Starting phenix.real_space_refine on Fri Jul 3 19:54:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c81_16468/07_2026/8c81_16468.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c81_16468/07_2026/8c81_16468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8c81_16468/07_2026/8c81_16468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c81_16468/07_2026/8c81_16468.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8c81_16468/07_2026/8c81_16468.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c81_16468/07_2026/8c81_16468.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c81_16468/07_2026/8c81_16468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c81_16468/07_2026/8c81_16468.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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 1 5.49 5 S 64 5.16 5 C 10122 2.51 5 N 2610 2.21 5 O 2912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15709 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1502 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 10, 'TRANS': 173} Chain: "B" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4228 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 26, 'TRANS': 512} Chain: "C" Number of atoms: 4435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4435 Classifications: {'peptide': 561} Link IDs: {'PTRANS': 30, 'TRANS': 530} Chain: "D" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 586 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "E" Number of atoms: 4726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4726 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 21, 'TRANS': 563} Chain breaks: 3 Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 159 Unusual residues: {'ERG': 1, 'Q7G': 1, 'Z8A': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ERG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.78, per 1000 atoms: 0.18 Number of scatterers: 15709 At special positions: 0 Unit cell: (146.916, 118.272, 123.816, 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 1 15.00 O 2912 8.00 N 2610 7.00 C 10122 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 668.3 milliseconds 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3650 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 14 sheets defined 48.5% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 62 through 72 removed outlier: 4.391A pdb=" N LEU A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 86 through 102 removed outlier: 4.369A pdb=" N VAL A 90 " --> pdb=" O TRP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 129 removed outlier: 3.958A pdb=" N LEU A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 152 through 155 Processing helix chain 'A' and resid 158 through 179 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.722A pdb=" N VAL A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 206 Proline residue: A 203 - end of helix Processing helix chain 'B' and resid 19 through 36 removed outlier: 3.819A pdb=" N PHE B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN B 30 " --> pdb=" O TRP B 26 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 31 " --> pdb=" O TYR B 27 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 32 " --> pdb=" O TYR B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 50 Processing helix chain 'B' and resid 53 through 72 removed outlier: 3.937A pdb=" N THR B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 100 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 157 through 160 removed outlier: 4.011A pdb=" N ALA B 160 " --> pdb=" O GLN B 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 160' Processing helix chain 'B' and resid 161 through 176 Processing helix chain 'B' and resid 189 through 203 removed outlier: 3.736A pdb=" N TYR B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.547A pdb=" N LEU B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 239 through 250 removed outlier: 4.049A pdb=" N ARG B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 279 removed outlier: 3.723A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 removed outlier: 4.024A pdb=" N LEU B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.899A pdb=" N HIS B 338 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 334 through 339' Processing helix chain 'B' and resid 342 through 347 removed outlier: 3.552A pdb=" N ILE B 347 " --> pdb=" O ARG B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 379 removed outlier: 4.096A pdb=" N ILE B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 384 Processing helix chain 'B' and resid 389 through 406 removed outlier: 3.781A pdb=" N VAL B 393 " --> pdb=" O PRO B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.829A pdb=" N GLN B 411 " --> pdb=" O ASN B 407 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 459 Processing helix chain 'B' and resid 461 through 476 Processing helix chain 'B' and resid 482 through 503 removed outlier: 3.648A pdb=" N GLU