Starting phenix.real_space_refine on Sat Aug 23 16:10:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ebp_27995/08_2025/8ebp_27995.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ebp_27995/08_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_27995/08_2025/8ebp_27995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ebp_27995/08_2025/8ebp_27995.map" model { file = "/net/cci-nas-00/data/ceres_data/8ebp_27995/08_2025/8ebp_27995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ebp_27995/08_2025/8ebp_27995.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.52, per 1000 atoms: 0.27 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: 1.03 Conformation dependent library (CDL) restraints added in 828.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.60 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: 2.53 Time building geometry restraints manager: 1.36 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: 0.01 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: 1.570 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.090 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.520 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG L 18 TYR 0.013 0.001 TYR I 145 PHE 0.010 0.001 PHE H 100E TRP 0.007 0.001 TRP H 47 HIS 0.008 0.001 HIS H 200 Details of bonding type rmsd covalent geometry : bond 0.00351 (13490) covalent geometry : angle 0.63196 (18336) SS BOND : bond 0.00305 ( 26) SS BOND : angle 0.85717 ( 52) hydrogen bonds : bond 0.27009 ( 473) hydrogen bonds : angle 9.75818 ( 1284) *********************** 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 : 0.539 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: 0.0915 time to fit residues: 13.5065 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 : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.0170 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 40.0000 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.0822 ------------------------------------------------------------------------------- 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 B 322 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 = 0.3853 r_free = 0.3853 target = 0.103746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.059102 restraints weight = 35791.162| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 4.18 r_work: 0.2689 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1100 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= 0.148 Angle : 0.637 9.748 18388 Z= 0.335 Chirality : 0.046 0.219 2114 Planarity : 0.004 0.054 2358 Dihedral : 4.214 18.649 1886 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.38 % Favored : 93.56 % Rotamer: Outliers : 0.34 % Allowed : 6.22 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.20), residues: 1740 helix: -0.43 (0.33), residues: 268 sheet: 0.75 (0.24), residues: 538 loop : -2.05 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 18 TYR 0.037 0.001 TYR I 194 PHE 0.012 0.001 PHE H 166 TRP 0.009 0.001 TRP B 284 HIS 0.008 0.001 HIS I 200 Details of bonding type rmsd covalent geometry : bond 0.00327 (13490) covalent geometry : angle 0.63639 (18336) SS BOND : bond 0.00315 ( 26) SS BOND : angle 0.73036 ( 52) hydrogen bonds : bond 0.05902 ( 473) hydrogen bonds : angle 6.62207 ( 1284) *********************** 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 84 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: L 139 ASP cc_start: 0.9469 (m-30) cc_final: 0.9244 (m-30) REVERT: I 148 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8519 (mm-30) outliers start: 5 outliers final: 2 residues processed: 82 average time/residue: 0.0909 time to fit residues: 12.0687 Evaluate side-chains 68 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 24 optimal weight: 3.9990 chunk 142 optimal weight: 40.0000 chunk 119 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 140 optimal weight: 30.0000 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.102296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.057397 restraints weight = 36031.205| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 4.07 r_work: 0.2642 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 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 0.040 13516 Z= 0.229 Angle : 0.642 7.933 18388 Z= 0.335 Chirality : 0.046 0.213 2114 Planarity : 0.004 0.060 2358 Dihedral : 4.307 18.414 1886 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.61 % Favored : 93.33 % Rotamer: Outliers : 1.01 % Allowed : 9.20 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.20), residues: 1740 helix: -0.45 (0.33), residues: 273 sheet: 0.63 (0.23), residues: 553 loop : -2.07 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 102 TYR 0.020 0.001 TYR M 141 PHE 0.016 0.001 PHE H 100E TRP 0.010 0.001 TRP H 47 HIS 0.010 0.001 HIS I 200 Details of bonding type rmsd covalent geometry : bond 0.00537 (13490) covalent geometry : angle 0.64107 (18336) SS BOND : bond 0.00401 ( 26) SS BOND : angle 0.88643 ( 52) hydrogen bonds : bond 0.05063 ( 473) hydrogen bonds : angle 6.07826 ( 1284) *********************** 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 89 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: L 139 ASP cc_start: 0.9475 (m-30) cc_final: 