Starting phenix.real_space_refine on Mon Dec 30 13:37:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ebp_27995/12_2024/8ebp_27995.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ebp_27995/12_2024/8ebp_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_27995/12_2024/8ebp_27995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ebp_27995/12_2024/8ebp_27995.map" model { file = "/net/cci-nas-00/data/ceres_data/8ebp_27995/12_2024/8ebp_27995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ebp_27995/12_2024/8ebp_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-5532/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: 7.91, per 1000 atoms: 0.60 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: 3.22 Conformation dependent library (CDL) restraints added in 1.7 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: 1.97 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: 4.76 Time building geometry restraints manager: 3.73 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: 0.00 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: 0.840 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.890 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.910 ------------------------------------------------------------------------------- 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 13490 Z= 0.223 Angle : 0.632 8.063 18336 Z= 0.349 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 *********************** 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 : 1.610 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: 0.2281 time to fit residues: 33.4533 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 : 1.643 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 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 13490 Z= 0.302 Angle : 0.665 8.864 18336 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 *********************** 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 : 1.709 Fit side-chains revert: symmetry clash REVERT: A 95 ILE cc_start: 0.8597 (mm) cc_final: 0.8348 (mm) REVERT: L 139 ASP cc_start: 0.9370 (m-30) cc_final: 0.9006 (m-30) REVERT: H 144 ASP cc_start: 0.8235 (m-30) cc_final: 0.7981 (m-30) REVERT: B 435 HIS cc_start: 0.7915 (m170) cc_final: 0.7614 (m170) outliers start: 4 outliers final: 2 residues processed: 78 average time/residue: 0.2223 time to fit residues: 28.1503 Evaluate side-chains 70 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 1.588 ------------------------------------------------------------------------------- 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 86 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 156 optimal weight: 0.9980 chunk 169 optimal weight: 50.0000 chunk 139 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13490 Z= 0.331 Angle : 0.630 6.827 18336 Z= 0.329 Chirality : 0.046 0.220 2114 Planarity : 0.004 0.059 2358 Dihedral : 4.350 18.696 1886 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.61 % Favored : 93.33 % Rotamer: Outliers : 0.88 % Allowed : 9.40 % Favored : 89.72 % 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: -1.30 (0.20), residues: 1740 helix: -0.47 (0.33), residues: 273 sheet: 0.53 (0.23), residues: 577 loop : -2.02 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.009 0.001 HIS I 200 PHE 0.016 0.001 PHE H 100E TYR 0.021 0.001 TYR M 141 ARG 0.005 0.000 ARG A 102 *********************** 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: 13 poor density : 74 time to evaluate : 1.599 Fit side-chains revert: symmetry clash REVERT: A 95 ILE cc_start: 0.8623 (mm) cc_final: 0.8379 (mm) REVERT: L 139 ASP cc_start: 0.9420 (m-30) cc_final: 0.9090 (m-30) REVERT: H 144 ASP cc_start: 0.8229 (m-30) cc_final: 0.7988 (m-30) REVERT: H 176 TYR cc_start: 0.8698 (m-80) cc_final: 0.8435 (m-10) REVERT: H 208 ASP cc_start: 0.9174 (m-30) cc_final: 0.8457 (t0) REVERT: H 212 GLU cc_start: 0.7868 (pm20) cc_final: 0.7379 (pp20) REVERT: B 435 HIS cc_start: 0.8014 (m170) cc_final: 0.7683 (m170) REVERT: M 30 ASP cc_start: 0.8258 (t0) cc_final: 0.8045 (t0) outliers start: 13 outliers final: 10 residues processed: 84 average time/residue: 0.2223 time to fit residues: 30.3789 Evaluate side-chains 77 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 H residue 197 ASN Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain M residue 20 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 