B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 Processing helix chain 'B' and resid 534 through 554 Processing helix chain 'C' and resid 19 through 28 Processing helix chain 'C' and resid 57 through 86 removed outlier: 4.032A pdb=" N SER C 61 " --> pdb=" O PRO C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.630A pdb=" N LEU C 94 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 114 Processing helix chain 'C' and resid 115 through 122 removed outlier: 5.563A pdb=" N ASP C 120 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE C 122 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 186 Processing helix chain 'C' and resid 200 through 215 removed outlier: 3.687A pdb=" N ILE C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 removed outlier: 4.322A pdb=" N PHE C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.529A pdb=" N ARG C 254 " --> pdb=" O HIS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 286 removed outlier: 3.511A pdb=" N VAL C 284 " --> pdb=" O ARG C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 325 removed outlier: 3.594A pdb=" N LEU C 317 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.602A pdb=" N ILE C 382 " --> pdb=" O ASP C 378 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'C' and resid 399 through 415 removed outlier: 3.669A pdb=" N LEU C 403 " --> pdb=" O PRO C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 444 Processing helix chain 'C' and resid 464 through 476 removed outlier: 4.184A pdb=" N ALA C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 470 " --> pdb=" O MET C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 523 Processing helix chain 'C' and resid 528 through 532 removed outlier: 3.722A pdb=" N SER C 531 " --> pdb=" O SER C 528 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER C 532 " --> pdb=" O GLY C 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 528 through 532' Processing helix chain 'C' and resid 541 through 549 Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 25 through 46 removed outlier: 3.585A pdb=" N ASN D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE D 31 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N HIS D 45 " --> pdb=" O THR D 41 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 71 removed outlier: 3.626A pdb=" N PHE D 58 " --> pdb=" O PHE D 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.808A pdb=" N GLU E 45 " --> pdb=" O GLY E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 121 Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 159 through 161 No H-bonds generated for 'chain 'E' and resid 159 through 161' Processing helix chain 'E' and resid 162 through 168 Processing helix chain 'E' and resid 169 through 179 removed outlier: 3.863A pdb=" N ASP E 172 " --> pdb=" O ALA E 169 " (cutoff:3.500A) Proline residue: E 173 - end of helix removed outlier: 3.796A pdb=" N SER E 177 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 218 removed outlier: 3.513A pdb=" N PHE E 217 " --> pdb=" O THR E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 297 Processing helix chain 'E' and resid 307 through 326 removed outlier: 3.844A pdb=" N GLU E 311 " --> pdb=" O GLN E 307 " (cutoff:3.500A) Proline residue: E 313 - end of helix removed outlier: 3.647A pdb=" N GLU E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN E 326 " --> pdb=" O VAL E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 355 removed outlier: 4.111A pdb=" N VAL E 349 " --> pdb=" O GLN E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 418 removed outlier: 3.543A pdb=" N GLN E 412 " --> pdb=" O GLN E 408 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS E 413 " --> pdb=" O TRP E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 429 removed outlier: 4.128A pdb=" N ASP E 429 " --> pdb=" O THR E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 426 through 429' Processing helix chain 'E' and resid 430 through 453 removed outlier: 3.787A pdb=" N LEU E 434 " --> pdb=" O ASN E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 490 removed outlier: 3.598A pdb=" N SER E 480 " --> pdb=" O ASP E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 502 removed outlier: 3.630A pdb=" N GLN E 495 " --> pdb=" O ASP E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 538 removed outlier: 3.809A pdb=" N ILE E 527 " --> pdb=" O TYR E 523 " (cutoff:3.500A) Proline residue: E 528 - end of helix Processing helix chain 'E' and resid 563 through 575 Processing helix chain 'E' and resid 576 through 579 Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 57 Processing sheet with id=AA2, first strand: chain 'B' and resid 123 through 124 removed outlier: 6.195A pdb=" N ILE B 133 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N LEU B 506 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE B 148 " --> pdb=" O LEU B 506 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 211 removed outlier: 3.577A pdb=" N PHE B 364 