Starting phenix.real_space_refine on Thu May 15 14:12:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ebp_27995/05_2025/8ebp_27995.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ebp_27995/05_2025/8ebp_27995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ebp_27995/05_2025/8ebp_27995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ebp_27995/05_2025/8ebp_27995.map" model { file = "/net/cci-nas-00/data/ceres_data/8ebp_27995/05_2025/8ebp_27995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ebp_27995/05_2025/8ebp_27995.cif" } resolution = 3.38 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= 0.005 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 8288 2.51 5 N 2278 2.21 5 O 2594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13230 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3320 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 15, 'TRANS': 419} Chain: "L" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1606 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 199} Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1689 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "B" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3320 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 15, 'TRANS': 419} Chain: "M" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1606 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 199} Chain: "I" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1689 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 12, 'TRANS': 212} Time building chain proxies: 7.62, per 1000 atoms: 0.58 Number of scatterers: 13230 At special positions: 0 Unit cell: (106.56, 103.23, 233.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2594 8.00 N 2278 7.00 C 8288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 407 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS L 212 " - pdb=" SG CYS H 216 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 292 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 390 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 135 " - pdb=" SG CYS M 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 212 " - pdb=" SG CYS I 216 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 140 " - pdb=" SG CYS I 196 " distance=2.03 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: 2.94 Conformation dependent library (CDL) restraints added in 1.8 seconds 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3232 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 36 sheets defined 17.9% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 65 through 92 removed outlier: 3.555A pdb=" N ASP A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 129 removed outlier: 4.272A pdb=" N THR A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 141 removed outlier: 3.566A pdb=" N LEU A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 removed outlier: 4.605A pdb=" N LYS A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 173 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 210 removed outlier: 3.557A pdb=" N GLN A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ARG A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N PHE A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.613A pdb=" N ALA A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.609A pdb=" N ASP A 325 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 347 Processing helix chain 'A' and resid 348 through 353 removed outlier: 3.516A pdb=" N ILE A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 189 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.692A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.823A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 92 removed outlier: 3.527A pdb=" N LEU B 73 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 129 removed outlier: 3.622A pdb=" N THR B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 141 removed outlier: 3.559A pdb=" N LEU B 141 " --> pdb=" O ILE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 173 removed outlier: 4.463A pdb=" N LYS B 171 " --> pdb=" O ASP B 167 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 211 removed outlier: 3.655A pdb=" N SER B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ARG B 199 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE B 200 " --> pdb=" O PHE B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.786A pdb=" N ARG B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 246 removed outlier: 3.699A pdb=" N ILE B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 322 through 326 removed outlier: 3.641A pdb=" N ASP B 325 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 347 Processing helix chain 'B' and resid 348 through 353 removed outlier: 3.802A pdb=" N ILE B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 128 removed outlier: 3.783A pdb=" N ALA M 128 " --> pdb=" O