154 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 157 optimal weight: 0.7980 chunk 166 optimal weight: 40.0000 chunk 82 optimal weight: 6.9990 chunk 148 optimal weight: 40.0000 chunk 44 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 189 HIS H 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13490 Z= 0.194 Angle : 0.577 10.715 18336 Z= 0.299 Chirality : 0.044 0.220 2114 Planarity : 0.004 0.058 2358 Dihedral : 4.135 18.410 1886 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.09 % Favored : 93.85 % Rotamer: Outliers : 0.88 % Allowed : 11.43 % Favored : 87.69 % 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: -1.18 (0.20), residues: 1740 helix: -0.24 (0.34), residues: 274 sheet: 0.80 (0.23), residues: 544 loop : -2.05 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 154 HIS 0.009 0.001 HIS I 200 PHE 0.014 0.001 PHE H 100E TYR 0.019 0.001 TYR M 141 ARG 0.003 0.000 ARG B 205 *********************** 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 91 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ILE cc_start: 0.8581 (mm) cc_final: 0.8368 (mm) REVERT: L 139 ASP cc_start: 0.9420 (m-30) cc_final: 0.9095 (m-30) REVERT: H 144 ASP cc_start: 0.8004 (m-30) cc_final: 0.7777 (m-30) REVERT: H 208 ASP cc_start: 0.9170 (m-30) cc_final: 0.8471 (t0) REVERT: H 212 GLU cc_start: 0.7823 (pm20) cc_final: 0.7315 (pp20) REVERT: B 197 ASN cc_start: 0.8667 (t0) cc_final: 0.8319 (t0) REVERT: B 435 HIS cc_start: 0.8068 (m170) cc_final: 0.7728 (m170) REVERT: I 176 TYR cc_start: 0.9268 (m-80) cc_final: 0.8908 (m-10) outliers start: 13 outliers final: 3 residues processed: 89 average time/residue: 0.2250 time to fit residues: 31.9937 Evaluate side-chains 74 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 281 THR 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 138 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 40.0000 chunk 149 optimal weight: 40.0000 chunk 41 optimal weight: 6.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 155 ASN B 247 ASN M 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.065 13490 Z= 0.652 Angle : 0.782 7.766 18336 Z= 0.407 Chirality : 0.050 0.219 2114 Planarity : 0.005 0.064 2358 Dihedral : 4.726 20.127 1886 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.53 % Favored : 92.41 % Rotamer: Outliers : 2.03 % Allowed : 12.45 % Favored : 85.52 % 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: -1.58 (0.20), residues: 1740 helix: -0.77 (0.31), residues: 278 sheet: 0.25 (0.23), residues: 563 loop : -2.06 (0.19), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 154 HIS 0.009 0.002 HIS H 35 PHE 0.022 0.002 PHE I 100E TYR 0.026 0.002 TYR H 176 ARG 0.009 0.001 ARG A 102 *********************** 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 105 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 1.581 Fit side-chains revert: symmetry clash REVERT: A 95 ILE cc_start: 0.8674 (mm) cc_final: 0.8469 (mm) REVERT: L 139 ASP cc_start: 0.9370 (m-30) cc_final: 0.9119 (m-30) REVERT: H 208 ASP cc_start: 0.9181 (m-30) cc_final: 0.8476 (t0) REVERT: B 435 HIS cc_start: 0.8129 (m170) cc_final: 0.7736 (m-70) REVERT: M 30 ASP cc_start: 0.8398 (t0) cc_final: 0.8193 (t0) REVERT: M 199 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8047 (mp0) outliers start: 30 outliers final: 17 residues processed: 98 average time/residue: 0.2113 time to fit residues: 33.9635 Evaluate side-chains 82 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR 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 270 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain H residue 148 GLU Chi-restraints excluded: chain H residue 197 ASN 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 20 ILE Chi-restraints excluded: chain M residue 75 ILE 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 55 optimal weight: 20.0000 chunk 149 optimal weight: 30.0000 chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 166 optimal weight: 40.0000 chunk 138 optimal weight: 0.9990 chunk 77 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 155 ASN M 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13490 Z= 0.191 Angle : 0.606 11.566 18336 Z= 0.313 Chirality : 0.045 0.219 2114 Planarity : 0.004 0.061 2358 Dihedral : 4.372 19.191 1886 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.26 % Favored : 93.62 % Rotamer: Outliers : 1.29 % Allowed : 14.01 % 