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS B 286 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE B 318 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE B 288 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASP B 320 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR B 290 " --> pdb=" O ASP B 320 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL B 231 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL B 289 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL B 233 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE B 232 " --> pdb=" O TYR B 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 434 through 436 removed outlier: 3.861A pdb=" N THR B 508 " --> pdb=" O LYS B 526 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 126 through 127 removed outlier: 3.987A pdb=" N ARG C 135 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ALA C 153 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N ILE C 140 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER C 151 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N HIS C 142 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR C 149 " --> pdb=" O HIS C 142 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ALA C 479 " --> pdb=" O PRO C 156 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N MET C 158 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 218 through 222 removed outlier: 3.844A pdb=" N GLY C 373 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE C 359 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 297 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N PHE C 329 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE C 299 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ASP C 331 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA C 301 " --> pdb=" O ASP C 331 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL C 243 " --> pdb=" O ARG C 265 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 455 through 460 removed outlier: 3.631A pdb=" N ARG C 494 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL C 481 " --> pdb=" O ARG C 496 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 38 through 41 removed outlier: 3.647A pdb=" N ILE E 14 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 57 through 63 removed outlier: 5.513A pdb=" N LEU E 58 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA E 73 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY E 60 " --> pdb=" O ILE E 71 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 76 through 82 removed outlier: 5.647A pdb=" N GLU E 78 " --> pdb=" O ARG E 89 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ARG E 89 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY E 80 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N PHE E 124 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 186 through 193 removed outlier: 6.603A pdb=" N LEU E 253 " --> pdb=" O SER E 386 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL E 388 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR E 255 " --> pdb=" O VAL E 388 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 387 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR E 300 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASN E 299 " --> pdb=" O HIS E 331 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL E 333 " --> pdb=" O ASN E 299 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU E 301 " --> pdb=" O VAL E 333 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 186 through 193 removed outlier: 3.815A pdb=" N ASN E 382 " --> pdb=" O HIS E 368 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL E 370 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE E 380 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 263 through 266 Processing sheet with id=AB5, first strand: chain 'E' and resid 591 through 597 removed outlier: 3.816A pdb=" N GLY E 605 " --> pdb=" O THR E 596 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 2028 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: 1.90 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4994 1.34 - 1.46: 3622 1.46 - 1.58: 7375 1.58 - 1.70: 6 1.70 - 1.82: 98 Bond restraints: 16095 Sorted by residual: bond pdb=" C10 ERG B 602 " pdb=" C9 ERG B 602 " ideal model delta sigma weight residual 1.556 1.621 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C10 ERG A 301 " pdb=" C9 ERG A 301 " ideal model delta sigma weight residual 1.556 1.613 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C13 ERG B 602 " pdb=" C17 ERG B 602 " ideal model delta sigma weight residual 1.545 1.601 -0.056 2.00e-02 2.50e+03 7.70e+00 bond pdb=" C10 ERG B 601 " pdb=" C9 ERG B 601 " ideal model delta sigma weight residual 1.556 1.609 -0.053 2.00e-02 2.50e+03 6.91e+00 bond pdb=" C19 Z8A A 302 " pdb=" N1 Z8A A 302 " ideal model delta sigma weight residual 1.345 1.390 -0.045 2.00e-02 2.50e+03 5.16e+00 ... (remaining 16090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 