0.9251 (m-30) REVERT: H 208 ASP cc_start: 0.9189 (m-30) cc_final: 0.8754 (t0) REVERT: H 212 GLU cc_start: 0.7886 (pm20) cc_final: 0.7503 (pp20) REVERT: M 30 ASP cc_start: 0.9002 (t0) cc_final: 0.8665 (t0) outliers start: 15 outliers final: 10 residues processed: 86 average time/residue: 0.0917 time to fit residues: 12.7438 Evaluate side-chains 75 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain B residue 236 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 19 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 0.0470 chunk 38 optimal weight: 20.0000 chunk 159 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 89 optimal weight: 0.6980 chunk 167 optimal weight: 30.0000 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.103497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.058194 restraints weight = 35639.585| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 4.09 r_work: 0.2701 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13516 Z= 0.112 Angle : 0.562 6.902 18388 Z= 0.291 Chirality : 0.044 0.217 2114 Planarity : 0.004 0.058 2358 Dihedral : 4.092 18.624 1886 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.09 % Favored : 93.85 % Rotamer: Outliers : 0.74 % Allowed : 11.10 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.21), residues: 1740 helix: -0.20 (0.34), residues: 274 sheet: 0.76 (0.23), residues: 568 loop : -1.96 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 205 TYR 0.025 0.001 TYR H 176 PHE 0.011 0.001 PHE H 100E TRP 0.010 0.001 TRP I 154 HIS 0.008 0.001 HIS H 200 Details of bonding type rmsd covalent geometry : bond 0.00255 (13490) covalent geometry : angle 0.56189 (18336) SS BOND : bond 0.00285 ( 26) SS BOND : angle 0.73683 ( 52) hydrogen bonds : bond 0.03869 ( 473) hydrogen bonds : angle 5.47727 ( 1284) *********************** 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 88 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: L 83 GLU cc_start: 0.8840 (tp30) cc_final: 0.8510 (mm-30) REVERT: H 208 ASP cc_start: 0.9205 (m-30) cc_final: 0.8751 (t0) REVERT: H 212 GLU cc_start: 0.7903 (pm20) cc_final: 0.7490 (pp20) outliers start: 11 outliers final: 5 residues processed: 85 average time/residue: 0.1018 time to fit residues: 13.9346 Evaluate side-chains 74 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 111 optimal weight: 2.9990 chunk 11 optimal weight: 0.0000 chunk 81 optimal weight: 30.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 149 optimal weight: 30.0000 chunk 76 optimal weight: 4.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- 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 B 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.102311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.056728 restraints weight = 35852.491| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 4.10 r_work: 0.2663 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13516 Z= 0.174 Angle : 0.596 10.998 18388 Z= 0.309 Chirality : 0.045 0.220 2114 Planarity : 0.004 0.060 2358 Dihedral : 4.114 17.729 1886 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 1.08 % Allowed : 12.58 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.21), residues: 1740 helix: -0.11 (0.34), residues: 275 sheet: 0.73 (0.23), residues: 567 loop : -1.97 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 102 TYR 0.020 0.001 TYR M 141 PHE 0.014 0.001 PHE H 100E TRP 0.025 0.001 TRP H 154 HIS 0.008 0.001 HIS I 200 Details of bonding type rmsd covalent geometry : bond 0.00408 (13490) covalent geometry : angle 0.59487 (18336) SS BOND : bond 0.00345 ( 26) SS BOND : angle 0.80369 ( 52) hydrogen bonds : bond 0.03948 ( 473) hydrogen bonds : angle 5.38694 ( 1284) *********************** 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 94 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: L 83 GLU cc_start: 0.8831 (tp30) cc_final: 0.8477 (mm-30) REVERT: H 212 GLU cc_start: 0.7899 (pm20) cc_final: 0.7487 (pp20) REVERT: I 148 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8175 (mm-30) outliers start: 16 outliers final: 7 residues processed: 91 average time/residue: 0.1002 time to fit residues: 14.7328 Evaluate side-chains 76 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 A residue 281 THR Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain B residue 45 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 171 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 166 optimal weight: 30.0000 chunk 143 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 M 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.101667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.056165 restraints weight = 35972.550| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 4.11 r_work: 0.2643 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13516 Z= 0.216 Angle : 0.615 9.401 18388 Z= 0.319 Chirality : 0.045 0.220 2114 Planarity : 0.004 0.060 2358 Dihedral : 4.214 18.475 1886 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.78 % Favored : 93.16 % Rotamer: Outliers : 1.42 % Allowed : 13.73 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.21), residues: 1740 helix: -0.21 (0.33), residues: 277 sheet: 0.66 (0.23), residues: 572 loop : -1.96 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 