GLU M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 189 removed outlier: 3.791A pdb=" N HIS M 189 " --> pdb=" O GLN M 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.549A pdb=" N SER I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.627A pdb=" N THR I 87 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 341 through 342 removed outlier: 6.781A pdb=" N CYS A 283 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY A 34 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LYS A 20 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLU A 21 " --> pdb=" O HIS A 435 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE A 437 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR A 23 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 276 through 278 removed outlier: 3.528A pdb=" N VAL A 278 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 38 " --> pdb=" O CYS A 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150 removed outlier: 6.282A pdb=" N VAL A 47 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 269 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL A 262 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE A 268 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 375 removed outlier: 3.557A pdb=" N MET A 372 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 removed outlier: 4.023A pdb=" N LYS A 401 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.557A pdb=" N VAL L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.557A pdb=" N VAL L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AB1, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.764A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU L 179 " --> pdb=" O LEU L 133 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TYR L 173 " --> pdb=" O ASP L 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 154 through 156 removed outlier: 4.259A pdb=" N TRP L 149 " --> pdb=" O VAL L 156 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR L 146 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL L 196 " --> pdb=" O VAL L 203 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 192 through 193 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.666A pdb=" N VAL H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.152A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 96 through 97 Processing sheet with id=AB7, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.587A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS H 140 " --> pdb=" O SER H 180 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER H 180 " --> pdb=" O CYS H 140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.587A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS H 140 " --> pdb=" O SER H 180 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER H 180 " --> pdb=" O CYS H 140 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER H 177 " --> pdb=" O VAL H 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 152 through 153 removed outlier: 3.598A pdb=" N LYS H 209 " --> pdb=" O CYS H 196 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL H 198 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL H 207 " --> pdb=" O VAL H 198 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 341 through 343 removed outlier: 3.545A pdb=" N THR B 317 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS B 283 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY B 34 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LYS B 20 " --> pdb=" O GLU B 33 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.847A pdb=" N VAL B 278 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 38 " --> pdb=" O CYS B 335 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 146 through 150 removed outlier: 5.739A pdb=" N THR B 45 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 158 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE B 268 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AC5, first strand: chain 'B' and resid 372 through 375 Processing sheet with id=AC6, first strand: chain 'B' and resid 401 through 402 removed outlier: 4.112A pdb=" N LYS B 401 " --> pdb=" O ILE B 392 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.447A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 9 through 13 Processing sheet with id=AC9, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AD1, first strand: chain 'M' and resid 115 through 119 removed outlier: 3.523A pdb=" N LEU M 179 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR M 173 " --> pdb=" O ASP M 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 145 through 148 removed outlier: 3.582A pdb=" N LYS M 205 " --> pdb=" O CYS M 194 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 150 through 151 Processing sheet with id=AD4, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.551A pdb=" N LEU I 18 " --> pdb=" O MET I 