Starting phenix.real_space_refine on Fri Jul 3 15:16:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g4c_29716/07_2026/8g4c_29716.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g4c_29716/07_2026/8g4c_29716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g4c_29716/07_2026/8g4c_29716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g4c_29716/07_2026/8g4c_29716.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8g4c_29716/07_2026/8g4c_29716.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g4c_29716/07_2026/8g4c_29716.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g4c_29716/07_2026/8g4c_29716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g4c_29716/07_2026/8g4c_29716.map" } resolution = 3.1 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= -0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 64 5.16 5 C 9388 2.51 5 N 2401 2.21 5 O 2643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14503 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5036 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 10, 'TRANS': 628} Chain breaks: 1 Chain: "B" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1940 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 5, 'TRANS': 242} Chain: "C" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1940 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 5, 'TRANS': 242} Chain: "D" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "E" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'6OU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.47, per 1000 atoms: 0.17 Number of scatterers: 14503 At special positions: 0 Unit cell: (108.128, 123.824, 192.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 7 15.00 O 2643 8.00 N 2401 7.00 C 9388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.78 Conformation dependent library (CDL) restraints added in 525.0 milliseconds 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3390 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 11 sheets defined 62.3% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 19 through 37 Processing helix chain 'A' and resid 41 through 47 removed outlier: 3.629A pdb=" N ASN A 45 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 82 removed outlier: 3.803A pdb=" N THR A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 94 Processing helix chain 'A' and resid 96 through 106 removed outlier: 3.938A pdb=" N ARG A 102 " --> pdb=" O HIS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 126 removed outlier: 3.776A pdb=" N ALA A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.625A pdb=" N VAL A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 177 removed outlier: 3.530A pdb=" N LEU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.624A pdb=" N SER A 182 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 183 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 184 " --> pdb=" O LEU A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 179 through 184' Processing helix chain 'A' and resid 198 through 223 removed outlier: 3.782A pdb=" N MET A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 267 removed outlier: 3.663A pdb=" N PHE A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL A 256 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 286 removed outlier: 3.798A pdb=" N SER A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 290 through 316 removed outlier: 3.605A pdb=" N THR A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 325 removed outlier: 3.998A pdb=" N THR A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 348 removed outlier: 4.122A pdb=" N GLU A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 416 Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 493 through 505 Processing helix chain 'A' and resid 513 through 554 removed outlier: 3.887A pdb=" N ALA A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LYS A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N MET A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A 553 " --> pdb=" O LYS A 549 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 Processing helix chain 'A' and resid 570 through 603 removed outlier: 3.810A pdb=" N LYS A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE A 588 " --> pdb=" O TYR A 584 " (cutoff:3.500A) Proline residue: A 589 - end of helix removed outlier: 4.146A pdb=" N SER A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 removed outlier: 4.270A pdb=" N LEU A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 603 through 608' Processing helix chain 'A' and resid 613 through 644 removed outlier: 4.199A pdb=" N ILE A 617 " --> pdb=" O TRP A 613 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 622 " --> pdb=" O MET A 618 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 623 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR A 624 " --> pdb=" O MET A 620 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 