102 TYR 0.020 0.001 TYR M 141 PHE 0.018 0.001 PHE M 62 TRP 0.009 0.001 TRP A 284 HIS 0.011 0.001 HIS I 200 Details of bonding type rmsd covalent geometry : bond 0.00507 (13490) covalent geometry : angle 0.61401 (18336) SS BOND : bond 0.00424 ( 26) SS BOND : angle 0.83057 ( 52) hydrogen bonds : bond 0.04102 ( 473) hydrogen bonds : angle 5.36756 ( 1284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8862 (m-80) REVERT: H 208 ASP cc_start: 0.9177 (m-30) cc_final: 0.8706 (t0) REVERT: I 87 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8691 (t) REVERT: I 148 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8322 (mm-30) outliers start: 21 outliers final: 10 residues processed: 91 average time/residue: 0.0990 time to fit residues: 14.5738 Evaluate side-chains 82 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 270 MET Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain L residue 171 ASN 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 171 ASN 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 77 optimal weight: 4.9990 chunk 151 optimal weight: 0.2980 chunk 85 optimal weight: 30.0000 chunk 26 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 65 optimal weight: 0.0170 chunk 111 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 overall best weight: 0.9220 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.102804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.057100 restraints weight = 35559.551| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 4.28 r_work: 0.2654 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.003 0.042 13516 Z= 0.125 Angle : 0.575 9.060 18388 Z= 0.296 Chirality : 0.044 0.222 2114 Planarity : 0.004 0.060 2358 Dihedral : 4.108 18.168 1886 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.03 % Favored : 93.91 % Rotamer: Outliers : 1.01 % Allowed : 14.68 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.21), residues: 1740 helix: -0.07 (0.34), residues: 279 sheet: 0.68 (0.23), residues: 572 loop : -1.92 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 205 TYR 0.020 0.001 TYR M 141 PHE 0.013 0.001 PHE H 100E TRP 0.008 0.001 TRP B 284 HIS 0.008 0.001 HIS I 200 Details of bonding type rmsd covalent geometry : bond 0.00289 (13490) covalent geometry : angle 0.57469 (18336) SS BOND : bond 0.00301 ( 26) SS BOND : angle 0.70674 ( 52) hydrogen bonds : bond 0.03626 ( 473) hydrogen bonds : angle 5.14242 ( 1284) *********************** 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 90 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9279 (t) cc_final: 0.8959 (m) REVERT: H 208 ASP cc_start: 0.9189 (m-30) cc_final: 0.8711 (t0) outliers start: 15 outliers final: 9 residues processed: 86 average time/residue: 0.1034 time to fit residues: 14.2905 Evaluate side-chains 80 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain L residue 171 ASN 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 M residue 135 CYS Chi-restraints excluded: chain I residue 100 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 101 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 131 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 M 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.102246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.056473 restraints weight = 35748.444| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 4.28 r_work: 0.2640 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13516 Z= 0.165 Angle : 0.594 12.551 18388 Z= 0.307 Chirality : 0.045 0.223 2114 Planarity : 0.004 0.059 2358 Dihedral : 4.098 18.027 1886 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.21 % Favored : 93.74 % Rotamer: Outliers : 1.08 % Allowed : 15.29 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.21), residues: 1740 helix: -0.05 (0.34), residues: 279 sheet: 0.68 (0.23), residues: 572 loop : -1.91 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.021 0.001 TYR M 141 PHE 0.023 0.001 PHE H 100E TRP 0.008 0.001 TRP A 284 HIS 0.008 0.001 HIS I 200 Details of bonding type rmsd covalent geometry : bond 0.00390 (13490) covalent geometry : angle 0.59349 (18336) SS BOND : bond 0.00328 ( 26) SS BOND : angle 0.75115 ( 52) hydrogen bonds : bond 0.03675 ( 473) hydrogen bonds : angle 5.12899 ( 1284) *********************** 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 89 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 87 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8595 (t) outliers start: 16 outliers final: 13 residues processed: 86 average time/residue: 0.1000 time to fit residues: 13.9075 Evaluate side-chains 86 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 L residue 171 ASN 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 M residue 135 CYS Chi-restraints excluded: chain M residue 171 ASN Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 140 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 93 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 9 optimal weight: 0.0050 chunk 171 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.102574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.056844 restraints weight = 35945.895| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 4.26 r_work: 0.2649 