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: -1.23 (0.20), residues: 1740 helix: -0.29 (0.33), residues: 277 sheet: 0.55 (0.23), residues: 568 loop : -1.99 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 154 HIS 0.007 0.001 HIS H 200 PHE 0.019 0.001 PHE H 100E TYR 0.020 0.001 TYR M 141 ARG 0.003 0.000 ARG B 205 *********************** 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 93 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 1.765 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9106 (t) cc_final: 0.8800 (m) REVERT: L 139 ASP cc_start: 0.9321 (m-30) cc_final: 0.9061 (m-30) REVERT: H 208 ASP cc_start: 0.9138 (m-30) cc_final: 0.8429 (t0) REVERT: B 281 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8644 (p) REVERT: B 435 HIS cc_start: 0.8192 (m170) cc_final: 0.7897 (m170) REVERT: M 30 ASP cc_start: 0.8259 (t0) cc_final: 0.8026 (t0) REVERT: I 87 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8572 (t) outliers start: 19 outliers final: 10 residues processed: 91 average time/residue: 0.2059 time to fit residues: 30.9492 Evaluate side-chains 77 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 281 THR 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 205 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 92 optimal weight: 0.7980 chunk 165 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13490 Z= 0.214 Angle : 0.588 10.388 18336 Z= 0.303 Chirality : 0.045 0.221 2114 Planarity : 0.004 0.061 2358 Dihedral : 4.212 18.164 1886 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.03 % Favored : 93.91 % Rotamer: Outliers : 0.95 % Allowed : 15.63 % Favored : 83.42 % 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: -1.11 (0.21), residues: 1740 helix: -0.15 (0.34), residues: 279 sheet: 0.64 (0.23), residues: 568 loop : -1.94 (0.20), residues: 893 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 0.017 0.001 PHE H 100E TYR 0.026 0.001 TYR M 141 ARG 0.003 0.000 ARG A 102 *********************** 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: 14 poor density : 74 time to evaluate : 1.618 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9086 (t) cc_final: 0.8765 (m) REVERT: A 392 ILE cc_start: 0.9039 (mp) cc_final: 0.8778 (pt) REVERT: L 139 ASP cc_start: 0.9331 (m-30) cc_final: 0.9073 (m-30) REVERT: H 208 ASP cc_start: 0.9171 (m-30) cc_final: 0.8468 (t0) REVERT: B 435 HIS cc_start: 0.8185 (m170) cc_final: 0.7840 (m-70) REVERT: I 87 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8542 (t) outliers start: 14 outliers final: 9 residues processed: 86 average time/residue: 0.2245 time to fit residues: 32.5860 Evaluate side-chains 80 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 281 THR Chi-restraints excluded: chain H residue 197 ASN 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 205 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 150 optimal weight: 0.0030 chunk 158 optimal weight: 3.9990 chunk 144 optimal weight: 0.0570 overall best weight: 0.9110 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13490 Z= 0.180 Angle : 0.578 12.629 18336 Z= 0.298 Chirality : 0.044 0.224 2114 Planarity : 0.004 0.059 2358 Dihedral : 4.094 18.367 1886 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.21 % Favored : 93.62 % Rotamer: Outliers : 1.15 % Allowed : 16.10 % Favored : 82.75 % 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: -0.02 (0.34), residues: 279 sheet: 0.70 (0.23), residues: 572 loop : -1.92 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 309 HIS 0.005 0.001 HIS H 200 PHE 0.017 0.001 PHE H 100E TYR 0.023 0.001 TYR M 141 ARG 0.003 0.000 ARG B 205 *********************** 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: 17 poor density : 75 time to evaluate : 1.616 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9025 (t) cc_final: 0.8758 (m) REVERT: A 392 ILE cc_start: 0.9044 (mp) cc_final: 0.8777 (tt) REVERT: L 139 ASP cc_start: 0.9398 (m-30) cc_final: 0.9150 (m-30) REVERT: H 208 ASP cc_start: 0.9179 (m-30) cc_final: 0.8467 (t0) REVERT: B 197 ASN cc_start: 0.8537 (t0) cc_final: 0.8221 (t0) REVERT: B 435 HIS cc_start: 0.8166 (m170) cc_final: 0.7823 (m-70) REVERT: I 87 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8544 (t) REVERT: I 138 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.6871 (pt) outliers start: 17 outliers final: 11 residues processed: 91 average time/residue: 0.2110 time to fit residues: 31.9328 Evaluate side-chains 86 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain H residue 197 ASN 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 138 LEU 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 154 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 153 optimal weight: 0.8980 chunk 101 optimal weight: 0.0770 chunk 163 optimal weight: 2.