19 removed outlier: 4.181A pdb=" N LYS B 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.536A pdb=" N SER B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 86 removed outlier: 3.644A pdb=" N GLN B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.626A pdb=" N ILE B 112 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 removed outlier: 4.174A pdb=" N LYS B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 125 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.899A pdb=" N ARG B 137 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.673A pdb=" N ILE B 144 " --> pdb=" O PRO B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 159 removed outlier: 3.599A pdb=" N LYS B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 231 through 248 removed outlier: 3.767A pdb=" N VAL B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 247 " --> pdb=" O GLN B 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 54 removed outlier: 3.654A pdb=" N LEU C 49 " --> pdb=" O GLY C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 101 through 107 Processing helix chain 'C' and resid 108 through 112 removed outlier: 3.778A pdb=" N ILE C 112 " --> pdb=" O PRO C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 132 Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.526A pdb=" N ARG C 137 " --> pdb=" O TYR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 157 removed outlier: 3.740A pdb=" N ALA C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 193 removed outlier: 3.543A pdb=" N GLN C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.840A pdb=" N TYR C 209 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS C 210 " --> pdb=" O ALA C 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 206 through 210' Processing helix chain 'C' and resid 233 through 248 removed outlier: 3.540A pdb=" N VAL C 245 " --> pdb=" O LYS C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 9 through 30 removed outlier: 3.701A pdb=" N ILE D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 61 removed outlier: 3.646A pdb=" N TYR D 40 " --> pdb=" O GLY D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 removed outlier: 4.109A pdb=" N ASN D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 138 removed outlier: 3.638A pdb=" N VAL D 90 " --> pdb=" O PHE D 86 " (cutoff:3.500A) Proline residue: D 129 - end of helix Processing helix chain 'D' and resid 143 through 169 Processing helix chain 'D' and resid 183 through 194 Processing helix chain 'D' and resid 194 through 202 Processing helix chain 'D' and resid 217 through 235 Processing helix chain 'D' and resid 268 through 273 removed outlier: 3.937A pdb=" N PHE D 272 " --> pdb=" O PRO D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 285 removed outlier: 3.562A pdb=" N ASP D 284 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 300 removed outlier: 3.546A pdb=" N ALA D 300 " --> pdb=" O LYS D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 326 No H-bonds generated for 'chain 'D' and resid 324 through 326' Processing helix chain 'D' and resid 327 through 334 removed outlier: 4.312A pdb=" N VAL D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 10 through 30 removed outlier: 3.781A pdb=" N GLN E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE E 28 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 61 removed outlier: 3.766A pdb=" N TYR E 40 " --> pdb=" O GLY E 36 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET E 41 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE E 48 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG E 58 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS E 59 " --> pdb=" O PHE E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 71 Processing helix chain 'E' and resid 84 through 138 removed outlier: 3.754A pdb=" N VAL E 90 " --> pdb=" O PHE E 86 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER E 93 " --> pdb=" O MET E 89 " (cutoff:3.500A) Proline residue: E 129 - end of helix Processing helix chain 'E' and resid 143 through 169 Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 194 through 202 removed outlier: 3.525A pdb=" N CYS E 198 " --> pdb=" O LEU E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 236 Processing helix chain 'E' and resid 264 through 268 removed outlier: 3.693A pdb=" N VAL E 268 " --> pdb=" O PRO E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 287 Processing helix chain 'E' and resid 290 through 300 Processing helix chain 'E' and resid 324 through 328 removed outlier: 3.541A pdb=" N PHE E 328 " --> pdb=" O ARG E 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 330 removed outlier: 3.772A pdb=" N LEU A 511 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 388 removed outlier: 7.711A pdb=" N ALA A 403 " --> pdb=" O GLY A 439 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ARG A 441 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N PHE A 