Starting phenix.real_space_refine on Fri Jun 13 06:32:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g4c_29716/06_2025/8g4c_29716.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g4c_29716/06_2025/8g4c_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g4c_29716/06_2025/8g4c_29716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g4c_29716/06_2025/8g4c_29716.map" model { file = "/net/cci-nas-00/data/ceres_data/8g4c_29716/06_2025/8g4c_29716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g4c_29716/06_2025/8g4c_29716.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.28, per 1000 atoms: 0.64 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: 3.92 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.56 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: 4.31 Time building geometry restraints manager: 4.47 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 - 32.91: 8609 32.91 - 65.82: 267 65.82 - 98.74: 30 98.74 - 131.65: 0 131.65 - 164.56: 6 Dihedral angle restraints: 8912 sinusoidal: 3672 harmonic: 5240 Sorted by residual: dihedral pdb=" C19 6OU A 701 " pdb=" C20 6OU A 701 " pdb=" O30 6OU A 701 " pdb=" C31 6OU A 701 " ideal model delta sinusoidal sigma weight residual 212.33 47.77 164.56 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C19 6OU A 701 " pdb=" C20 6OU A 701 " pdb=" C21 6OU A 701 " pdb=" O22 6OU A 701 " ideal model delta sinusoidal sigma weight residual -59.00 103.83 -162.83 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C21 6OU A 701 " pdb=" C20 6OU A 701 " pdb=" O30 6OU A 701 " pdb=" C31 6OU A 701 " ideal model delta sinusoidal sigma weight residual 85.49 -75.42 160.91 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 8909 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: 3.940 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: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.660 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 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 : 16.586 164.560 5522 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.06 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (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 TRP 0.026 0.001 TRP A 605 HIS 0.003 0.001 HIS A 596 PHE 0.013 0.001 PHE C 235 TYR 0.023 0.001 TYR A 623 ARG 0.002 0.000 ARG E 168 Details of bonding type rmsd hydrogen bonds : bond 0.15143 ( 797) hydrogen bonds : angle 5.33399 ( 2310) covalent geometry : bond 0.00378 (14780) covalent geometry : angle 0.59273 (19911) *********************** 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 : 1.478 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: 0.2740 time to fit residues: 56.4299 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 : 1.482 ------------------------------------------------------------------------------- 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 149 optimal weight: 0.6980 chunk 134 optimal weight: 0.0980 chunk 74 optimal weight: 3.9990 chunk 45 optimal weight: 30.0000 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 138 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.220622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.168708 restraints weight = 18699.368| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 1.95 r_work: 0.3447 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.0669 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= 0.135 Angle : 0.495 7.692 19911 Z= 0.264 Chirality : 0.041 0.145 2268 Planarity : 0.003 0.043 2479 Dihedral : 11.531 153.942 1999 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.95 % Allowed : 5.92 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1791 helix: 1.64 (0.17), residues: 1036 sheet: -0.00 (0.40), residues: 189 loop : -1.21 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 605 HIS 0.007 0.001 HIS A 510 PHE 0.012 0.001 PHE D 52 TYR 0.019 0.001 TYR A 623 ARG 0.003 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.05441 ( 797) hydrogen bonds : angle 4.20772 ( 2310) covalent geometry : bond 0.00296 (14780) covalent geometry : angle 0.49488 (19911) *********************** 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: 15 poor density : 119 time to evaluate : 1.473 Fit side-chains revert: symmetry clash REVERT: A 319 LYS cc_start: 0.7746 (ttpt) cc_final: 0.7486 (ttmt) REVERT: D 58 ARG cc_start: 0.6917 (tmm-80) cc_final: 0.6677 (ttt180) REVERT: D 89 MET cc_start: 0.6680 (tpp) cc_final: 0.5348 (mtt) REVERT: D 100 HIS cc_start: 0.5074 (t-90) cc_final: 0.4755 (t70) outliers start: 15 outliers final: 10 residues processed: 127 average time/residue: 0.2710 time to fit residues: 50.6674 Evaluate side-chains 123 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 93 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 560 SER 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 D residue 94 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 23 