21454 1.87 - 3.73: 329 3.73 - 5.60: 62 5.60 - 7.46: 15 7.46 - 9.33: 3 Bond angle restraints: 21863 Sorted by residual: angle pdb=" N ILE C 118 " pdb=" CA ILE C 118 " pdb=" C ILE C 118 " ideal model delta sigma weight residual 111.88 107.27 4.61 1.06e+00 8.90e-01 1.89e+01 angle pdb=" N VAL E 537 " pdb=" CA VAL E 537 " pdb=" C VAL E 537 " ideal model delta sigma weight residual 113.16 108.39 4.77 1.49e+00 4.50e-01 1.03e+01 angle pdb=" C HIS C 96 " pdb=" N ASP C 97 " pdb=" CA ASP C 97 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.72e+00 angle pdb=" C20 ERG B 601 " pdb=" C22 ERG B 601 " pdb=" C23 ERG B 601 " ideal model delta sigma weight residual 125.47 134.80 -9.33 3.00e+00 1.11e-01 9.67e+00 angle pdb=" N GLY A 132 " pdb=" CA GLY A 132 " pdb=" C GLY A 132 " ideal model delta sigma weight residual 110.43 114.10 -3.67 1.35e+00 5.49e-01 7.38e+00 ... (remaining 21858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.69: 9253 27.69 - 55.37: 399 55.37 - 83.06: 43 83.06 - 110.75: 18 110.75 - 138.43: 8 Dihedral angle restraints: 9721 sinusoidal: 4054 harmonic: 5667 Sorted by residual: dihedral pdb=" C5A PLP C 601 " pdb=" O4P PLP C 601 " pdb=" P PLP C 601 " pdb=" O1P PLP C 601 " ideal model delta sinusoidal sigma weight residual 76.43 -162.96 -120.62 1 2.00e+01 2.50e-03 3.62e+01 dihedral pdb=" C16 Z8A A 302 " pdb=" C17 Z8A A 302 " pdb=" C18 Z8A A 302 " pdb=" C6 Z8A A 302 " ideal model delta sinusoidal sigma weight residual 59.65 -161.92 -138.43 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" C5 Q7G A 303 " pdb=" C1 Q7G A 303 " pdb=" O5 Q7G A 303 " pdb=" O1 Q7G A 303 " ideal model delta sinusoidal sigma weight residual 176.24 -50.66 -133.10 1 3.00e+01 1.11e-03 1.80e+01 ... (remaining 9718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2082 0.059 - 0.119: 324 0.119 - 0.178: 42 0.178 - 0.238: 3 0.238 - 0.297: 8 Chirality restraints: 2459 Sorted by residual: chirality pdb=" C5 Q7G A 303 " pdb=" C4 Q7G A 303 " pdb=" C6 Q7G A 303 " pdb=" O5 Q7G A 303 " both_signs ideal model delta sigma weight residual False -2.23 -2.52 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C14 ERG B 602 " pdb=" C13 ERG B 602 " pdb=" C15 ERG B 602 " pdb=" C8 ERG B 602 " both_signs ideal model delta sigma weight residual False -2.26 -1.97 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C14 ERG A 301 " pdb=" C13 ERG A 301 " pdb=" C15 ERG A 301 " pdb=" C8 ERG A 301 " both_signs ideal model delta sigma weight residual False -2.26 -1.98 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2456 not shown) Planarity restraints: 2759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 259 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO E 260 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 260 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 260 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 155 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO C 156 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 156 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 156 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 492 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.43e+00 pdb=" N PRO E 493 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 493 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 493 " 0.022 5.00e-02 4.00e+02 ... (remaining 2756 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2373 2.76 - 3.29: 14017 3.29 - 3.83: 23643 3.83 - 4.36: 25479 4.36 - 4.90: 48867 Nonbonded interactions: 114379 Sorted by model distance: nonbonded pdb=" OE2 GLU C 517 " pdb=" OG1 THR D 13 " model vdw 2.225 3.040 nonbonded pdb=" O ASN A 74 " pdb=" OG1 THR A 78 " model vdw 2.248 3.040 nonbonded pdb=" OG SER B 476 " pdb=" OD2 ASP C 238 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR B 460 " pdb=" OE1 GLU B 488 " model vdw 2.253 3.040 nonbonded pdb=" O SER D 7 " pdb=" OG SER D 7 " model vdw 2.261 3.040 ... (remaining 114374 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 7.710 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 11.940 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 0.065 16096 Z= 0.167 Angle : 0.605 9.327 21863 Z= 0.309 Chirality : 0.046 0.297 2459 Planarity : 0.004 0.049 2759 Dihedral : 16.033 138.435 6071 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.19), residues: 1922 helix: 2.26 (0.19), residues: 777 sheet: 0.38 (0.30), residues: 302 loop : -1.40 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 50 TYR 0.020 0.001 TYR C 510 PHE 0.015 0.001 PHE C 168 TRP 0.013 0.001 TRP E 346 HIS 0.004 0.001 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (16095) covalent geometry : angle 0.60513 / 0.31 (21863) hydrogen bonds : bond 0.15968 / 10.56 ( 707) hydrogen bonds : angle 5.64964 / 4.24 ( 2028) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.527 Fit side-chains REVERT: E 366 PHE cc_start: 0.7357 (p90) cc_final: 0.6854 (p90) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1021 