8431 Evaluate side-chains 30 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 85 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.1976 r_free = 0.1976 target = 0.024254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.1810 r_free = 0.1810 target = 0.020807 restraints weight = 29362.527| |-----------------------------------------------------------------------------| r_work (start): 0.1808 rms_B_bonded: 0.92 r_work: 0.1750 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.1676 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.1676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9486 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10544 Z= 0.162 Angle : 0.439 5.164 14292 Z= 0.234 Chirality : 0.044 0.133 1592 Planarity : 0.003 0.041 1844 Dihedral : 4.144 44.770 1476 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.03 % Allowed : 16.98 % 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: -0.25 (0.22), residues: 1380 helix: 0.55 (0.25), residues: 464 sheet: 0.38 (0.30), residues: 292 loop : -0.93 (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 B 138 PHE 0.013 0.001 PHE D 11 TYR 0.018 0.001 TYR A 258 ARG 0.002 0.000 ARG B 260 *********************** 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: 11 poor density : 25 time to evaluate : 1.126 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 36 average time/residue: 1.2593 time to fit residues: 50.0394 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 : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.1949 r_free = 0.1949 target = 0.023657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.1780 r_free = 0.1780 target = 0.020209 restraints weight = 29749.749| |-----------------------------------------------------------------------------| r_work (start): 0.1778 rms_B_bonded: 0.92 r_work: 0.1719 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.1644 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.1644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9502 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10544 Z= 0.210 Angle : 0.457 5.200 14292 Z= 0.243 Chirality : 0.044 0.135 1592 Planarity : 0.003 0.040 1844 Dihedral : 4.166 41.693 1476 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.31 % Allowed : 17.35 % Favored : 81.34 % 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: -0.19 (0.22), residues: 1380 helix: 0.59 (0.25), residues: 464 sheet: 0.40 (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 0.014 0.002 PHE B 221 TYR 0.016 0.001 TYR A 258 ARG 0.001 0.000 ARG B 260 *********************** 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 39 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 1.107 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 39 average time/residue: 1.1937 time to fit residues: 51.6762 Evaluate side-chains 31 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 94 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 29 optimal weight: 0.2980 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 110 optimal weight: 0.0030 overall best weight: 2.6596 ------------------------------------------------------------------------------- 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 = 0.1918 r_free = 0.1918 target = 0.022991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.1746 r_free = 0.1746 target = 0.019547 restraints weight = 30014.188| |-----------------------------------------------------------------------------| r_work (start): 0.1744 rms_B_bonded: 0.92 r_work: 0.1684 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.1609 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.1609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9520 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10544 Z= 0.275 Angle : 0.483 5.246 14292 Z= 0.257 Chirality : 0.045 0.136 1592 Planarity : 0.003 0.040 1844 Dihedral : 4.297 41.723 1476 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.12 % Allowed : 17.82 % 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: -0.26 (0.22), residues: 1380 helix: 0.51 (0.25), residues: 464 sheet: 0.38 (0.30), residues: 292 loop : -0.91 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 92 HIS 0.003 0.001 HIS B 138 PHE 0.016 0.002 PHE B 221 TYR 0.014 0.001 TYR A 258 ARG 0.001 0.000 ARG A 211 *********************** 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 37 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 25 time to evaluate : 1.188 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 37 average time/residue: 1.2186 time to fit residues: 49.9998 Evaluate side-chains 31 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 9 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 = 0.1934 r_free = 0.1934 target = 0.023326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.1763 r_free = 0.1763 target = 0.019874 restraints weight = 29847.144| |-----------------------------------------------------------------------------| r_work (start): 0.1761 rms_B_bonded: 0.92 r_work: 0.1701 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.1626 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.1626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9511 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10544 Z= 0.224 Angle : 0.464 5.183 14292 Z= 0.247 Chirality : 0.045 0.134 1592 Planarity : 0.003 0.040 1844 Dihedral : 4.234 40.509 1476 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.84 % Allowed : 18.19 % Favored : 80.97 % 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: -0.19 (0.22), residues: 1380 helix: 0.57 (0.25), residues: 464 sheet: 0.39 (0.30), residues: 292 loop : -0.86 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 92 HIS 0.003 0.001 HIS B 138 PHE 0.015 0.002 PHE B 221 TYR 0.016 0.001 TYR A 258 ARG 0.001 0.000 ARG D 260 *********************** 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 34 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 1.231 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 34 average time/residue: 1.2763 time to fit residues: 48.1229 Evaluate side-chains 31 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.1970 r_free = 0.1970 target = 0.024113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.1803 r_free = 0.1803 target = 0.020649 restraints weight = 29895.590| |-----------------------------------------------------------------------------| r_work (start): 0.1801 rms_B_bonded: 0.93 r_work: 0.1742 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.1668 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.1668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9489 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10544 Z= 0.159 Angle : 0.437 5.108 14292 Z= 0.232 Chirality : 0.044 0.133 1592 Planarity : 0.003 0.040 1844 Dihedral : 4.047 36.793 1476 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.93 % Allowed : 18.38 % 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: -0.03 (0.22), residues: 1380 helix: 0.73 (0.25), residues: 464 sheet: 0.41 (0.30), residues: 292 loop : -0.74 (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 B 138 PHE 0.013 0.001 PHE A 11 TYR 0.017 0.001 TYR A 258 ARG 0.002 0.000 ARG B 260 *********************** 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 35 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 1.141 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 35 average time/residue: 1.2536 time to fit residues: 48.5563 Evaluate side-chains 31 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 40 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 93 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.1957 r_free = 0.1957 target = 0.023820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.1788 r_free = 0.1788 target = 0.020357 restraints weight = 29569.250| |-----------------------------------------------------------------------------| r_work (start): 0.1785 rms_B_bonded: 0.92 r_work: 0.1727 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.1653 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.1653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9497 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10544 Z= 0.191 Angle : 0.449 5.159 14292 Z= 0.239 Chirality : 0.044 0.135 1592 Planarity : 0.003 0.040 1844 Dihedral : 4.072 36.037 1476 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.65 % Allowed : 18.47 % Favored : 80.88 % 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: -0.01 (0.22), residues: 1380 helix: 0.74 (0.25), residues: 464 sheet: 0.41 (0.30), residues: 292 loop : -0.72 (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 A 11 TYR 0.015 0.001 TYR A 258 ARG 0.002 0.000 ARG B 260 ********************** 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 32 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 1.245 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 32 average time/residue: 1.2780 time to fit residues: 45.5543 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 : 1.384 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 81 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 91 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 118 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.1984 r_free = 0.1984 target = 0.024421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.1819 r_free = 0.1819 target = 0.020959 restraints weight = 29298.362| |-----------------------------------------------------------------------------| r_work (start): 0.1816 rms_B_bonded: 0.92 r_work: 0.1758 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.1685 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.1685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9480 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10544 Z= 0.150 Angle : 0.432 5.105 14292 Z= 0.229 Chirality : 0.043 0.133 1592 Planarity : 0.003 0.040 1844 Dihedral : 3.939 32.949 1476 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.75 % Allowed : 18.66 % Favored : 80.60 % 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: 0.10 (0.22), residues: 1380 helix: 0.84 (0.25), residues: 464 sheet: 0.42 (0.30), residues: 292 loop : -0.63 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 92 HIS 0.003 0.000 HIS B 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4185.31 seconds wall clock time: 75 minutes 31.58 seconds (4531.58 seconds total)