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 144 optimal weight: 0.9980 chunk 43 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 333 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.220820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.152436 restraints weight = 18729.839| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 8.59 r_work: 0.3145 rms_B_bonded: 5.97 restraints_weight: 2.0000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14780 Z= 0.119 Angle : 0.462 7.498 19911 Z= 0.246 Chirality : 0.040 0.154 2268 Planarity : 0.003 0.042 2479 Dihedral : 11.050 154.531 1996 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.95 % Allowed : 8.59 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1791 helix: 1.68 (0.17), residues: 1037 sheet: 0.02 (0.40), residues: 188 loop : -1.22 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 605 HIS 0.004 0.001 HIS B 202 PHE 0.012 0.001 PHE D 52 TYR 0.018 0.001 TYR A 623 ARG 0.002 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.05077 ( 797) hydrogen bonds : angle 3.98409 ( 2310) covalent geometry : bond 0.00258 (14780) covalent geometry : angle 0.46218 (19911) *********************** 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 130 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.478 Fit side-chains REVERT: A 319 LYS cc_start: 0.7654 (ttpt) cc_final: 0.7380 (ttmt) REVERT: C 246 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6682 (tp) REVERT: D 58 ARG cc_start: 0.6808 (tmm-80) cc_final: 0.6582 (ttt180) REVERT: D 100 HIS cc_start: 0.4774 (t-90) cc_final: 0.4490 (t70) outliers start: 15 outliers final: 9 residues processed: 125 average time/residue: 0.2644 time to fit residues: 49.1773 Evaluate side-chains 120 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 1.678 ------------------------------------------------------------------------------- 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 167 ILE 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 C residue 246 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 24 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 119 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 132 optimal weight: 40.0000 chunk 77 optimal weight: 0.9980 chunk 173 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.218908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.149777 restraints weight = 18651.739| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 8.65 r_work: 0.3128 rms_B_bonded: 5.76 restraints_weight: 2.0000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14780 Z= 0.144 Angle : 0.489 7.747 19911 Z= 0.259 Chirality : 0.041 0.156 2268 Planarity : 0.003 0.040 2479 Dihedral : 10.950 155.119 1996 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.34 % Allowed : 10.12 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1791 helix: 1.61 (0.17), residues: 1040 sheet: -0.04 (0.40), residues: 188 loop : -1.21 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 605 HIS 0.005 0.001 HIS B 202 PHE 0.012 0.001 PHE A 160 TYR 0.016 0.001 TYR A 623 ARG 0.001 0.000 ARG E 261 Details of bonding type rmsd hydrogen bonds : bond 0.05426 ( 797) hydrogen bonds : angle 3.95606 ( 2310) covalent geometry : bond 0.00333 (14780) covalent geometry : angle 0.48915 (19911) *********************** 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 130 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.500 Fit side-chains REVERT: A 319 LYS cc_start: 0.7594 (ttpt) cc_final: 0.7362 (ttmt) REVERT: A 607 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7948 (pp) REVERT: C 246 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6922 (tp) REVERT: D 58 ARG cc_start: 0.6889 (tmm-80) cc_final: 0.6654 (ttt180) REVERT: D 100 HIS cc_start: 0.4656 (t-90) cc_final: 0.4400 (t70) outliers start: 21 outliers final: 12 residues processed: 122 average time/residue: 0.2790 time to fit residues: 50.2876 Evaluate side-chains 121 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 93 ILE Chi-restraints excluded: chain A residue 167 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 63 THR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 124 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 21 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 111 optimal weight: 0.2980 chunk 154 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 162 optimal weight: 8.9990 chunk 108 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.221186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.152790 restraints weight = 18864.343| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 9.14 r_work: 0.3169 rms_B_bonded: 5.62 restraints_weight: 2.0000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14780 Z= 0.099 Angle : 0.442 7.257 19911 Z= 0.235 Chirality : 0.039 0.150 2268 Planarity : 0.003 0.038 2479 Dihedral : 10.659 154.838 1996 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.95 % Allowed : 11.20 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.21), residues: 1791 helix: 1.78 (0.17), residues: 1039 sheet: 0.05 (0.40), residues: 188 loop : -1.17 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 605 HIS 0.003 0.000 HIS B 202 PHE 0.012 0.001 PHE D 52 TYR 0.014 0.001 TYR A 623 ARG 0.002 0.000 ARG E 168 Details of bonding type rmsd hydrogen bonds : bond 0.04500 ( 797) hydrogen bonds : angle 3.75846 ( 2310) covalent geometry : bond 0.00198 (14780) covalent geometry : angle 0.44197 (19911) *********************** 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 127 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 1.456 Fit side-chains REVERT: A 319 LYS cc_start: 0.7504 (ttpt) cc_final: 0.7284 (ttmt) REVERT: A 376 MET cc_start: 0.0914 (mmm) cc_final: -0.0608 (pmm) REVERT: A 607 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7935 (pp) REVERT: C 138 ASP cc_start: 0.8217 (m-30) cc_final: 0.7986 (m-30) REVERT: C 246 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6778 (tp) REVERT: D 58 ARG cc_start: 0.6799 (tmm-80) cc_final: 0.6566 (ttt180) REVERT: D 100 HIS cc_start: 0.4545 (t-90) cc_final: 0.4281 (t70) outliers start: 15 outliers final: 11 residues processed: 122 average time/residue: 0.2670 time to fit residues: 48.6543 Evaluate side-chains 122 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 607 LEU 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 246 LEU 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 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 0 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 167 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 132 optimal weight: 30.0000 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.214955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.142547 restraints weight = 18872.614| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 11.61 r_work: 0.3079 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 14780 Z= 0.305 Angle : 0.659 9.514 19911 Z= 0.343 Chirality : 0.047 0.206 2268 Planarity : 0.004 0.055 2479 Dihedral : 11.029 156.911 1996 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 1.72 % Allowed : 12.09 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.20), residues: 1791 helix: 1.20 (0.17), residues: 1043 sheet: -0.36 (0.40), residues: 188 loop : -1.46 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 605 HIS 0.007 0.001 HIS C 29 PHE 0.019 0.002 PHE A 599 TYR 0.020 0.002 TYR B 140 ARG 0.005 0.001 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.07682 ( 797) hydrogen bonds : angle 4.27176 ( 2310) covalent geometry : bond 0.00753 (14780) covalent geometry : angle 0.65866 (19911) *********************** 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 134 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 1.567 Fit side-chains revert: symmetry clash REVERT: A 70 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8923 (mt) REVERT: A 319 LYS cc_start: 0.7689 (ttpt) cc_final: 0.7475 (ttmt) REVERT: A 607 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8207 (pp) REVERT: D 58 ARG cc_start: 0.7222 (tmm-80) cc_final: 0.6999 (ttt180) REVERT: D 100 HIS cc_start: 0.4806 (t-90) cc_final: 0.4503 (t70) REVERT: E 167 LYS cc_start: -0.0097 (mmtt) cc_final: -0.1640 (ttmm) outliers start: 27 outliers final: 19 residues processed: 126 average time/residue: 0.2834 time to fit residues: 53.0615 Evaluate side-chains 126 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 1.670 ------------------------------------------------------------------------------- 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 202 MET 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 B residue 9 ILE 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 29 VAL 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 D residue 125 GLU Chi-restraints excluded: chain E residue 39 LEU 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 30 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 137 optimal weight: 0.0040 chunk 27 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.219751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.151696 restraints weight = 18893.899| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 9.16 r_work: 0.3146 rms_B_bonded: 5.94 restraints_weight: 2.0000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1293 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= 0.108 Angle : 0.463 7.233 19911 Z= 0.247 Chirality : 0.040 0.149 2268 Planarity : 0.003 0.039 2479 Dihedral : 10.661 156.229 1996 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.26 % Rotamer: Outliers : 1.02 % Allowed : 13.