Starting phenix.real_space_refine on Sun Nov 17 22:11:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4c_29716/11_2024/8g4c_29716.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4c_29716/11_2024/8g4c_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4c_29716/11_2024/8g4c_29716.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4c_29716/11_2024/8g4c_29716.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4c_29716/11_2024/8g4c_29716.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4c_29716/11_2024/8g4c_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-5513/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: 9.55, per 1000 atoms: 0.66 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: 3.50 Conformation dependent library (CDL) restraints added in 2.0 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: 1.57 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: 4.76 Time building geometry restraints manager: 4.10 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: 2.720 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: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 34.800 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.910 ------------------------------------------------------------------------------- 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= 0.245 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 *********************** 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 : 1.382 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: 0.2821 time to fit residues: 57.7657 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 : 1.426 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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= 0.189 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 *********************** 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 : 1.531 Fit side-chains revert: symmetry clash REVERT: A 37 THR cc_start: 0.8352 (t) cc_final: 0.8139 (t) REVERT: A 319 LYS cc_start: 0.7721 (ttpt) cc_final: 0.7491 (ttmt) REVERT: D 58 ARG cc_start: 0.6647 (tmm-80) cc_final: 0.6404 (ttt180) REVERT: D 89 MET cc_start: 0.6445 (tpp) cc_final: 0.5483 (mtt) REVERT: D 100 HIS cc_start: 0.5375 (t-90) cc_final: 0.5051 (t70) REVERT: D 125 GLU cc_start: 0.2201 (OUTLIER) cc_final: 0.2001 (pm20) outliers start: 15 outliers final: 10 residues processed: 127 average time/residue: 0.2872 time to fit residues: 53.9447 Evaluate side-chains 124 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 1.563 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 125 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 161 optimal weight: 0.0020 chunk 173 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14780 Z= 0.187 Angle : 0.478 7.636 19911 Z= 0.254 Chirality : 0.040 0.155 2268 Planarity : 0.003 0.042 2479 Dihedral : 11.064 154.702 1996 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.95 % Allowed : 8.91 % Favored : 90.13 % 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: 0.83 (0.21), residues: 1791 helix: 1.61 (0.17), residues: 1042 sheet: -0.02 (0.40), residues: 188 loop : -1.25 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 605 HIS 0.004 0.001 HIS B 202 PHE 0.012 0.001 PHE D 52 TYR 0.019 0.001 TYR A 623 ARG 0.002 0.000 ARG E 10 *********************** 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 128 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 1.727 Fit side-chains REVERT: A 70 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8561 (mp) REVERT: A 319 LYS cc_start: 0.7713 (ttpt) cc_final: 0.7465 (ttmt) REVERT: C 246 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6782 (tp) REVERT: D 58 ARG cc_start: 0.6680 (tmm-80) cc_final: 0.6428 (ttt180) REVERT: D 100 HIS cc_start: 0.5329 (t-90) cc_final: 0.4984 (t70) outliers start: 15 outliers final: 9 residues processed: 122 average time/residue: 0.2878 time to fit residues: 52.0875 Evaluate side-chains 121 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 1.725 ------------------------------------------------------------------------------- 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 167 ILE Chi-restraints excluded: chain A residue 194 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 171 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14780 Z= 0.231 Angle : 0.505 7.841 19911 Z= 0.267 Chirality : 0.041 0.156 2268 Planarity : 0.003 0.039 2479 Dihedral : 10.930 155.521 1996 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.65 % Allowed : 10.31 % Favored : 88.03 % 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: 