82 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 removed outlier: 7.048A pdb=" N MET I 34 " --> pdb=" O SER I 50 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SER I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 96 through 97 Processing sheet with id=AD7, first strand: chain 'I' and resid 120 through 124 removed outlier: 3.587A pdb=" N GLY I 139 " --> pdb=" O LEU I 124 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER I 180 " --> pdb=" O CYS I 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 120 through 124 removed outlier: 3.587A pdb=" N GLY I 139 " --> pdb=" O LEU I 124 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER I 180 " --> pdb=" O CYS I 140 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 195 through 198 removed outlier: 3.712A pdb=" N CYS I 196 " --> pdb=" O LYS I 209 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS I 209 " --> pdb=" O CYS I 196 " (cutoff:3.500A) 505 hydrogen bonds defined for protein. 1284 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: 4.40 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4337 1.34 - 1.46: 2996 1.46 - 1.58: 6069 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 13490 Sorted by residual: bond pdb=" C ARG A 329 " pdb=" N GLY A 330 " ideal model delta sigma weight residual 1.331 1.291 0.039 1.46e-02 4.69e+03 7.19e+00 bond pdb=" C ARG B 329 " pdb=" N GLY B 330 " ideal model delta sigma weight residual 1.331 1.301 0.029 1.46e-02 4.69e+03 4.00e+00 bond pdb=" C TYR L 141 " pdb=" N PRO L 142 " ideal model delta sigma weight residual 1.333 1.350 -0.017 1.01e-02 9.80e+03 2.79e+00 bond pdb=" C ASP L 152 " pdb=" N SER L 153 " ideal model delta sigma weight residual 1.331 1.312 0.019 1.43e-02 4.89e+03 1.73e+00 bond pdb=" C PHE H 146 " pdb=" N PRO H 147 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.41e+00 ... (remaining 13485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 17776 1.61 - 3.23: 467 3.23 - 4.84: 68 4.84 - 6.45: 19 6.45 - 8.06: 6 Bond angle restraints: 18336 Sorted by residual: angle pdb=" N VAL B 52 " pdb=" CA VAL B 52 " pdb=" C VAL B 52 " ideal model delta sigma weight residual 113.53 108.44 5.09 9.80e-01 1.04e+00 2.70e+01 angle pdb=" C ASP L 152 " pdb=" CA ASP L 152 " pdb=" CB ASP L 152 " ideal model delta sigma weight residual 116.54 110.74 5.80 1.15e+00 7.56e-01 2.54e+01 angle pdb=" N VAL A 52 " pdb=" CA VAL A 52 " pdb=" C VAL A 52 " ideal model delta sigma weight residual 113.53 109.09 4.44 9.80e-01 1.04e+00 2.06e+01 angle pdb=" N SER L 153 " pdb=" CA SER L 153 " pdb=" C SER L 153 " ideal model delta sigma weight residual 113.02 118.24 -5.22 1.20e+00 6.94e-01 1.89e+01 angle pdb=" N PHE B 103 " pdb=" CA PHE B 103 " pdb=" C PHE B 103 " ideal model delta sigma weight residual 112.12 107.08 5.04 1.34e+00 5.57e-01 1.41e+01 ... (remaining 18331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 7505 17.86 - 35.73: 583 35.73 - 53.59: 91 53.59 - 71.46: 16 71.46 - 89.32: 11 Dihedral angle restraints: 8206 sinusoidal: 3162 harmonic: 5044 Sorted by residual: dihedral pdb=" CB CYS B 113 " pdb=" SG CYS B 113 " pdb=" SG CYS B 339 " pdb=" CB CYS B 339 " ideal model delta sinusoidal sigma weight residual -86.00 -159.73 73.73 1 1.00e+01 1.00e-02 6.91e+01 dihedral pdb=" CB CYS A 350 " pdb=" SG CYS A 350 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 153.33 -60.33 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " pdb=" SG CYS A 339 " pdb=" CB CYS A 339 " ideal model delta sinusoidal sigma weight residual -86.00 -145.72 59.72 1 1.00e+01 1.00e-02 4.76e+01 ... (remaining 8203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1573 0.045 - 0.090: 387 0.090 - 0.135: 140 0.135 - 0.181: 8 0.181 - 0.226: 6 Chirality restraints: 2114 Sorted by residual: chirality pdb=" CB VAL B 104 " pdb=" CA VAL B 104 " pdb=" CG1 VAL B 104 " pdb=" CG2 VAL B 104 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ASP L 152 " pdb=" N ASP L 152 " pdb=" C ASP L 152 " pdb=" CB ASP L 152 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE H 100 " pdb=" CA ILE H 100 " pdb=" CG1 ILE H 100 " pdb=" CG2 ILE H 100 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2111 not shown) Planarity restraints: 2358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 184 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO B 185 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 185 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 185 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP L 152 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.05e+00 pdb=" C ASP L 152 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP L 152 " 0.013 2.00e-02 2.50e+03 pdb=" N SER L 153 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 97 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO B 98 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 98 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 