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.21), residues: 1791 helix: 1.62 (0.17), residues: 1038 sheet: -0.20 (0.40), residues: 190 loop : -1.24 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 605 HIS 0.005 0.001 HIS B 202 PHE 0.013 0.001 PHE D 52 TYR 0.014 0.001 TYR A 623 ARG 0.002 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.04797 ( 797) hydrogen bonds : angle 3.82718 ( 2310) covalent geometry : bond 0.00221 (14780) covalent geometry : angle 0.46250 (19911) *********************** 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 121 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 1.749 Fit side-chains revert: symmetry clash REVERT: A 70 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8942 (mt) REVERT: A 319 LYS cc_start: 0.7676 (ttpt) cc_final: 0.7463 (ttmt) REVERT: A 376 MET cc_start: 0.1162 (mmm) cc_final: -0.0485 (pmm) REVERT: A 607 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8045 (pp) REVERT: C 203 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.7414 (t70) REVERT: D 58 ARG cc_start: 0.6827 (tmm-80) cc_final: 0.6598 (ttt180) REVERT: D 84 THR cc_start: 0.7461 (OUTLIER) cc_final: 0.7230 (m) REVERT: D 100 HIS cc_start: 0.4701 (t-90) cc_final: 0.4469 (t-170) outliers start: 16 outliers final: 11 residues processed: 115 average time/residue: 0.2840 time to fit residues: 48.6673 Evaluate side-chains 117 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 93 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 607 LEU 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 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 D residue 125 GLU 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 166 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 chunk 164 optimal weight: 0.0050 chunk 144 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.220178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.169521 restraints weight = 18691.855| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.08 r_work: 0.3445 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1314 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= 0.100 Angle : 0.443 7.966 19911 Z= 0.235 Chirality : 0.039 0.154 2268 Planarity : 0.003 0.039 2479 Dihedral : 10.378 155.429 1996 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.96 % Favored : 95.98 % Rotamer: Outliers : 0.76 % Allowed : 13.69 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.21), residues: 1791 helix: 1.78 (0.17), residues: 1039 sheet: -0.09 (0.40), residues: 190 loop : -1.17 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 605 HIS 0.003 0.000 HIS B 202 PHE 0.014 0.001 PHE D 52 TYR 0.015 0.001 TYR D 57 ARG 0.001 0.000 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.04517 ( 797) hydrogen bonds : angle 3.71040 ( 2310) covalent geometry : bond 0.00205 (14780) covalent geometry : angle 0.44307 (19911) *********************** 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 119 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 1.957 Fit side-chains revert: symmetry clash REVERT: A 70 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8910 (mt) REVERT: A 319 LYS cc_start: 0.7683 (ttpt) cc_final: 0.7471 (ttmt) REVERT: A 376 MET cc_start: 0.0799 (mmm) cc_final: -0.0783 (pmm) REVERT: A 607 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8164 (pp) REVERT: C 138 ASP cc_start: 0.8053 (m-30) cc_final: 0.7851 (m-30) REVERT: D 58 ARG cc_start: 0.6909 (tmm-80) cc_final: 0.6648 (ttt180) REVERT: D 100 HIS cc_start: 0.5025 (t-90) cc_final: 0.4661 (t-170) outliers start: 12 outliers final: 9 residues processed: 116 average time/residue: 0.4049 time to fit residues: 69.3190 Evaluate side-chains 117 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 607 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 121 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 91 optimal weight: 0.6980 chunk 167 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.217987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148773 restraints weight = 18648.382| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 9.45 r_work: 0.3088 rms_B_bonded: 5.54 restraints_weight: 2.0000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1419 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= 0.168 Angle : 0.517 8.093 19911 Z= 0.273 Chirality : 0.042 0.166 2268 Planarity : 0.003 0.039 2479 Dihedral : 10.517 156.024 1996 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.86 % Favored : 95.09 % Rotamer: Outliers : 1.15 % Allowed : 13.88 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1791 helix: 1.62 (0.17), residues: 1036 sheet: -0.21 (0.40), residues: 190 loop : -1.21 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 605 HIS 0.006 0.001 HIS B 202 PHE 0.013 0.001 PHE A 524 TYR 0.016 0.002 TYR A 164 ARG 0.002 0.000 ARG E 168 Details of bonding type rmsd hydrogen bonds : bond 0.05862 ( 797) hydrogen bonds : angle 3.90309 ( 2310) covalent geometry : bond 0.00397 (14780) covalent geometry : angle 0.51728 (19911) *********************** 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 126 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 1.744 Fit side-chains