0.79 (0.21), residues: 1791 helix: 1.57 (0.17), residues: 1040 sheet: -0.10 (0.40), residues: 188 loop : -1.22 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 605 HIS 0.006 0.001 HIS B 202 PHE 0.012 0.001 PHE D 52 TYR 0.018 0.001 TYR A 623 ARG 0.001 0.000 ARG C 83 *********************** 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 133 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 1.664 Fit side-chains REVERT: A 70 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8543 (mp) REVERT: A 319 LYS cc_start: 0.7707 (ttpt) cc_final: 0.7464 (ttmt) REVERT: A 376 MET cc_start: -0.0213 (pmm) cc_final: -0.1193 (mmm) REVERT: A 607 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8079 (pp) REVERT: C 246 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.7056 (tp) REVERT: D 58 ARG cc_start: 0.6738 (tmm-80) cc_final: 0.6487 (ttt180) REVERT: D 100 HIS cc_start: 0.5300 (t-90) cc_final: 0.4929 (t70) REVERT: E 167 LYS cc_start: 0.1051 (OUTLIER) cc_final: 0.0829 (mmtp) outliers start: 26 outliers final: 17 residues processed: 126 average time/residue: 0.2681 time to fit residues: 50.6926 Evaluate side-chains 125 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 601 VAL 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 9 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 63 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 E residue 167 LYS Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 40.0000 chunk 97 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14780 Z= 0.199 Angle : 0.490 7.621 19911 Z= 0.259 Chirality : 0.041 0.159 2268 Planarity : 0.003 0.039 2479 Dihedral : 10.789 155.610 1996 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.40 % Allowed : 11.58 % Favored : 87.01 % 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: 0.83 (0.21), residues: 1791 helix: 1.60 (0.17), residues: 1039 sheet: -0.09 (0.40), residues: 188 loop : -1.20 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 605 HIS 0.005 0.001 HIS B 202 PHE 0.013 0.001 PHE D 52 TYR 0.015 0.001 TYR A 623 ARG 0.001 0.000 ARG C 83 *********************** 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 126 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.597 Fit side-chains REVERT: A 70 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8545 (mp) REVERT: A 319 LYS cc_start: 0.7707 (ttpt) cc_final: 0.7502 (ttmt) REVERT: A 376 MET cc_start: -0.0289 (pmm) cc_final: -0.1163 (mmm) REVERT: A 607 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8064 (pp) REVERT: C 246 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.7063 (tp) REVERT: D 58 ARG cc_start: 0.6716 (tmm-80) cc_final: 0.6460 (ttt180) REVERT: D 100 HIS cc_start: 0.5264 (t-90) cc_final: 0.4904 (t70) REVERT: E 167 LYS cc_start: 0.1079 (OUTLIER) cc_final: 0.0827 (mmtp) outliers start: 22 outliers final: 14 residues processed: 119 average time/residue: 0.2862 time to fit residues: 50.2727 Evaluate side-chains 121 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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 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 9 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 29 VAL 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 167 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 171 optimal weight: 0.0000 chunk 142 optimal weight: 7.9990 chunk 79 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1188 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= 0.133 Angle : 0.444 7.295 19911 Z= 0.235 Chirality : 0.039 0.152 2268 Planarity : 0.003 0.037 2479 Dihedral : 10.541 155.371 1996 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.08 % Favored : 95.87 % Rotamer: Outliers : 1.34 % Allowed : 12.29 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.21), residues: 1791 helix: 1.75 (0.17), residues: 1039 sheet: 0.01 (0.40), residues: 188 loop : -1.13 (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 0.013 0.001 PHE D 52 TYR 0.013 0.001 TYR A 623 ARG 0.002 0.000 ARG B 156 *********************** 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: 21 poor density : 113 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: A 70 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8551 (mp) REVERT: A 319 LYS cc_start: 0.7673 (ttpt) cc_final: 0.7427 (ttmt) REVERT: A 376 MET cc_start: -0.0275 (pmm) cc_final: -0.1138 (mmm) REVERT: A 607 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8053 (pp) REVERT: C 246 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7076 (tp) REVERT: D 58 ARG cc_start: 0.6634 (tmm-80) cc_final: 0.6368 (ttt180) REVERT: D 100 HIS cc_start: 0.5231 (t-90) cc_final: 0.4838 (t-170) REVERT: E 167 LYS cc_start: 0.1043 (OUTLIER) cc_final: 0.0798 (mmtp) outliers start: 21 outliers final: 14 residues processed: 125 average time/residue: 0.2865 time to fit residues: 52.9201 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 : 1.618 ------------------------------------------------------------------------------- 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 486 VAL 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 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 167 LYS 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 165 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 97 optimal weight: 0.3980 chunk 125 optimal weight: 0.0770 chunk 96 optimal weight: 0.9990 chunk 144 optimal weight: 0.0970 chunk 95 optimal weight: 0.9980 chunk 170 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 91 GLN D 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1295 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= 0.115 Angle : 0.431 7.951 19911 Z= 0.229 Chirality : 0.039 0.150 2268 Planarity : 0.002 0.037 2479 Dihedral : 10.150 154.629 1996 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.34 % Allowed : 12.99 % 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 (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: 1.16 (0.21), residues: 1791 helix: 1.88 (0.17), residues: 1038 sheet: 0.08 (0.41), residues: 190 loop : -1.09 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 605 HIS 0.002 0.000 HIS B 202 PHE 0.013 0.001 PHE D 52 TYR 0.015 0.001 TYR C 134 ARG 0.002 0.000 ARG C 83 *********************** 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 133 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.572 Fit side-chains REVERT: A 319 LYS cc_start: 0.7611 (ttpt) cc_final: 0.7379 (ttmt) REVERT: A 376 MET cc_start: -0.0361 (pmm) cc_final: -0.1019 (mmm) REVERT: A 607 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8000 (pp) REVERT: C 246 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.7022 (tp) REVERT: D 58 ARG cc_start: 0.6530 (tmm-80) cc_final: 0.6262 (ttt180) REVERT: D 100 HIS cc_start: 0.5251 (t-90) cc_final: 0.4833 (t-170) outliers start: 21 outliers final: 16 residues processed: 127 average time/residue: 0.2846 time to fit residues: 54.0918 Evaluate side-chains 127 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL 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 75 LYS 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 131 LEU Chi-restraints excluded: chain C residue 246 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 134 optimal weight: 0.3980 chunk 155 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14780 Z= 0.164 Angle : 0.458 7.539 19911 Z= 0.242 Chirality : 0.040 0.159 2268 Planarity : 0.003 0.037 2479 Dihedral : 10.133 154.884 1996 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.24 % Favored : 95.70 % Rotamer: Outliers : 1.59 % Allowed : 13.18 % Favored : 85.23 % 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: 1.13 (0.21), residues: 1791 helix: 1.84 (0.17), residues: 1040 sheet: 0.04 (0.40), residues: 190 loop : -1.08 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 605 HIS 0.004 0.001 HIS B 202 PHE 0.012 0.001 PHE D 52 TYR 0.013 0.001 TYR A 164 ARG 0.002 0.000 ARG E 168 *********************** 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 135 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.656 Fit side-chains REVERT: A 319 LYS cc_start: 0.7633 (ttpt) cc_final: 0.7402 (ttmt) REVERT: A 376 MET cc_start: -0.0364 (pmm) cc_final: -0.0892 (mmm) REVERT: A 607 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8030 (pp) REVERT: D 58 ARG cc_start: 0.6604 (tmm-80) cc_final: 0.6342 (ttt180) REVERT: D 100 HIS cc_start: 0.5284 (t-90) cc_final: 0.4886 (t70) outliers start: 25 outliers final: 22 residues processed: 129 average time/residue: 0.2927 time to fit residues: 55.8000 Evaluate side-chains 132 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 194 VAL Chi-restraints excluded: chain A residue 230 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 75 LYS 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 C residue 131 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 20.0000 chunk 149 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 48 optimal weight: 0.1980 chunk 143 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1346 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= 0.157 Angle : 0.457 7.754 19911 Z= 0.241 Chirality : 0.040 0.159 