time to fit residues: 23.5147 Evaluate side-chains 122 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN E 254 GLN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.124762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.096982 restraints weight = 23160.762| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.08 r_work: 0.3017 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16096 Z= 0.216 Angle : 0.635 9.711 21863 Z= 0.326 Chirality : 0.046 0.246 2459 Planarity : 0.004 0.047 2759 Dihedral : 11.856 131.348 2374 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.76 % Allowed : 6.37 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 1922 helix: 2.21 (0.19), residues: 793 sheet: 0.35 (0.30), residues: 294 loop : -1.51 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 250 TYR 0.029 0.002 TYR E 318 PHE 0.020 0.002 PHE D 67 TRP 0.011 0.001 TRP A 110 HIS 0.006 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.22 (16095) covalent geometry : angle 0.63463 / 0.33 (21863) hydrogen bonds : bond 0.06980 / 4.72 ( 707) hydrogen bonds : angle 4.49332 / 3.34 ( 2028) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: E 245 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7188 (tm-30) REVERT: E 366 PHE cc_start: 0.8357 (p90) cc_final: 0.7928 (p90) outliers start: 13 outliers final: 9 residues processed: 135 average time/residue: 0.1049 time to fit residues: 21.9231 Evaluate side-chains 130 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 18 optimal weight: 7.9990 chunk 165 optimal weight: 0.0470 chunk 102 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 187 optimal weight: 0.0770 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 375 GLN C 291 ASN D 21 ASN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.130632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.103255 restraints weight = 23202.245| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.03 r_work: 0.3107 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16096 Z= 0.101 Angle : 0.527 9.370 21863 Z= 0.264 Chirality : 0.042 0.236 2459 Planarity : 0.004 0.044 2759 Dihedral : 9.966 112.248 2374 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.70 % Allowed : 7.31 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.20), residues: 1922 helix: 2.41 (0.19), residues: 796 sheet: 0.58 (0.31), residues: 297 loop : -1.41 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 39 TYR 0.017 0.001 TYR C 510 PHE 0.010 0.001 PHE E 335 TRP 0.010 0.001 TRP E 441 HIS 0.004 0.001 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (16095) covalent geometry : angle 0.52726 / 0.26 (21863) hydrogen bonds : bond 0.04353 / 2.98 ( 707) hydrogen bonds : angle 4.15739 / 3.10 ( 2028) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.510 Fit side-chains REVERT: A 81 ASP cc_start: 0.8771 (t70) cc_final: 0.8506 (t0) REVERT: D 16 GLU cc_start: 0.8370 (tt0) cc_final: 0.8131 (tt0) REVERT: E 366 PHE cc_start: 0.8338 (p90) cc_final: 0.7927 (p90) outliers start: 12 outliers final: 11 residues processed: 142 average time/residue: 0.1094 time to fit residues: 24.0809 Evaluate side-chains 129 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 133 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.127027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.099358 restraints weight = 23235.655| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.01 r_work: 0.3055 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16096 Z= 0.150 Angle : 0.559 8.323 21863 Z= 0.283 Chirality : 0.043 0.247 2459 Planarity : 0.004 0.043 2759 Dihedral : 9.422 112.101 2374 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.99 % Allowed : 9.64 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1922 helix: 2.40 (0.19), residues: 797 sheet: 0.48 (0.31), residues: 299 loop : -1.39 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 39 TYR 0.022 0.001 TYR C 510 PHE 0.017 0.001 PHE D 67 TRP 0.009 0.001 TRP A 110 HIS 0.004 0.001 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (16095) covalent geometry : angle 0.55902 / 0.28 (21863) hydrogen bonds : bond 0.05506 / 3.75 ( 707) hydrogen bonds : angle 4.13339 / 3.07 ( 2028) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.592 Fit side-chains REVERT: A 81 ASP cc_start: 0.8777 (t70) cc_final: 0.8489 (t0) REVERT: D 16 GLU cc_start: 0.8483 (tt0) cc_final: 0.8195 (tt0) REVERT: E 245 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7165 (tm-30) REVERT: E 366 PHE cc_start: 0.8427 (p90) cc_final: 0.7811 (p90) REVERT: E 414 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7401 (mm-30) outliers start: 17 outliers final: 14 residues processed: 136 average time/residue: 0.1147 time to fit residues: 23.5149 Evaluate side-chains 136 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN B 295 HIS ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.091051 restraints weight = 23422.315| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.99 