405 " --> pdb=" O ARG A 441 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 426 through 427 removed outlier: 3.506A pdb=" N GLN A 433 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 31 removed outlier: 6.513A pdb=" N LYS B 11 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS B 24 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE B 9 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 26 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN B 7 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 28 " --> pdb=" O GLU B 5 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU B 5 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE B 30 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE B 9 " --> pdb=" O HIS B 61 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N HIS B 61 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 87 through 91 removed outlier: 6.527A pdb=" N GLY B 88 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ASP B 168 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE B 90 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE B 165 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL B 200 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA B 167 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE B 35 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ILE B 214 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER B 37 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE B 216 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N MET B 39 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR B 223 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 18 through 31 removed outlier: 3.512A pdb=" N ASN C 18 " --> pdb=" O ASN C 15 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS C 11 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS C 24 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE C 9 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE C 26 " --> pdb=" O ASN C 7 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN C 7 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE C 28 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLU C 5 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE C 30 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR C 63 " --> pdb=" O ASN C 7 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE C 9 " --> pdb=" O HIS C 61 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N HIS C 61 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.388A pdb=" N GLY C 88 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL C 36 " --> pdb=" O MET C 199 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N THR C 201 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ILE C 38 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL C 213 " --> pdb=" O GLN C 224 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN C 224 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE C 215 " --> pdb=" O TYR C 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 179 through 182 removed outlier: 3.860A pdb=" N GLU D 179 " --> pdb=" O SER D 216 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER D 216 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 205 through 209 removed outlier: 6.168A pdb=" N ASP D 206 " --> pdb=" O ILE D 243 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N SER D 245 " --> pdb=" O ASP D 206 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLN D 208 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N GLN D 247 " --> pdb=" O GLN D 208 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS D 248 " --> pdb=" O GLN D 251 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS D 305 " --> pdb=" O THR D 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 181 through 182 removed outlier: 4.303A pdb=" N ILE E 181 " --> pdb=" O VAL E 214 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 214 " --> pdb=" O ILE E 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 205 through 209 removed outlier: 3.710A pdb=" N SER E 245 " --> pdb=" O GLN E 208 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS E 305 " --> pdb=" O THR E 321 " (cutoff:3.500A) 797 hydrogen bonds defined for protein. 