2268 Planarity : 0.003 0.042 2479 Dihedral : 10.066 155.235 1996 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.08 % Favored : 95.87 % Rotamer: Outliers : 1.59 % Allowed : 13.24 % Favored : 85.17 % 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: 1.16 (0.21), residues: 1791 helix: 1.87 (0.17), residues: 1034 sheet: 0.04 (0.40), residues: 190 loop : -1.04 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 605 HIS 0.004 0.001 HIS B 202 PHE 0.012 0.001 PHE D 52 TYR 0.012 0.001 TYR A 164 ARG 0.001 0.000 ARG E 9 *********************** 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 133 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 1.646 Fit side-chains REVERT: A 319 LYS cc_start: 0.7628 (ttpt) cc_final: 0.7390 (ttmt) REVERT: A 376 MET cc_start: -0.0295 (pmm) cc_final: -0.0719 (mmm) REVERT: A 607 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8051 (pp) REVERT: D 58 ARG cc_start: 0.6580 (tmm-80) cc_final: 0.6314 (ttt180) REVERT: D 100 HIS cc_start: 0.5285 (t-90) cc_final: 0.4887 (t70) outliers start: 25 outliers final: 23 residues processed: 125 average time/residue: 0.2966 time to fit residues: 55.0612 Evaluate side-chains 132 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.821 ------------------------------------------------------------------------------- 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 194 VAL 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 75 LYS 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 C residue 131 LEU 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 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 102 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 140 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 111 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1395 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= 0.134 Angle : 0.442 8.599 19911 Z= 0.233 Chirality : 0.039 0.160 2268 Planarity : 0.003 0.043 2479 Dihedral : 9.858 155.174 1996 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.85 % Favored : 96.09 % Rotamer: Outliers : 1.53 % Allowed : 13.43 % Favored : 85.04 % 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: 1.26 (0.21), residues: 1791 helix: 1.95 (0.17), residues: 1034 sheet: 0.13 (0.41), residues: 188 loop : -1.02 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 605 HIS 0.003 0.001 HIS B 202 PHE 0.012 0.001 PHE D 52 TYR 0.015 0.001 TYR C 134 ARG 0.002 0.000 ARG A 513 ********************** 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 130 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 1.622 Fit side-chains REVERT: A 319 LYS cc_start: 0.7603 (ttpt) cc_final: 0.7371 (ttmt) REVERT: A 376 MET cc_start: -0.0366 (pmm) cc_final: -0.0674 (mmm) REVERT: A 607 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8062 (pp) REVERT: D 58 ARG cc_start: 0.6544 (tmm-80) cc_final: 0.6285 (ttt180) REVERT: D 100 HIS cc_start: 0.5273 (t-90) cc_final: 0.4872 (t70) outliers start: 24 outliers final: 23 residues processed: 123 average time/residue: 0.2858 time to fit residues: 52.7694 Evaluate side-chains 129 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 194 VAL 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 75 LYS 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 C residue 131 LEU 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 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 43 optimal weight: 0.0170 chunk 129 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 144 optimal weight: 0.0040 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.5030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.223529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.155935 restraints weight = 18814.402| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 8.51 r_work: 0.3236 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14780 Z= 0.116 Angle : 0.434 7.780 19911 Z= 0.229 Chirality : 0.039 0.161 2268 Planarity : 0.003 0.043 2479 Dihedral : 9.632 154.746 1996 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.80 % Favored : 96.15 % Rotamer: Outliers : 1.34 % Allowed : 13.69 % 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: 1.33 (0.21), residues: 1791 helix: 2.02 (0.17), residues: 1039 sheet: 0.18 (0.41), residues: 188 loop : -1.06 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 605 HIS 0.002 0.000 HIS B 202 PHE 0.012 0.001 PHE D 52 TYR 0.015 0.001 TYR C 134 ARG 0.002 0.000 ARG E 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2839.51 seconds wall clock time: 53 minutes 58.43 seconds (3238.43 seconds total)