Starting phenix.real_space_refine on Thu Jul 31 07:23:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ebp_27995/07_2025/8ebp_27995.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ebp_27995/07_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_27995/07_2025/8ebp_27995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ebp_27995/07_2025/8ebp_27995.map" model { file = "/net/cci-nas-00/data/ceres_data/8ebp_27995/07_2025/8ebp_27995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ebp_27995/07_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-5711/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: 8.17, per 1000 atoms: 0.62 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: 3.13 Conformation dependent library (CDL) restraints added in 2.1 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: 2.22 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: 4.96 Time building geometry restraints manager: 3.79 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: 1.090 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.200 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.080 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.580 ------------------------------------------------------------------------------- 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 : 1.433 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: 0.2175 time to fit residues: 32.0547 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 : 1.485 ------------------------------------------------------------------------------- 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 = 35775.712| |-----------------------------------------------------------------------------| 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: 0.8543 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 18.086 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 : 1.505 Fit side-chains revert: symmetry clash REVERT: L 139 ASP cc_start: 0.9455 (m-30) cc_final: 0.9221 (m-30) REVERT: B 372 MET cc_start: 0.8690 (tmm) cc_final: 0.8485 (tmm) REVERT: B 435 HIS cc_start: 0.8436 (m170) cc_final: 0.8089 (m170) REVERT: I 148 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8481 (mm-30) outliers start: 4 outliers final: 2 residues processed: 78 average time/residue: 0.2135 time to fit residues: 27.2363 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 : 1.475 ------------------------------------------------------------------------------- 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: 0.0970 chunk 144 optimal weight: 6.9990 chunk 11 optimal weight: 0.0670 chunk 45 optimal weight: 5.9990 chunk 48 optimal weight: 0.0170 chunk 84 optimal weight: 30.0000 chunk 146 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 overall best weight: 0.8358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.103373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.057853 restraints weight = 35769.687| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 4.14 r_work: 0.2694 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1383 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= 0.124 Angle : 0.583 8.272 18388 Z= 0.303 Chirality : 0.044 0.212 2114 Planarity : 0.004 0.056 2358 Dihedral : 4.153 18.824 1886 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.02 % Rotamer: Outliers : 0.95 % Allowed : 8.93 % Favored : 90.12 % 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: -0.29 (0.34), residues: 269 sheet: 0.75 (0.23), residues: 549 loop : -2.01 (0.20), residues: 922 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 0.011 0.001 PHE H 100E TYR 0.020 0.001 TYR M 141 ARG 0.004 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.04549 ( 473) hydrogen bonds : angle 5.90656 ( 1284) SS BOND : bond 0.00296 ( 26) SS BOND : angle 0.69623 ( 52) covalent geometry : bond 0.00279 (13490) covalent geometry : angle 0.58302 (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 90 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 1.529 Fit side-chains revert: symmetry clash REVERT: L 139 ASP cc_start: 0.9471 (m-30) cc_final: 0.9243 (m-30) REVERT: H 208 ASP cc_start: 0.9183 (m-30) cc_final: 0.8746 (t0) REVERT: H 212 GLU cc_start: 0.7907 (pm20) cc_final: 0.7532 (pp20) REVERT: B 372 MET cc_start: 0.8691 (tmm) cc_final: 0.8460 (tmm) REVERT: B 435 HIS cc_start: 0.8506 (m170) cc_final: 0.8128 (m170) outliers start: 14 outliers final: 6 residues processed: 88 average time/residue: 0.2133 time to fit residues: 30.6637 Evaluate side-chains 75 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL 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 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: 2.9990 chunk 113 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 118 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.103850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.058719 restraints weight = 35180.391| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 4.08 r_work: 0.2716 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13516 Z= 0.112 Angle : 0.556 6.826 18388 Z= 0.287 Chirality : 0.044 0.219 2114 Planarity : 0.004 0.057 2358 Dihedral : 4.009 18.444 1886 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.69 % Favored : 94.25 % Rotamer: Outliers : 0.68 % Allowed : 10.96 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.21), residues: 1740 helix: -0.14 (0.34), residues: 272 sheet: 0.86 (0.23), residues: 548 loop : -2.00 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 154 HIS 0.008 0.001 HIS H 200 PHE 0.014 0.001 PHE M 62 TYR 0.022 0.001 TYR M 141 ARG 0.003 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 473) hydrogen bonds : angle 5.43885 ( 1284) SS BOND : bond 0.00473 ( 26) SS BOND : angle 0.74081 ( 52) covalent geometry : bond 0.00256 (13490) covalent geometry : angle 0.55516 (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 90 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 ILE cc_start: 0.9023 (mp) cc_final: 0.8754 (pt) REVERT: L 83 GLU cc_start: 0.8861 (tp30) cc_final: 0.8550 (mm-30) REVERT: H 146 PHE cc_start: 0.8546 (t80) cc_final: 0.8339 (t80) REVERT: H 212 GLU cc_start: 0.7902 (pm20) cc_final: 0.7494 (pp20) REVERT: B 372 MET cc_start: 0.8717 (tmm) cc_final: 0.8463 (tmm) REVERT: B 435 HIS cc_start: 0.8540 (m170) cc_final: 0.8136 (m170) outliers start: 10 outliers final: 4 residues processed: 87 average time/residue: 0.2181 time to fit residues: 30.8284 Evaluate side-chains 75 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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: 10.0000 chunk 158 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 147 optimal weight: 30.0000 chunk 79 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 163 optimal weight: 20.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.101546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.056813 restraints weight = 36031.472| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 4.04 r_work: 0.2626 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 13516 Z= 0.292 Angle : 0.673 10.002 18388 Z= 0.350 Chirality : 0.047 0.219 2114 Planarity : 0.005 0.059 2358 Dihedral : 4.297 18.867 1886 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.26 % Favored : 93.68 % Rotamer: Outliers : 1.22 % Allowed : 12.31 % Favored : 86.47 % 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: -1.20 (0.20), residues: 1740 helix: -0.33 (0.33), residues: 277 sheet: 0.59 (0.23), residues: 577 loop : -1.98 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 103 HIS 0.008 0.002 HIS I 200 PHE 0.017 0.002 PHE H 100E TYR 0.023 0.002 TYR M 141 ARG 0.008 0.001 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.04567 ( 473) hydrogen bonds : angle 5.61444 ( 1284) SS BOND : bond 0.00455 ( 26) SS BOND : angle 0.92906 ( 52) covalent geometry : bond 0.00683 (13490) covalent geometry : angle 0.67165 (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 92 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 1 GLN cc_start: 0.9459 (tp40) cc_final: 0.9165 (tp40) REVERT: H 208 ASP cc_start: 0.9197 (m-30) cc_final: 0.8753 (t0) REVERT: B 372 MET cc_start: 0.8703 (tmm) cc_final: 0.8448 (tmm) REVERT: B 435 HIS cc_start: 0.8538 (m170) cc_final: 0.8119 (m170) REVERT: I 148 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8256 (mm-30) outliers start: 18 outliers final: 12 residues processed: 88 average time/residue: 0.2086 time to fit residues: 29.8042 Evaluate side-chains 79 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 270 MET Chi-restraints excluded: chain L residue 51 ASP 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 281 THR Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 77 optimal weight: 0.0770 chunk 144 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 61 optimal weight: 0.0670 chunk 101 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 63 optimal weight: 30.0000 chunk 60 optimal weight: 9.9990 overall best weight: 0.9678 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.102849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.057287 restraints weight = 36139.374| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 4.08 r_work: 0.2676 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13516 Z= 0.123 Angle : 0.572 9.344 18388 Z= 0.297 Chirality : 0.044 0.221 2114 Planarity : 0.004 0.058 2358 Dihedral : 4.134 18.289 1886 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.26 % Favored : 93.68 % Rotamer: Outliers : 1.01 % Allowed : 14.28 % Favored : 84.71 % 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: -1.02 (0.21), residues: 1740 helix: -0.05 (0.34), residues: 277 sheet: 0.73 (0.23), residues: 568 loop : -1.91 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 309 HIS 0.010 0.001 HIS I 200 PHE 0.014 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 0.03737 ( 473) hydrogen bonds : angle 5.22649 ( 1284) SS BOND : bond 0.00297 ( 26) SS BOND : angle 0.73243 ( 52) covalent geometry : bond 0.00283 (13490) covalent geometry : angle 0.57114 (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 89 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 1.443 Fit side-chains revert: symmetry clash REVERT: A 392 ILE cc_start: 0.9040 (mp) cc_final: 0.8797 (pt) REVERT: H 208 ASP cc_start: 0.9177 (m-30) cc_final: 0.8678 (t0) REVERT: H 212 GLU cc_start: 0.7878 (pm20) cc_final: 0.7455 (pp20) REVERT: B 372 MET cc_start: 0.8704 (tmm) cc_final: 0.8442 (tmm) REVERT: B 435 HIS cc_start: 0.8622 (m170) cc_final: 0.8230 (m170) REVERT: I 87 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8490 (t) REVERT: I 148 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8292 (mm-30) outliers start: 15 outliers final: 5 residues processed: 87 average time/residue: 0.2279 time to fit residues: 32.2983 Evaluate side-chains 75 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 47 optimal weight: 5.9990 chunk 171 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 162 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.101497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.056072 restraints weight = 36008.773| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 4.11 r_work: 0.2638 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13516 Z= 0.215 Angle : 0.620 8.734 18388 Z= 0.321 Chirality : 0.045 0.221 2114 Planarity : 0.004 0.060 2358 Dihedral : 4.233 18.511 1886 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.49 % Favored : 93.45 % Rotamer: Outliers : 1.01 % Allowed : 15.02 % Favored : 83.96 % 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: -1.12 (0.20), residues: 1740 helix: -0.18 (0.33), residues: 279 sheet: 0.61 (0.23), residues: 573 loop : -1.94 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 284 HIS 0.008 0.001 HIS I 200 PHE 0.023 0.001 PHE H 100E TYR 0.021 0.001 TYR M 141 ARG 0.006 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 473) hydrogen bonds : angle 5.30617 ( 1284) SS BOND : bond 0.00466 ( 26) SS BOND : angle 0.87337 ( 52) covalent geometry : bond 0.00507 (13490) covalent geometry : angle 0.61950 (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 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: A 392 ILE cc_start: 0.9033 (mp) cc_final: 0.8795 (pt) REVERT: H 1 GLN cc_start: 0.9443 (tp40) cc_final: 0.9153 (tp40) REVERT: H 100 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8612 (m-80) REVERT: H 146 PHE cc_start: 0.8667 (t80) cc_final: 0.8419 (t80) REVERT: H 208 ASP cc_start: 0.9192 (m-30) cc_final: 0.8733 (t0) REVERT: B 435 HIS cc_start: 0.8645 (m170) cc_final: 0.8245 (m170) REVERT: M 30 ASP cc_start: 0.9034 (t0) cc_final: 0.8626 (t0) REVERT: I 87 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8670 (t) outliers start: 15 outliers final: 11 residues processed: 85 average time/residue: 0.2084 time to fit residues: 29.0973 Evaluate side-chains 80 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 189 MET 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 L residue 51 ASP Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain I residue 87 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: 6.9990 chunk 162 optimal weight: 20.0000 chunk 156 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.101780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.056385 restraints weight = 36070.355| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 4.05 r_work: 0.2652 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2095 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= 0.184 Angle : 0.611 11.878 18388 Z= 0.317 Chirality : 0.045 0.255 2114 Planarity : 0.004 0.060 2358 Dihedral : 4.216 18.649 1886 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.38 % Favored : 93.56 % Rotamer: Outliers : 1.08 % Allowed : 15.36 % Favored : 83.56 % 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: -1.10 (0.21), residues: 1740 helix: -0.16 (0.33), residues: 279 sheet: 0.60 (0.23), residues: 577 loop : -1.91 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.007 0.001 HIS I 200 PHE 0.022 0.001 PHE H 100E TYR 0.020 0.001 TYR M 141 ARG 0.004 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 473) hydrogen bonds : angle 5.21423 ( 1284) SS BOND : bond 0.00377 ( 26) SS BOND : angle 0.80601 ( 52) covalent geometry : bond 0.00432 (13490) covalent geometry : angle 0.61064 (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 88 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: A 392 ILE cc_start: 0.9013 (mp) cc_final: 0.8769 (pt) REVERT: H 1 GLN cc_start: 0.9439 (tp40) cc_final: 0.9149 (tp40) REVERT: H 208 ASP cc_start: 0.9198 (m-30) cc_final: 0.8710 (t0) REVERT: B 435 HIS cc_start: 0.8653 (m170) cc_final: 0.8278 (m170) REVERT: I 87 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8614 (t) REVERT: I 199 ASN cc_start: 0.9099 (t0) cc_final: 0.8874 (t0) outliers start: 16 outliers final: 13 residues processed: 86 average time/residue: 0.2393 time to fit residues: 32.9258 Evaluate side-chains 84 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 2.254 ------------------------------------------------------------------------------- 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 L residue 51 ASP 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 271 VAL Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 132 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 145 optimal weight: 0.0770 chunk 143 optimal weight: 7.9990 chunk 166 optimal weight: 30.0000 chunk 28 optimal weight: 8.9990 chunk 13 optimal weight: 0.0370 chunk 3 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.103056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.057824 restraints weight = 35485.117| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 4.11 r_work: 0.2690 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13516 