revert: symmetry clash REVERT: A 70 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8932 (mt) REVERT: A 376 MET cc_start: 0.1012 (mmm) cc_final: -0.0571 (pmm) REVERT: A 383 MET cc_start: 0.3610 (mpp) cc_final: 0.3221 (mpp) REVERT: A 607 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8121 (pp) REVERT: D 58 ARG cc_start: 0.6844 (tmm-80) cc_final: 0.6618 (ttt180) REVERT: D 100 HIS cc_start: 0.4640 (t-90) cc_final: 0.4348 (t70) outliers start: 18 outliers final: 15 residues processed: 122 average time/residue: 0.4003 time to fit residues: 74.1695 Evaluate side-chains 124 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 2.473 ------------------------------------------------------------------------------- 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 167 ILE Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 9 ILE 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 29 VAL 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 D residue 308 VAL 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 110 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 104 optimal weight: 0.0670 chunk 100 optimal weight: 0.2980 chunk 126 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 1 optimal weight: 0.2980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.219999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.152903 restraints weight = 18718.721| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 8.36 r_work: 0.3139 rms_B_bonded: 5.82 restraints_weight: 2.0000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14780 Z= 0.114 Angle : 0.469 8.956 19911 Z= 0.247 Chirality : 0.040 0.157 2268 Planarity : 0.003 0.039 2479 Dihedral : 10.337 155.701 1996 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.02 % Favored : 95.92 % Rotamer: Outliers : 1.15 % Allowed : 13.94 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.21), residues: 1791 helix: 1.76 (0.17), residues: 1034 sheet: -0.14 (0.40), residues: 190 loop : -1.15 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 605 HIS 0.004 0.001 HIS B 202 PHE 0.013 0.001 PHE D 52 TYR 0.013 0.001 TYR A 623 ARG 0.001 0.000 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.04837 ( 797) hydrogen bonds : angle 3.74949 ( 2310) covalent geometry : bond 0.00247 (14780) covalent geometry : angle 0.46874 (19911) ********************** 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 128 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.8937 (mt) REVERT: A 376 MET cc_start: 0.0983 (mmm) cc_final: -0.0547 (pmm) REVERT: A 607 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8111 (pp) REVERT: C 138 ASP cc_start: 0.8237 (m-30) cc_final: 0.8034 (m-30) REVERT: D 58 ARG cc_start: 0.6897 (tmm-80) cc_final: 0.6654 (ttt180) REVERT: D 100 HIS cc_start: 0.4674 (t-90) cc_final: 0.4411 (t-170) outliers start: 18 outliers final: 14 residues processed: 123 average time/residue: 0.3830 time to fit residues: 71.3213 Evaluate side-chains 125 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 3.327 ------------------------------------------------------------------------------- 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 93 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 607 LEU 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 29 VAL 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 D residue 308 VAL 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 166 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 144 optimal weight: 0.4980 chunk 159 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 176 optimal weight: 0.3980 chunk 163 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN D 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.222872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.155523 restraints weight = 18906.304| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 8.53 r_work: 0.3197 rms_B_bonded: 5.43 restraints_weight: 2.0000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1459 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= 0.094 Angle : 0.440 8.312 19911 Z= 0.232 Chirality : 0.039 0.159 2268 Planarity : 0.003 0.040 2479 Dihedral : 9.893 155.028 1996 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.02 % Favored : 95.92 % Rotamer: Outliers : 0.95 % Allowed : 14.39 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.21), residues: 1791 helix: 1.95 (0.17), residues: 1033 sheet: 0.07 (0.41), residues: 187 loop : -1.11 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 605 HIS 0.002 0.000 HIS B 202 PHE 0.013 0.001 PHE D 52 TYR 0.011 0.001 TYR D 57 ARG 0.002 0.000 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 797) hydrogen bonds : angle 3.60242 ( 2310) covalent geometry : bond 0.00191 (14780) covalent geometry : angle 0.43951 (19911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10223.91 seconds wall clock time: 181 minutes 18.33 seconds (10878.33 seconds total)