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2138 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= 0.146 Angle : 0.582 11.749 18388 Z= 0.301 Chirality : 0.045 0.280 2114 Planarity : 0.004 0.058 2358 Dihedral : 4.082 18.181 1886 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.15 % Favored : 93.79 % Rotamer: Outliers : 1.29 % Allowed : 15.36 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.21), residues: 1740 helix: 0.02 (0.34), residues: 279 sheet: 0.70 (0.23), residues: 572 loop : -1.89 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.022 0.001 TYR M 141 PHE 0.021 0.001 PHE H 100E TRP 0.008 0.001 TRP A 284 HIS 0.007 0.001 HIS I 200 Details of bonding type rmsd covalent geometry : bond 0.00343 (13490) covalent geometry : angle 0.58102 (18336) SS BOND : bond 0.00311 ( 26) SS BOND : angle 0.73118 ( 52) hydrogen bonds : bond 0.03564 ( 473) hydrogen bonds : angle 5.05723 ( 1284) *********************** 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 91 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8671 (m-80) REVERT: I 87 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8588 (t) outliers start: 19 outliers final: 13 residues processed: 88 average time/residue: 0.1004 time to fit residues: 14.3718 Evaluate side-chains 86 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 281 THR 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 50 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 140 CYS Chi-restraints excluded: chain I residue 197 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 59 optimal weight: 8.9990 chunk 20 optimal weight: 0.1980 chunk 148 optimal weight: 40.0000 chunk 77 optimal weight: 20.0000 chunk 169 optimal weight: 40.0000 chunk 130 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 101 optimal weight: 0.4980 chunk 55 optimal weight: 5.9990 chunk 145 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.103199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.057811 restraints weight = 35885.372| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 4.14 r_work: 0.2691 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2235 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= 0.119 Angle : 0.573 11.506 18388 Z= 0.296 Chirality : 0.044 0.229 2114 Planarity : 0.004 0.057 2358 Dihedral : 3.988 18.349 1886 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.80 % Favored : 94.14 % Rotamer: Outliers : 1.01 % Allowed : 15.83 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.21), residues: 1740 helix: 0.15 (0.34), residues: 279 sheet: 0.73 (0.23), residues: 580 loop : -1.86 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 205 TYR 0.021 0.001 TYR M 141 PHE 0.020 0.001 PHE H 100E TRP 0.008 0.001 TRP A 309 HIS 0.007 0.001 HIS I 200 Details of bonding type rmsd covalent geometry : bond 0.00278 (13490) covalent geometry : angle 0.57252 (18336) SS BOND : bond 0.00269 ( 26) SS BOND : angle 0.67622 ( 52) hydrogen bonds : bond 0.03271 ( 473) hydrogen bonds : angle 4.90343 ( 1284) ********************** 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 89 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9250 (t) cc_final: 0.8931 (m) REVERT: I 87 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8477 (t) outliers start: 15 outliers final: 12 residues processed: 87 average time/residue: 0.0993 time to fit residues: 14.0027 Evaluate side-chains 85 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 H residue 197 ASN 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 I residue 87 THR Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 140 CYS Chi-restraints excluded: chain I residue 197 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 21 optimal weight: 0.6980 chunk 162 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 50 optimal weight: 0.2980 chunk 125 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 94 optimal weight: 0.3980 chunk 103 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 M 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.103750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.058605 restraints weight = 35741.646| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 4.17 r_work: 0.2712 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2377 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= 0.110 Angle : 0.570 11.234 18388 Z= 0.294 Chirality : 0.044 0.230 2114 Planarity : 0.004 0.057 2358 Dihedral : 3.893 18.398 1886 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.80 % Favored : 94.14 % Rotamer: Outliers : 1.01 % Allowed : 15.76 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.21), residues: 1740 helix: 0.30 (0.34), residues: 277 sheet: 0.79 (0.23), residues: 585 loop : -1.81 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 205 TYR 0.021 0.001 TYR M 141 PHE 0.020 0.001 PHE H 100E TRP 0.008 0.001 TRP B 309 HIS 0.006 0.001 HIS I 200 Details of bonding type rmsd covalent geometry : bond 0.00258 (13490) covalent geometry : angle 0.56962 (18336) SS BOND : bond 0.00261 ( 26) SS BOND : angle 0.67834 ( 52) hydrogen bonds : bond 0.03080 ( 473) hydrogen bonds : angle 4.78218 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3756.25 seconds wall clock time: 65 minutes 8.52 seconds (3908.52 seconds total)