98 " 0.027 5.00e-02 4.00e+02 ... (remaining 2355 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 255 2.68 - 3.24: 12510 3.24 - 3.79: 19147 3.79 - 4.35: 25535 4.35 - 4.90: 43003 Nonbonded interactions: 100450 Sorted by model distance: nonbonded pdb=" OG SER B 391 " pdb=" OE1 GLN B 402 " model vdw 2.126 3.040 nonbonded pdb=" OG SER A 391 " pdb=" OE1 GLN A 402 " model vdw 2.159 3.040 nonbonded pdb=" O CYS B 60 " pdb=" NZ LYS B 68 " model vdw 2.187 3.120 nonbonded pdb=" OE2 GLU M 204 " pdb=" OG1 THR M 206 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR M 146 " pdb=" OG1 THR M 197 " model vdw 2.229 3.040 ... (remaining 100445 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' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.650 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13516 Z= 0.163 Angle : 0.633 8.063 18388 Z= 0.350 Chirality : 0.046 0.226 2114 Planarity : 0.004 0.051 2358 Dihedral : 12.803 89.323 4896 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.07 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.20), residues: 1740 helix: -1.25 (0.30), residues: 277 sheet: 0.30 (0.24), residues: 537 loop : -2.02 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.008 0.001 HIS H 200 PHE 0.010 0.001 PHE H 100E TYR 0.013 0.001 TYR I 145 ARG 0.009 0.001 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.27009 ( 473) hydrogen bonds : angle 9.75818 ( 1284) SS BOND : bond 0.00305 ( 26) SS BOND : angle 0.85717 ( 52) covalent geometry : bond 0.00351 (13490) covalent geometry : angle 0.63196 (18336) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.429 Fit side-chains revert: symmetry clash REVERT: A 95 ILE cc_start: 0.8518 (mm) cc_final: 0.8276 (mm) REVERT: L 139 ASP cc_start: 0.9348 (m-30) cc_final: 0.9025 (m-30) REVERT: H 144 ASP cc_start: 0.8146 (m-30) cc_final: 0.7871 (m-30) REVERT: H 146 PHE cc_start: 0.8406 (t80) cc_final: 0.8199 (t80) REVERT: H 212 GLU cc_start: 0.7893 (pm20) cc_final: 0.7330 (tm-30) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2092 time to fit residues: 30.5017 Evaluate side-chains 67 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 134 optimal weight: 0.0980 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 171 ASN H 155 ASN H 199 ASN B 202 ASN M 29 ASN M 79 GLN I 199 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.102761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.058047 restraints weight = 35775.750| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 4.13 r_work: 0.2660 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13516 Z= 0.203 Angle : 0.666 8.864 18388 Z= 0.351 Chirality : 0.047 0.218 2114 Planarity : 0.005 0.055 2358 Dihedral : 4.322 18.085 1886 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.55 % Favored : 93.39 % Rotamer: Outliers : 0.27 % Allowed : 6.83 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.20), residues: 1740 helix: -0.52 (0.32), residues: 269 sheet: 0.70 (0.24), residues: 533 loop : -2.08 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.008 0.002 HIS I 200 PHE 0.014 0.001 PHE H 100E TYR 0.040 0.002 TYR I 194 ARG 0.005 0.001 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.05799 ( 473) hydrogen bonds : angle 6.66303 ( 1284) SS BOND : bond 0.00363 ( 26) SS BOND : angle 0.82723 ( 52) covalent geometry : bond 0.00469 (13490) covalent geometry : angle 0.66537 (18336) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: L 139 ASP cc_start: 0.9453 (m-30) cc_final: 0.9220 (m-30) REVERT: B 372 MET cc_start: 0.8692 (tmm) cc_final: 0.8487 (tmm) REVERT: B 435 HIS cc_start: 0.8433 (m170) cc_final: 0.8084 (m170) REVERT: I 148 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8480 (mm-30) outliers start: 4 outliers final: 2 residues processed: 78 average time/residue: 0.2066 time to fit residues: 26.0652 Evaluate side-chains 69 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain B residue 392 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 134 optimal weight: 0.9980 chunk 144 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 84 optimal weight: 30.0000 chunk 146 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 171 ASN H 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.102899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.057225 restraints weight = 35662.503| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 4.36 r_work: 0.2660 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13516 Z= 0.139 Angle : 0.592 8.289 18388 Z= 0.309 Chirality : 0.044 0.214 2114 Planarity : 0.004 0.058 2358 Dihedral : 4.197 18.535 1886 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 0.95 % Allowed : 9.07 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.20), residues: 1740 helix: -0.34 (0.33), residues: 271 sheet: 0.62 (0.23), residues: 577 loop : -1.97 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.010 0.001 HIS I 200 PHE 0.012 0.001 