2310 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: 2.00 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 4574 1.34 - 1.50: 3705 1.50 - 1.65: 6383 1.65 - 1.80: 62 1.80 - 1.95: 56 Bond restraints: 14780 Sorted by residual: bond pdb=" C16 6OU A 701 " pdb=" O18 6OU A 701 " ideal model delta sigma weight residual 1.327 1.463 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" C31 6OU A 701 " pdb=" O30 6OU A 701 " ideal model delta sigma weight residual 1.331 1.423 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C14 6OU A 701 " pdb=" C15 6OU A 701 " ideal model delta sigma weight residual 1.521 1.607 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C15 6OU A 701 " pdb=" C16 6OU A 701 " ideal model delta sigma weight residual 1.501 1.583 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C41 6OU A 701 " pdb=" C42 6OU A 701 " ideal model delta sigma weight residual 1.497 1.568 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 14775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.11: 19889 5.11 - 10.23: 19 10.23 - 15.34: 1 15.34 - 20.46: 1 20.46 - 25.57: 1 Bond angle restraints: 19911 Sorted by residual: angle pdb=" C40 6OU A 701 " pdb=" C41 6OU A 701 " pdb=" C42 6OU A 701 " ideal model delta sigma weight residual 127.56 153.13 -25.57 3.00e+00 1.11e-01 7.27e+01 angle pdb=" CA PRO E 129 " pdb=" N PRO E 129 " pdb=" CD PRO E 129 " ideal model delta sigma weight residual 112.00 102.89 9.11 1.40e+00 5.10e-01 4.24e+01 angle pdb=" O22 6OU A 701 " pdb=" P23 6OU A 701 " pdb=" O26 6OU A 701 " ideal model delta sigma weight residual 93.95 109.56 -15.61 3.00e+00 1.11e-01 2.71e+01 angle pdb=" C39 6OU A 701 " pdb=" C40 6OU A 701 " pdb=" C41 6OU A 701 " ideal model delta sigma weight residual 127.60 112.85 14.75 3.00e+00 1.11e-01 2.42e+01 angle pdb=" N ASP A 556 " pdb=" CA ASP A 556 " pdb=" C ASP A 556 " ideal model delta sigma weight residual 112.89 106.81 6.08 1.24e+00 6.50e-01 2.41e+01 ... (remaining 19906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.94: 8575 31.94 - 63.88: 268 63.88 - 95.82: 33 95.82 - 127.76: 0 127.76 - 159.70: 3 Dihedral angle restraints: 8879 sinusoidal: 3639 harmonic: 5240 Sorted by residual: dihedral pdb=" O1A AGS C 301 " pdb=" O3A AGS C 301 " pdb=" PA AGS C 301 " pdb=" PB AGS C 301 " ideal model delta sinusoidal sigma weight residual 292.27 132.57 159.70 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" O1A AGS B 301 " pdb=" O3A AGS B 301 " pdb=" PA AGS B 301 " pdb=" PB AGS B 301 " ideal model delta sinusoidal sigma weight residual -67.73 88.27 -156.00 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C12 6OU A 701 " pdb=" C13 6OU A 701 " pdb=" C14 6OU A 701 " pdb=" C15 6OU A 701 " ideal model delta sinusoidal sigma weight residual 186.47 40.88 145.59 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 8876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1559 0.035 - 0.070: 496 0.070 - 0.105: 151 0.105 - 0.140: 57 0.140 - 0.176: 5 Chirality restraints: 2268 Sorted by residual: chirality pdb=" CA PRO E 129 " pdb=" N PRO E 129 " pdb=" C PRO E 129 " pdb=" CB PRO E 129 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA VAL C 245 " pdb=" N VAL C 245 " pdb=" C VAL C 245 " pdb=" CB VAL C 245 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CG LEU E 119 " pdb=" CB LEU E 119 " pdb=" CD1 LEU E 119 " pdb=" CD2 LEU E 119 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 2265 not shown) Planarity restraints: 2479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 128 " 0.062 5.00e-02 4.00e+02 8.82e-02 1.25e+01 pdb=" N PRO E 129 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO E 129 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 129 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET C 240 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C MET C 240 " -0.035 2.00e-02 2.50e+03 pdb=" O MET C 240 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS C 241 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 84 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO D 85 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 85 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 85 " 0.024 5.00e-02 4.00e+02 ... (remaining 2476 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2437 2.77 - 3.30: 13449 3.30 - 3.83: 22790 3.83 - 4.37: 25311 4.37 - 4.90: 45802 Nonbonded interactions: 109789 Sorted by model distance: nonbonded pdb=" O SER A 125 " pdb=" OH TYR E 40 " model vdw 2.236 3.040 nonbonded pdb=" OG SER B 145 " pdb=" OE1 GLN B 148 " model vdw 2.245 3.040 nonbonded pdb=" OG SER A 406 " pdb=" O GLU A 443 " model vdw 2.282 3.040 nonbonded pdb=" O SER A 316 " pdb=" OG SER A 316 " model vdw 2.303 3.040 nonbonded pdb=" OD1 ASP A 410 " pdb=" N LEU A 411 " model vdw 2.306 3.120 ... (remaining 109784 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 3.620 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: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.300 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.010 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 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 0.136 14780 Z= 0.197 Angle : 0.593 25.574 19911 Z= 0.303 Chirality : 0.041 0.176 2268 Planarity : 0.003 0.088 2479 Dihedral : 15.899 159.702 5489 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.25 % Allowed : 0.83 % Favored : 98.92 % 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 are not related in a simple way. whole: 0.73 (0.21), residues: 1791 helix: 1.53 (0.17), residues: 1034 sheet: -0.16 (0.40), residues: 190 loop : -1.22 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 168 TYR 0.023 0.001 