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13490 Z= 0.167 Angle : 0.569 12.147 18336 Z= 0.292 Chirality : 0.044 0.226 2114 Planarity : 0.004 0.058 2358 Dihedral : 3.985 18.063 1886 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 0.81 % Allowed : 16.64 % Favored : 82.54 % 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: 0.12 (0.34), residues: 279 sheet: 0.80 (0.23), residues: 576 loop : -1.89 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 309 HIS 0.006 0.001 HIS I 200 PHE 0.023 0.001 PHE H 100E TYR 0.024 0.001 TYR M 141 ARG 0.003 0.000 ARG B 205 *********************** 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 85 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8997 (t) cc_final: 0.8721 (m) REVERT: A 392 ILE cc_start: 0.9031 (mp) cc_final: 0.8795 (tt) REVERT: L 139 ASP cc_start: 0.9371 (m-30) cc_final: 0.9113 (m-30) REVERT: B 197 ASN cc_start: 0.8465 (t0) cc_final: 0.8179 (t0) REVERT: B 435 HIS cc_start: 0.8165 (m170) cc_final: 0.7827 (m-70) REVERT: I 87 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8500 (t) outliers start: 12 outliers final: 8 residues processed: 84 average time/residue: 0.2204 time to fit residues: 29.9327 Evaluate side-chains 79 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain H residue 197 ASN 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 205 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 171 optimal weight: 20.0000 chunk 157 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 chunk 108 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13490 Z= 0.371 Angle : 0.644 11.394 18336 Z= 0.333 Chirality : 0.046 0.225 2114 Planarity : 0.004 0.059 2358 Dihedral : 4.201 18.654 1886 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.67 % Favored : 93.28 % Rotamer: Outliers : 0.81 % Allowed : 16.64 % Favored : 82.54 % 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: -1.05 (0.21), residues: 1740 helix: -0.05 (0.33), residues: 280 sheet: 0.63 (0.23), residues: 573 loop : -1.90 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.006 0.001 HIS H 35 PHE 0.023 0.002 PHE H 100E TYR 0.025 0.001 TYR M 141 ARG 0.005 0.000 ARG A 102 ********************** 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: 12 poor density : 72 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 ILE cc_start: 0.9015 (mp) cc_final: 0.8738 (tt) REVERT: L 139 ASP cc_start: 0.9374 (m-30) cc_final: 0.9130 (m-30) REVERT: H 208 ASP cc_start: 0.9158 (m-30) cc_final: 0.8422 (t0) REVERT: B 435 HIS cc_start: 0.8190 (m170) cc_final: 0.7838 (m-70) REVERT: I 87 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8658 (t) outliers start: 12 outliers final: 9 residues processed: 84 average time/residue: 0.2225 time to fit residues: 30.6077 Evaluate side-chains 81 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 271 VAL 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 41 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 20 optimal weight: 0.0060 chunk 37 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 overall best weight: 1.2398 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.102211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.057122 restraints weight = 35610.955| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 4.07 r_work: 0.2670 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13490 Z= 0.206 Angle : 0.585 11.571 18336 Z= 0.301 Chirality : 0.044 0.229 2114 Planarity : 0.004 0.058 2358 Dihedral : 4.103 17.827 1886 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.32 % Favored : 93.62 % Rotamer: Outliers : 0.88 % Allowed : 16.71 % Favored : 82.41 % 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: 0.10 (0.34), residues: 280 sheet: 0.73 (0.23), residues: 586 loop : -1.85 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 284 HIS 0.005 0.001 HIS H 200 PHE 0.022 0.001 PHE H 100E TYR 0.022 0.001 TYR M 141 ARG 0.002 0.000 ARG A 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2361.57 seconds wall clock time: 45 minutes 13.47 seconds (2713.47 seconds total)