PHE H 100E TYR 0.020 0.001 TYR M 141 ARG 0.003 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.04677 ( 473) hydrogen bonds : angle 5.97240 ( 1284) SS BOND : bond 0.00311 ( 26) SS BOND : angle 0.72333 ( 52) covalent geometry : bond 0.00315 (13490) covalent geometry : angle 0.59189 (18336) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 1.612 Fit side-chains revert: symmetry clash REVERT: L 139 ASP cc_start: 0.9462 (m-30) cc_final: 0.9232 (m-30) REVERT: H 208 ASP cc_start: 0.9180 (m-30) cc_final: 0.8753 (t0) REVERT: H 212 GLU cc_start: 0.7908 (pm20) cc_final: 0.7534 (pp20) REVERT: B 372 MET cc_start: 0.8706 (tmm) cc_final: 0.8474 (tmm) REVERT: B 435 HIS cc_start: 0.8525 (m170) cc_final: 0.8148 (m170) outliers start: 14 outliers final: 9 residues processed: 85 average time/residue: 0.2154 time to fit residues: 29.4129 Evaluate side-chains 73 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 165 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 171 ASN H 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.103279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.058091 restraints weight = 35111.330| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 4.06 r_work: 0.2700 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13516 Z= 0.118 Angle : 0.565 6.954 18388 Z= 0.293 Chirality : 0.044 0.219 2114 Planarity : 0.004 0.058 2358 Dihedral : 4.076 18.473 1886 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 0.74 % Allowed : 10.76 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.21), residues: 1740 helix: -0.21 (0.34), residues: 273 sheet: 0.74 (0.23), residues: 573 loop : -1.92 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 284 HIS 0.008 0.001 HIS I 200 PHE 0.012 0.001 PHE H 100E TYR 0.021 0.001 TYR M 141 ARG 0.003 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 473) hydrogen bonds : angle 5.56910 ( 1284) SS BOND : bond 0.00276 ( 26) SS BOND : angle 0.66354 ( 52) covalent geometry : bond 0.00270 (13490) covalent geometry : angle 0.56456 (18336) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 1.430 Fit side-chains revert: symmetry clash REVERT: L 139 ASP cc_start: 0.9494 (m-30) cc_final: 0.9288 (m-30) REVERT: H 208 ASP cc_start: 0.9203 (m-30) cc_final: 0.8748 (t0) REVERT: H 212 GLU cc_start: 0.7905 (pm20) cc_final: 0.7488 (pp20) REVERT: B 372 MET cc_start: 0.8725 (tmm) cc_final: 0.8492 (tmm) REVERT: B 435 HIS cc_start: 0.8525 (m170) cc_final: 0.8126 (m170) outliers start: 11 outliers final: 4 residues processed: 85 average time/residue: 0.2139 time to fit residues: 28.9916 Evaluate side-chains 77 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain H residue 197 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 147 optimal weight: 30.0000 chunk 79 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 171 ASN L 189 HIS H 155 ASN B 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.099756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.054009 restraints weight = 35877.396| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 4.13 r_work: 0.2584 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 13516 Z= 0.373 Angle : 0.744 10.963 18388 Z= 0.387 Chirality : 0.049 0.219 2114 Planarity : 0.005 0.063 2358 Dihedral : 4.541 19.531 1886 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.24 % Favored : 92.70 % Rotamer: Outliers : 1.49 % Allowed : 12.38 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.20), residues: 1740 helix: -0.59 (0.32), residues: 277 sheet: 0.39 (0.23), residues: 583 loop : -2.07 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 154 HIS 0.009 0.002 HIS I 200 PHE 0.021 0.002 PHE I 100E TYR 0.025 0.002 TYR M 141 ARG 0.009 0.001 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.05061 ( 473) hydrogen bonds : angle 5.87849 ( 1284) SS BOND : bond 0.00524 ( 26) SS BOND : angle 1.08144 ( 52) covalent geometry : bond 0.00873 (13490) covalent geometry : angle 0.74306 (18336) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 1.588 Fit side-chains revert: symmetry clash REVERT: H 146 PHE cc_start: 0.8732 (t80) cc_final: 0.8367 (t80) REVERT: H 208 ASP cc_start: 0.9192 (m-30) cc_final: 0.8758 (t0) REVERT: B 435 HIS cc_start: 0.8541 (m170) cc_final: 0.8067 (m-70) REVERT: M 30 ASP cc_start: 0.9087 (t0) cc_final: 0.8725 (t0) outliers start: 22 outliers final: 17 residues processed: 92 average time/residue: 0.2081 time to fit residues: 31.1014 Evaluate side-chains 83 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 205 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 77 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 171 ASN H 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.101930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.056284 restraints weight = 36054.678| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 4.12 r_work: 0.2650 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13516 