TYR A 623 PHE 0.013 0.001 PHE C 235 TRP 0.026 0.001 TRP A 605 HIS 0.003 0.001 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.20 (14780) covalent geometry : angle 0.59273 / 0.30 (19911) hydrogen bonds : bond 0.15143 / 9.90 ( 797) hydrogen bonds : angle 5.33399 / 3.84 ( 2310) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 37 THR cc_start: 0.8183 (t) cc_final: 0.7967 (t) REVERT: A 319 LYS cc_start: 0.7671 (ttpt) cc_final: 0.7467 (ttmt) REVERT: D 58 ARG cc_start: 0.6598 (tmm-80) cc_final: 0.6352 (ttt180) REVERT: D 100 HIS cc_start: 0.5351 (t-90) cc_final: 0.4991 (t-170) outliers start: 4 outliers final: 1 residues processed: 140 average time/residue: 0.1084 time to fit residues: 22.6421 Evaluate side-chains 119 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 243 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 0.0170 chunk 107 optimal weight: 0.0060 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.6980 overall best weight: 0.3834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN C 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.224754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.168152 restraints weight = 18897.355| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.93 r_work: 0.3468 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.0695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14780 Z= 0.104 Angle : 0.459 7.249 19911 Z= 0.246 Chirality : 0.039 0.140 2268 Planarity : 0.003 0.043 2479 Dihedral : 8.890 153.747 1966 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.70 % Allowed : 5.54 % Favored : 93.76 % 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 are not related in a simple way. whole: 1.04 (0.21), residues: 1791 helix: 1.79 (0.17), residues: 1032 sheet: 0.12 (0.40), residues: 188 loop : -1.18 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 102 TYR 0.016 0.001 TYR A 623 PHE 0.012 0.001 PHE D 52 TRP 0.013 0.001 TRP A 605 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.10 (14780) covalent geometry : angle 0.45911 / 0.25 (19911) hydrogen bonds : bond 0.04680 / 3.14 ( 797) hydrogen bonds : angle 4.11002 / 2.89 ( 2310) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 37 THR cc_start: 0.8244 (t) cc_final: 0.8035 (t) REVERT: A 319 LYS cc_start: 0.7643 (ttpt) cc_final: 0.7396 (ttmt) REVERT: D 58 ARG cc_start: 0.6777 (tmm-80) cc_final: 0.6536 (ttt180) REVERT: D 89 MET cc_start: 0.6567 (tpp) cc_final: 0.5305 (mtt) REVERT: D 100 HIS cc_start: 0.4996 (t-90) cc_final: 0.4666 (t-170) outliers start: 11 outliers final: 6 residues processed: 129 average time/residue: 0.1277 time to fit residues: 24.2528 Evaluate side-chains 122 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain D residue 94 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 175 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 103 optimal weight: 0.0020 chunk 109 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 40 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 ASN E 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.223564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.174226 restraints weight = 18915.880| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.05 r_work: 0.3489 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14780 Z= 0.096 Angle : 0.426 7.309 19911 Z= 0.228 Chirality : 0.039 0.138 2268 Planarity : 0.003 0.041 2479 Dihedral : 8.363 152.735 1963 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.57 % Allowed : 8.02 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.21), residues: 1791 helix: 1.89 (0.17), residues: 1032 sheet: 0.20 (0.41), residues: 188 loop : -1.15 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 168 TYR 0.016 0.001 TYR A 623 PHE 0.011 0.001 PHE A 501 TRP 0.012 0.001 TRP A 605 HIS 0.002 0.000 HIS E 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.10 (14780) covalent geometry : angle 0.42647 / 0.23 (19911) hydrogen bonds : bond 0.04331 / 2.91 ( 797) hydrogen bonds : angle 3.86521 / 2.72 ( 2310) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.442 Fit side-chains REVERT: A 315 TYR cc_start: 0.6546 (OUTLIER) cc_final: 0.6276 (t80) REVERT: A 319 LYS cc_start: 0.7691 (ttpt) cc_final: 0.7447 (ttmt) REVERT: C 138 ASP cc_start: 0.7951 (m-30) cc_final: 0.7681 (m-30) REVERT: D 58 ARG cc_start: 0.6798 (tmm-80) cc_final: 0.6545 (ttt180) REVERT: D 100 HIS cc_start: 0.5087 (t-90) cc_final: 0.4710 (t-170) outliers start: 9 outliers final: 5 residues processed: 125 average time/residue: 0.1135 time to fit residues: 21.0183 Evaluate side-chains 121 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 124 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 175 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 92 optimal weight: 0.0980 chunk 85 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 142 ASN C 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.218325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.148541 