r_work: 0.2915 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 16096 Z= 0.345 Angle : 0.734 9.944 21863 Z= 0.383 Chirality : 0.050 0.253 2459 Planarity : 0.005 0.048 2759 Dihedral : 10.007 115.545 2374 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.46 % Allowed : 10.75 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.19), residues: 1922 helix: 1.98 (0.19), residues: 798 sheet: 0.00 (0.31), residues: 281 loop : -1.66 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 256 TYR 0.038 0.002 TYR E 318 PHE 0.021 0.002 PHE B 256 TRP 0.012 0.002 TRP A 79 HIS 0.008 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00874 / 0.34 (16095) covalent geometry : angle 0.73361 / 0.38 (21863) hydrogen bonds : bond 0.08725 / 5.89 ( 707) hydrogen bonds : angle 4.56028 / 3.36 ( 2028) Misc. bond : bond 0.00054 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.489 Fit side-chains REVERT: E 245 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7405 (tm-30) REVERT: E 366 PHE cc_start: 0.8533 (p90) cc_final: 0.8171 (p90) REVERT: E 414 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7885 (mm-30) outliers start: 25 outliers final: 22 residues processed: 138 average time/residue: 0.1120 time to fit residues: 23.6240 Evaluate side-chains 138 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 10 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 190 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.125819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.097857 restraints weight = 22965.596| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.05 r_work: 0.3017 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16096 Z= 0.120 Angle : 0.544 8.570 21863 Z= 0.277 Chirality : 0.042 0.239 2459 Planarity : 0.004 0.048 2759 Dihedral : 9.116 109.050 2374 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.99 % Allowed : 11.92 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.20), residues: 1922 helix: 2.29 (0.19), residues: 795 sheet: 0.27 (0.30), residues: 306 loop : -1.51 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 50 TYR 0.019 0.001 TYR C 510 PHE 0.018 0.001 PHE D 67 TRP 0.013 0.001 TRP A 188 HIS 0.005 0.001 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (16095) covalent geometry : angle 0.54357 / 0.28 (21863) hydrogen bonds : bond 0.05013 / 3.43 ( 707) hydrogen bonds : angle 4.15067 / 3.09 ( 2028) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.366 Fit side-chains REVERT: A 81 ASP cc_start: 0.8811 (t70) cc_final: 0.8537 (t0) REVERT: B 127 MET cc_start: 0.8451 (mtp) cc_final: 0.8098 (mtp) REVERT: E 245 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7425 (tm-30) REVERT: E 366 PHE cc_start: 0.8465 (p90) cc_final: 0.7973 (p90) REVERT: E 414 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7798 (mm-30) outliers start: 17 outliers final: 15 residues processed: 138 average time/residue: 0.1153 time to fit residues: 24.0248 Evaluate side-chains 137 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 150 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 95 optimal weight: 0.0570 chunk 49 optimal weight: 5.9990 overall best weight: 1.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.125358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.097327 restraints weight = 22964.181| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.06 r_work: 0.3005 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16096 Z= 0.136 Angle : 0.550 9.684 21863 Z= 0.280 Chirality : 0.043 0.286 2459 Planarity : 0.004 0.046 2759 Dihedral : 8.696 108.502 2374 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.05 % Allowed : 12.22 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1922 helix: 2.34 (0.19), residues: 796 sheet: 0.34 (0.30), residues: 306 loop : -1.46 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 39 TYR 0.021 0.001 TYR C 510 PHE 0.032 0.001 PHE E 337 TRP 0.010 0.001 TRP A 110 HIS 0.004 0.001 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (16095) covalent geometry : angle 0.54970 / 0.28 (21863) hydrogen bonds : bond 0.05350 / 3.66 ( 707) hydrogen bonds : angle 4.10856 / 3.05 ( 2028) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.613 Fit side-chains REVERT: A 81 ASP cc_start: 0.8820 (t70) cc_final: 0.8547 (t0) REVERT: B 127 MET cc_start: 0.8424 (mtp) cc_final: 0.8040 (mtp) REVERT: E 245 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7429 (tm-30) REVERT: E 366 PHE cc_start: 0.8443 (p90) cc_final: 0.7948 (p90) REVERT: E 414 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7797 (mm-30) outliers start: 18 outliers final: 16 residues processed: 135 average time/residue: 0.1201 time to fit residues: 24.7140 Evaluate side-chains 137 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 95 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 138 optimal weight: 0.4980 chunk 153 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.125716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.097565 