Z= 0.151 Angle : 0.597 8.492 18388 Z= 0.310 Chirality : 0.045 0.231 2114 Planarity : 0.004 0.062 2358 Dihedral : 4.334 19.006 1886 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.38 % Favored : 93.56 % Rotamer: Outliers : 1.49 % Allowed : 13.33 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.20), residues: 1740 helix: -0.33 (0.33), residues: 279 sheet: 0.60 (0.23), residues: 563 loop : -1.97 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 154 HIS 0.008 0.001 HIS I 200 PHE 0.017 0.001 PHE H 100E TYR 0.021 0.001 TYR M 141 ARG 0.003 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 473) hydrogen bonds : angle 5.43106 ( 1284) SS BOND : bond 0.00373 ( 26) SS BOND : angle 0.87426 ( 52) covalent geometry : bond 0.00353 (13490) covalent geometry : angle 0.59603 (18336) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 1.588 Fit side-chains revert: symmetry clash REVERT: H 146 PHE cc_start: 0.8699 (t80) cc_final: 0.8466 (t80) REVERT: H 208 ASP cc_start: 0.9190 (m-30) cc_final: 0.8732 (t0) REVERT: B 435 HIS cc_start: 0.8656 (m170) cc_final: 0.8273 (m170) REVERT: I 87 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8597 (t) outliers start: 22 outliers final: 12 residues processed: 93 average time/residue: 0.2087 time to fit residues: 31.4421 Evaluate side-chains 78 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 205 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 162 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 171 ASN H 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.100974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.055586 restraints weight = 35938.476| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 4.10 r_work: 0.2627 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13516 Z= 0.235 Angle : 0.642 11.644 18388 Z= 0.333 Chirality : 0.046 0.222 2114 Planarity : 0.004 0.061 2358 Dihedral : 4.377 18.922 1886 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.67 % Favored : 93.28 % Rotamer: Outliers : 1.56 % Allowed : 14.75 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1740 helix: -0.35 (0.33), residues: 279 sheet: 0.42 (0.23), residues: 583 loop : -2.02 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 149 HIS 0.006 0.001 HIS I 200 PHE 0.018 0.002 PHE H 100E TYR 0.020 0.001 TYR M 141 ARG 0.005 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 473) hydrogen bonds : angle 5.42803 ( 1284) SS BOND : bond 0.00412 ( 26) SS BOND : angle 0.87685 ( 52) covalent geometry : bond 0.00553 (13490) covalent geometry : angle 0.64090 (18336) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: H 146 PHE cc_start: 0.8739 (t80) cc_final: 0.8432 (t80) REVERT: H 208 ASP cc_start: 0.9179 (m-30) cc_final: 0.8730 (t0) REVERT: B 435 HIS cc_start: 0.8670 (m170) cc_final: 0.8226 (m-70) REVERT: I 87 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8693 (t) REVERT: I 148 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7969 (mm-30) outliers start: 23 outliers final: 15 residues processed: 91 average time/residue: 0.2119 time to fit residues: 31.2443 Evaluate side-chains 85 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 205 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 148 optimal weight: 30.0000 chunk 35 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 156 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.102648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.057231 restraints weight = 36006.498| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 4.11 r_work: 0.2677 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13516 Z= 0.123 Angle : 0.579 10.013 18388 Z= 0.300 Chirality : 0.044 0.224 2114 Planarity : 0.004 0.061 2358 Dihedral : 4.176 18.663 1886 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.03 % Favored : 93.85 % Rotamer: Outliers : 1.08 % Allowed : 15.43 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.21), residues: 1740 helix: -0.09 (0.34), residues: 279 sheet: 0.64 (0.23), residues: 573 loop : -1.89 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 309 HIS 0.007 0.001 HIS I 200 PHE 0.016 0.001 PHE H 100E TYR 0.018 0.001 TYR M 141 ARG 0.003 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 473) hydrogen bonds : angle 5.09128 ( 1284) SS BOND : bond 0.00287 ( 26) SS BOND : angle 0.72323 ( 52) covalent geometry : bond 0.00282 (13490) covalent geometry : angle 0.57848 (18336) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9268 (t) cc_final: 0.8958 (m) REVERT: A 392 ILE cc_start: 0.9027 (mp) cc_final: 0.8787 (pt) REVERT: H 208 ASP cc_start: 0.9193 (m-30) cc_final: 0.8725 (t0) REVERT: B 435 HIS cc_start: 0.8667 (m170) cc_final: 0.8281 (m170) REVERT: I 87 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8489 (t) outliers start: 16 outliers final: 8 residues processed: 89 average time/residue: 0.2197 time to fit residues: 31.6772 Evaluate side-chains 81 