restraints weight = 18727.284| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 9.16 r_work: 0.3105 rms_B_bonded: 6.05 restraints_weight: 2.0000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14780 Z= 0.162 Angle : 0.508 7.970 19911 Z= 0.269 Chirality : 0.041 0.150 2268 Planarity : 0.003 0.040 2479 Dihedral : 8.398 154.431 1963 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.21 % Allowed : 9.55 % Favored : 89.24 % 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 are not related in a simple way. whole: 0.93 (0.21), residues: 1791 helix: 1.69 (0.17), residues: 1036 sheet: 0.00 (0.40), residues: 186 loop : -1.19 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 83 TYR 0.019 0.002 TYR A 623 PHE 0.015 0.001 PHE A 599 TRP 0.023 0.001 TRP A 605 HIS 0.006 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (14780) covalent geometry : angle 0.50808 / 0.27 (19911) hydrogen bonds : bond 0.05798 / 3.86 ( 797) hydrogen bonds : angle 3.96732 / 2.80 ( 2310) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.569 Fit side-chains REVERT: A 70 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8789 (mp) REVERT: A 319 LYS cc_start: 0.7620 (ttpt) cc_final: 0.7362 (ttmt) REVERT: A 607 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8076 (pp) REVERT: C 134 TYR cc_start: 0.8323 (t80) cc_final: 0.8062 (t80) REVERT: C 138 ASP cc_start: 0.8272 (m-30) cc_final: 0.8018 (m-30) REVERT: D 58 ARG cc_start: 0.6859 (tmm-80) cc_final: 0.6633 (ttt180) REVERT: D 100 HIS cc_start: 0.4600 (t-90) cc_final: 0.4349 (t70) outliers start: 19 outliers final: 14 residues processed: 125 average time/residue: 0.1267 time to fit residues: 23.4689 Evaluate side-chains 126 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 125 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 113 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 107 optimal weight: 0.0970 chunk 124 optimal weight: 9.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.219432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.149893 restraints weight = 18873.758| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 9.26 r_work: 0.3135 rms_B_bonded: 5.88 restraints_weight: 2.0000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14780 Z= 0.127 Angle : 0.466 7.594 19911 Z= 0.248 Chirality : 0.040 0.144 2268 Planarity : 0.003 0.039 2479 Dihedral : 8.181 153.903 1963 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.21 % Allowed : 10.82 % Favored : 87.97 % 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 are not related in a simple way. whole: 0.97 (0.21), residues: 1791 helix: 1.74 (0.17), residues: 1035 sheet: -0.01 (0.40), residues: 188 loop : -1.17 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 261 TYR 0.015 0.001 TYR A 623 PHE 0.011 0.001 PHE A 160 TRP 0.016 0.001 TRP A 605 HIS 0.005 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (14780) covalent geometry : angle 0.46638 / 0.25 (19911) hydrogen bonds : bond 0.05166 / 3.45 ( 797) hydrogen bonds : angle 3.83941 / 2.71 ( 2310) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 70 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8764 (mp) REVERT: A 315 TYR cc_start: 0.6702 (OUTLIER) cc_final: 0.6367 (t80) REVERT: A 319 LYS cc_start: 0.7534 (ttpt) cc_final: 0.7303 (ttmt) REVERT: A 376 MET cc_start: 0.0965 (mmm) cc_final: -0.0570 (pmm) REVERT: A 607 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8021 (pp) REVERT: C 134 TYR cc_start: 0.8321 (t80) cc_final: 0.8042 (t80) REVERT: C 138 ASP cc_start: 0.8224 (m-30) cc_final: 0.7995 (m-30) REVERT: D 58 ARG cc_start: 0.6863 (tmm-80) cc_final: 0.6634 (ttt180) REVERT: D 100 HIS cc_start: 0.4608 (t-90) cc_final: 0.4356 (t70) outliers start: 19 outliers final: 15 residues processed: 121 average time/residue: 0.1222 time to fit residues: 21.9698 Evaluate side-chains 126 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 141 optimal weight: 30.0000 chunk 25 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.219333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.150603 restraints weight = 18787.329| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 8.84 r_work: 0.3128 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14780 Z= 0.124 Angle : 0.464 7.532 19911 Z= 0.247 Chirality : 0.040 0.144 2268 Planarity : 0.003 0.038 2479 Dihedral : 8.062 153.669 1963 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.24 % Favored : 95.70 % Rotamer: Outliers : 1.34 % Allowed : 11.71 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.21), residues: 1791 helix: 1.77 (0.17), residues: 1035 sheet: -0.01 (0.40), residues: 188 loop : -1.15 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 9 TYR 0.014 0.001 TYR A 623 PHE 0.011 0.001 PHE D 52 TRP 0.016 0.001 TRP A 605 HIS 0.005 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (14780) covalent geometry : angle 0.46421 / 0.25 (19911) hydrogen bonds : bond 0.05075 / 3.39 ( 