Z= 0.114 Angle : 0.579 13.103 18388 Z= 0.298 Chirality : 0.044 0.226 2114 Planarity : 0.004 0.057 2358 Dihedral : 4.056 18.571 1886 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.15 % Favored : 93.79 % Rotamer: Outliers : 1.01 % Allowed : 16.04 % Favored : 82.95 % 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: -0.90 (0.21), residues: 1740 helix: 0.05 (0.34), residues: 279 sheet: 0.78 (0.23), residues: 578 loop : -1.84 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 309 HIS 0.008 0.001 HIS I 200 PHE 0.021 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 0.03356 ( 473) hydrogen bonds : angle 4.96370 ( 1284) SS BOND : bond 0.00284 ( 26) SS BOND : angle 0.69489 ( 52) covalent geometry : bond 0.00266 (13490) covalent geometry : angle 0.57910 (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 88 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9261 (t) cc_final: 0.8944 (m) REVERT: A 372 MET cc_start: 0.8741 (tpp) cc_final: 0.8518 (tpt) REVERT: A 392 ILE cc_start: 0.9017 (mp) cc_final: 0.8736 (tt) REVERT: H 1 GLN cc_start: 0.9427 (tp40) cc_final: 0.9124 (tp40) REVERT: B 435 HIS cc_start: 0.8665 (m170) cc_final: 0.8291 (m170) REVERT: I 87 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8451 (t) outliers start: 15 outliers final: 7 residues processed: 86 average time/residue: 0.2858 time to fit residues: 39.8319 Evaluate side-chains 77 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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 L residue 51 ASP Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 PHE 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: 30.0000 chunk 133 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.102091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.056908 restraints weight = 35626.599| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 4.07 r_work: 0.2664 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2266 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= 0.172 Angle : 0.603 12.308 18388 Z= 0.312 Chirality : 0.045 0.226 2114 Planarity : 0.004 0.058 2358 Dihedral : 4.099 18.550 1886 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.49 % Favored : 93.45 % Rotamer: Outliers : 0.95 % Allowed : 16.37 % Favored : 82.68 % 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: 0.05 (0.34), residues: 279 sheet: 0.75 (0.23), residues: 573 loop : -1.85 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 284 HIS 0.006 0.001 HIS I 200 PHE 0.021 0.001 PHE H 100E TYR 0.019 0.001 TYR M 141 ARG 0.005 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 473) hydrogen bonds : angle 5.00993 ( 1284) SS BOND : bond 0.00345 ( 26) SS BOND : angle 0.75922 ( 52) covalent geometry : bond 0.00407 (13490) covalent geometry : angle 0.60279 (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 84 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 ILE cc_start: 0.9026 (mp) cc_final: 0.8741 (tt) REVERT: H 1 GLN cc_start: 0.9434 (tp40) cc_final: 0.9135 (tp40) REVERT: H 100 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8613 (m-80) REVERT: B 435 HIS cc_start: 0.8640 (m170) cc_final: 0.8262 (m170) REVERT: I 87 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8582 (t) outliers start: 14 outliers final: 11 residues processed: 82 average time/residue: 0.2452 time to fit residues: 32.8035 Evaluate side-chains 82 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 L residue 51 ASP Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain M residue 189 HIS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 194 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 27 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 168 optimal weight: 30.0000 chunk 58 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 9 optimal weight: 0.0030 chunk 51 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 0.0870 chunk 1 optimal weight: 1.9990 overall best weight: 0.4568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN H 39 GLN H 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.103547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.058465 restraints weight = 35631.761| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 4.16 r_work: 0.2708 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13516 Z= 0.107 Angle : 0.567 12.294 18388 Z= 0.291 Chirality : 0.044 0.228 2114 Planarity : 0.004 0.057 2358 Dihedral : 3.962 18.579 1886 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.09 % Favored : 93.85 % Rotamer: Outliers : 0.81 % Allowed : 16.31 % 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: -0.77 (0.21), residues: 1740 helix: 0.23 (0.34), residues: 279 sheet: 0.90 (0.23), residues: 574 loop : -1.80 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 309 HIS 0.006 0.001 HIS I 200 PHE 0.020 0.001 PHE H 100E TYR 0.016 0.001 TYR M 141 ARG 0.004 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03164 ( 473) hydrogen bonds : angle 4.79195 ( 1284) SS BOND : bond 0.00261 ( 26) SS BOND : angle 0.67276 ( 52) covalent geometry : bond 0.00247 (13490) covalent geometry : angle 0.56650 (18336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7710.87 seconds wall clock time: 136 minutes 42.43 seconds (8202.43 seconds total)