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 205 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 132 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 166 optimal weight: 30.0000 chunk 28 optimal weight: 8.9990 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.101867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.056601 restraints weight = 35584.578| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 4.06 r_work: 0.2658 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13516 Z= 0.169 Angle : 0.602 11.722 18388 Z= 0.311 Chirality : 0.045 0.226 2114 Planarity : 0.004 0.060 2358 Dihedral : 4.153 17.775 1886 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.09 % Favored : 93.85 % Rotamer: Outliers : 0.95 % Allowed : 15.90 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.21), residues: 1740 helix: -0.06 (0.34), residues: 279 sheet: 0.62 (0.23), residues: 577 loop : -1.92 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 284 HIS 0.005 0.001 HIS H 200 PHE 0.024 0.001 PHE H 100E TYR 0.019 0.001 TYR M 141 ARG 0.004 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 473) hydrogen bonds : angle 5.09729 ( 1284) SS BOND : bond 0.00339 ( 26) SS BOND : angle 0.77241 ( 52) covalent geometry : bond 0.00399 (13490) covalent geometry : angle 0.60103 (18336) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 1.507 Fit side-chains revert: symmetry clash REVERT: A 392 ILE cc_start: 0.9038 (mp) cc_final: 0.8737 (tt) REVERT: B 435 HIS cc_start: 0.8651 (m170) cc_final: 0.8203 (m-70) REVERT: M 30 ASP cc_start: 0.9004 (t0) cc_final: 0.8729 (t0) REVERT: I 87 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8612 (t) outliers start: 14 outliers final: 12 residues processed: 85 average time/residue: 0.2059 time to fit residues: 28.3113 Evaluate side-chains 85 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 205 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 46 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.102068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.056553 restraints weight = 35604.101| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 4.20 r_work: 0.2648 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13516 Z= 0.153 Angle : 0.599 13.335 18388 Z= 0.310 Chirality : 0.044 0.228 2114 Planarity : 0.004 0.059 2358 Dihedral : 4.152 18.779 1886 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.26 % Favored : 93.68 % Rotamer: Outliers : 1.01 % Allowed : 16.10 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.21), residues: 1740 helix: 0.02 (0.34), residues: 279 sheet: 0.68 (0.23), residues: 577 loop : -1.89 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 284 HIS 0.006 0.001 HIS I 200 PHE 0.023 0.001 PHE H 100E TYR 0.019 0.001 TYR M 141 ARG 0.003 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 473) hydrogen bonds : angle 5.01242 ( 1284) SS BOND : bond 0.00328 ( 26) SS BOND : angle 0.74845 ( 52) covalent geometry : bond 0.00362 (13490) covalent geometry : angle 0.59828 (18336) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9282 (t) cc_final: 0.8955 (m) REVERT: A 392 ILE cc_start: 0.9021 (mp) cc_final: 0.8724 (tt) REVERT: B 435 HIS cc_start: 0.8675 (m170) cc_final: 0.8223 (m-70) REVERT: M 30 ASP cc_start: 0.9051 (t0) cc_final: 0.8761 (t0) REVERT: I 87 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8588 (t) outliers start: 15 outliers final: 13 residues processed: 86 average time/residue: 0.2067 time to fit residues: 28.7331 Evaluate side-chains 85 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 205 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 169 optimal weight: 8.9990 chunk 9 optimal weight: 0.0570 chunk 51 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.102313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.057261 restraints weight = 35760.945| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 4.11 r_work: 0.2673 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13516 Z= 0.143 Angle : 0.589 12.640 18388 Z= 0.303 Chirality : 0.044 0.229 2114 Planarity : 0.004 0.060 2358 Dihedral : 4.079 18.030 1886 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.15 % Favored : 93.79 % Rotamer: Outliers : 1.01 % Allowed : 15.90 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.21), residues: 1740 helix: 0.10 (0.34), residues: 280 sheet: 0.74 (0.23), residues: 578 loop : -1.88 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 309 HIS 0.005 0.001 HIS H 200 PHE 0.021 0.001 PHE H 100E TYR 0.017 0.001 TYR M 141 ARG 0.003 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 473) hydrogen bonds : angle 4.94012 ( 1284) SS BOND : bond 0.00315 ( 26) SS BOND : angle 0.72624 ( 52) covalent geometry : bond 0.00338 (13490) covalent geometry : angle 0.58816 (18336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6990.12 seconds wall clock time: 121 minutes 41.90 seconds (7301.90 seconds total)