797) hydrogen bonds : angle 3.78616 / 2.68 ( 2310) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.448 Fit side-chains REVERT: A 70 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8749 (mp) REVERT: A 315 TYR cc_start: 0.6663 (OUTLIER) cc_final: 0.6403 (t80) REVERT: A 319 LYS cc_start: 0.7576 (ttpt) cc_final: 0.7339 (ttmt) REVERT: A 376 MET cc_start: 0.1127 (mmm) cc_final: -0.0528 (pmm) REVERT: A 607 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8051 (pp) REVERT: C 134 TYR cc_start: 0.8337 (t80) cc_final: 0.8053 (t80) REVERT: D 58 ARG cc_start: 0.6785 (tmm-80) cc_final: 0.6565 (ttt180) REVERT: D 100 HIS cc_start: 0.4595 (t-90) cc_final: 0.4312 (t70) outliers start: 21 outliers final: 15 residues processed: 121 average time/residue: 0.1227 time to fit residues: 22.1361 Evaluate side-chains 124 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 6 optimal weight: 0.7980 chunk 36 optimal weight: 20.0000 chunk 9 optimal weight: 0.0370 chunk 166 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.0060 overall best weight: 0.4474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 162 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.222291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.171906 restraints weight = 18676.310| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.92 r_work: 0.3488 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14780 Z= 0.092 Angle : 0.433 7.937 19911 Z= 0.231 Chirality : 0.039 0.137 2268 Planarity : 0.002 0.037 2479 Dihedral : 7.733 153.169 1963 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.95 % Allowed : 12.35 % Favored : 86.70 % 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 are not related in a simple way. whole: 1.22 (0.21), residues: 1791 helix: 1.93 (0.17), residues: 1038 sheet: 0.12 (0.41), residues: 188 loop : -1.09 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 83 TYR 0.012 0.001 TYR A 623 PHE 0.012 0.001 PHE D 52 TRP 0.007 0.001 TRP A 605 HIS 0.002 0.000 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00179 / 0.09 (14780) covalent geometry : angle 0.43347 / 0.23 (19911) hydrogen bonds : bond 0.04011 / 2.70 ( 797) hydrogen bonds : angle 3.61355 / 2.56 ( 2310) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.447 Fit side-chains REVERT: A 70 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8775 (mp) REVERT: A 319 LYS cc_start: 0.7629 (ttpt) cc_final: 0.7387 (ttmt) REVERT: A 376 MET cc_start: 0.0577 (mmm) cc_final: -0.0988 (pmm) REVERT: C 138 ASP cc_start: 0.7857 (m-30) cc_final: 0.7547 (m-30) REVERT: C 203 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.7210 (t70) REVERT: D 58 ARG cc_start: 0.6756 (tmm-80) cc_final: 0.6502 (ttt180) REVERT: D 100 HIS cc_start: 0.4936 (t-90) cc_final: 0.4537 (t70) outliers start: 15 outliers final: 11 residues processed: 118 average time/residue: 0.1211 time to fit residues: 21.2522 Evaluate side-chains 121 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 53 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.217672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.147266 restraints weight = 18740.147| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 9.89 r_work: 0.3104 rms_B_bonded: 5.43 restraints_weight: 2.0000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14780 Z= 0.178 Angle : 0.520 7.863 19911 Z= 0.274 Chirality : 0.042 0.152 2268 Planarity : 0.003 0.038 2479 Dihedral : 8.026 154.271 1963 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 1.27 % Allowed : 12.79 % Favored : 85.93 % 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 are not related in a simple way. whole: 1.00 (0.21), residues: 1791 helix: 1.75 (0.17), residues: 1031 sheet: -0.11 (0.40), residues: 190 loop : -1.09 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 83 TYR 0.017 0.002 TYR A 164 PHE 0.014 0.002 PHE A 524 TRP 0.021 0.001 TRP A 605 HIS 0.006 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (14780) covalent geometry : angle 0.52021 / 0.27 (19911) hydrogen bonds : bond 0.05856 / 3.90 ( 797) hydrogen bonds : angle 3.85523 / 2.73 ( 2310) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8749 (mp) REVERT: A 319 LYS cc_start: 0.7637 (ttpt) cc_final: 0.7386 (ttmt) REVERT: A 607 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8053 (pp) REVERT: C 134 TYR cc_start: 0.8317 (t80) cc_final: 0.8038 (t80) REVERT: C 138 ASP cc_start: 0.8081 (m-30) cc_final: 0.7814 (m-30) REVERT: D 58 ARG cc_start: 0.6865 (tmm-80) cc_final: 0.6635 (ttt180) REVERT: D 100 HIS cc_start: 0.4684 (t-90) cc_final: 0.4368 (t70) outliers start: 20 outliers final: 18 residues processed: 126 average time/residue: 0.1212 time to fit residues: 22.8573 Evaluate side-chains 134 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 108 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.220273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.151266 restraints weight = 18906.340| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 9.57 r_work: 0.3145 rms_B_bonded: 5.83 restraints_weight: 2.0000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14780 Z= 0.106 Angle : 0.453 7.933 19911 Z= 0.239 Chirality : 0.039 0.137 2268 Planarity : 0.003 0.037 2479 Dihedral : 7.802 153.331 1963 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.85 % Favored : 96.09 % Rotamer: Outliers : 0.95 % Allowed : 13.11 % Favored : 85.93 % 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 are not related in a simple way. whole: 1.17 (0.21), residues: 1791 helix: 1.89 (0.17), residues: 1033 sheet: 0.04 (0.41), residues: 188 loop : -1.05 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 156 TYR 0.014 0.001 TYR A 623 PHE 0.011 0.001 PHE D 52 TRP 0.011 0.001 TRP A 605 HIS 0.004 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (14780) covalent geometry : angle 0.45264 / 0.24 (19911) hydrogen bonds : bond 0.04615 / 3.09 ( 797) hydrogen bonds : angle 3.67534 / 2.60 ( 2310) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 70 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8742 (mp) REVERT: A 319 LYS cc_start: 0.7493 (ttpt) cc_final: 0.7256 (ttmt) REVERT: A 607 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7998 (pp) REVERT: C 138 ASP cc_start: 0.8102 (m-30) cc_final: 0.7850 (m-30) REVERT: D 58 ARG cc_start: 0.6823 (tmm-80) cc_final: 0.6583 (ttt180) REVERT: D 100 HIS cc_start: 0.4434 (t-90) cc_final: 0.4176 (t70) outliers start: 15 outliers final: 13 residues processed: 121 average time/residue: 0.1057 time to fit residues: 19.2830 Evaluate side-chains 125 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 113 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 0.0470 chunk 77 optimal weight: 0.9980 chunk 126 optimal weight: 30.0000 chunk 92 optimal weight: 0.1980 chunk 100 optimal weight: 0.0570 chunk 68 optimal weight: 1.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.224752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.157257 restraints weight = 18843.178| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 8.57 r_work: 0.3222 rms_B_bonded: 5.43 restraints_weight: 2.0000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14780 Z= 0.087 Angle : 0.422 7.650 19911 Z= 0.223 Chirality : 0.039 0.134 2268 Planarity : 0.002 0.038 2479 Dihedral : 7.502 152.828 1963 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.26 % Rotamer: Outliers : 0.89 % Allowed : 13.18 % Favored : 85.93 % 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 are not related in a simple way. whole: 1.39 (0.21), residues: 1791 helix: 2.08 (0.17), residues: 1031 sheet: 0.23 (0.41), residues: 186 loop : -1.01 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 513 TYR 0.011 0.001 TYR A 623 PHE 0.013 0.001 PHE D 52 TRP 0.007 0.001 TRP A 613 HIS 0.003 0.000 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00169 / 0.09 (14780) covalent geometry : angle 0.42237 / 0.22 (19911) hydrogen bonds : bond 0.03801 / 2.56 ( 797) hydrogen bonds : angle 3.52009 / 2.49 ( 2310) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 70 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8765 (mp) REVERT: A 319 LYS cc_start: 0.7468 (ttpt) cc_final: 0.7237 (ttmt) REVERT: A 376 MET cc_start: 0.0920 (mmm) cc_final: -0.0678 (pmm) REVERT: A 607 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8017 (pp) REVERT: C 138 ASP cc_start: 0.7966 (m-30) cc_final: 0.7720 (m-30) REVERT: D 58 ARG cc_start: 0.6680 (tmm-80) cc_final: 0.6437 (ttt180) outliers start: 14 outliers final: 10 residues processed: 121 average time/residue: 0.1238 time to fit residues: 22.4329 Evaluate side-chains 121 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 176 optimal weight: 20.0000 chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.221654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.153324 restraints weight = 18790.623| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 9.10 r_work: 0.3176 rms_B_bonded: 5.61 restraints_weight: 2.0000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14780 Z= 0.105 Angle : 0.446 8.074 19911 Z= 0.234 Chirality : 0.039 0.140 2268 Planarity : 0.003 0.036 2479 Dihedral : 7.517 152.522 1963 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.08 % Favored : 95.87 % Rotamer: Outliers : 1.02 % Allowed : 13.30 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.21), residues: 1791 helix: 2.04 (0.17), residues: 1033 sheet: 0.18 (0.41), residues: 188 loop : -1.00 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 10 TYR 0.012 0.001 TYR A 164 PHE 0.011 0.001 PHE A 160 TRP 0.013 0.001 TRP A 605 HIS 0.004 0.000 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (14780) covalent geometry : angle 0.44598 / 0.23 (19911) hydrogen bonds : bond 0.04398 / 2.95 ( 797) hydrogen bonds : angle 3.56859 / 2.52 ( 2310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4467.94 seconds wall clock time: 76 minutes 58.71 seconds (4618.71 seconds total)