restraints weight = 23034.840| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.07 r_work: 0.3015 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16096 Z= 0.127 Angle : 0.535 8.509 21863 Z= 0.272 Chirality : 0.042 0.271 2459 Planarity : 0.004 0.046 2759 Dihedral : 7.981 106.018 2374 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.29 % Allowed : 12.74 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.20), residues: 1922 helix: 2.40 (0.19), residues: 795 sheet: 0.40 (0.30), residues: 308 loop : -1.46 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 39 TYR 0.020 0.001 TYR C 510 PHE 0.026 0.001 PHE E 337 TRP 0.010 0.001 TRP E 346 HIS 0.005 0.001 HIS E 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (16095) covalent geometry : angle 0.53489 / 0.27 (21863) hydrogen bonds : bond 0.05013 / 3.43 ( 707) hydrogen bonds : angle 4.04957 / 3.01 ( 2028) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.599 Fit side-chains REVERT: A 81 ASP cc_start: 0.8844 (t70) cc_final: 0.8581 (t0) REVERT: B 127 MET cc_start: 0.8394 (mtp) cc_final: 0.8001 (mtp) REVERT: D 16 GLU cc_start: 0.8514 (tt0) cc_final: 0.8229 (tt0) REVERT: E 170 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.7216 (t70) REVERT: E 245 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7373 (tm-30) REVERT: E 345 GLN cc_start: 0.6782 (mm-40) cc_final: 0.6481 (mm-40) REVERT: E 366 PHE cc_start: 0.8436 (p90) cc_final: 0.7950 (p90) REVERT: E 414 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7699 (mm-30) outliers start: 22 outliers final: 20 residues processed: 137 average time/residue: 0.1157 time to fit residues: 24.0118 Evaluate side-chains 143 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 126 optimal weight: 0.4980 chunk 173 optimal weight: 7.9990 chunk 68 optimal weight: 0.0000 chunk 114 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 165 optimal weight: 0.3980 chunk 71 optimal weight: 4.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.129676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.101947 restraints weight = 23034.538| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.03 r_work: 0.3079 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16096 Z= 0.095 Angle : 0.499 9.075 21863 Z= 0.250 Chirality : 0.041 0.241 2459 Planarity : 0.004 0.045 2759 Dihedral : 7.680 106.177 2374 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.94 % Allowed : 13.15 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.20), residues: 1922 helix: 2.51 (0.19), residues: 795 sheet: 0.60 (0.31), residues: 299 loop : -1.39 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 39 TYR 0.015 0.001 TYR C 510 PHE 0.023 0.001 PHE E 337 TRP 0.012 0.001 TRP A 188 HIS 0.004 0.000 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (16095) covalent geometry : angle 0.49924 / 0.25 (21863) hydrogen bonds : bond 0.03761 / 2.58 ( 707) hydrogen bonds : angle 3.92450 / 2.93 ( 2028) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.546 Fit side-chains REVERT: A 81 ASP cc_start: 0.8806 (t70) cc_final: 0.8530 (t0) REVERT: B 127 MET cc_start: 0.8161 (mtp) cc_final: 0.7904 (mtp) REVERT: D 16 GLU cc_start: 0.8486 (tt0) cc_final: 0.8209 (tt0) REVERT: E 345 GLN cc_start: 0.6878 (mm-40) cc_final: 0.6630 (mm-40) REVERT: E 366 PHE cc_start: 0.8462 (p90) cc_final: 0.7845 (p90) REVERT: E 414 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7363 (mm-30) outliers start: 16 outliers final: 14 residues processed: 143 average time/residue: 0.1045 time to fit residues: 22.9600 Evaluate side-chains 139 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 104 optimal weight: 0.0980 chunk 119 optimal weight: 2.9990 chunk 126 optimal weight: 0.0670 chunk 83 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 187 optimal weight: 0.0050 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 GLN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.102670 restraints weight = 22879.824| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.05 r_work: 0.3084 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16096 Z= 0.094 Angle : 0.500 8.912 21863 Z= 0.251 Chirality : 0.041 0.237 2459 Planarity : 0.004 0.044 2759 Dihedral : 7.510 105.913 2374 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.99 % Allowed : 13.50 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.20), residues: 1922 helix: 2.63 (0.19), residues: 793 sheet: 0.73 (0.31), residues: 294 loop : -1.32 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 39 TYR 0.015 0.001 TYR C 510 PHE 0.023 0.001 PHE D 67 TRP 0.011 0.001 TRP A 188 HIS 0.004 0.000 HIS E 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (16095) covalent geometry : angle 0.49967 / 0.25 (21863) hydrogen bonds : bond 0.03684 / 2.53 ( 707) hydrogen bonds : angle 3.85882 / 2.88 ( 2028) Misc. bond : bond 0.00008 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.586 Fit side-chains REVERT: A 81 ASP cc_start: 0.8839 (t70) cc_final: 0.8555 (t0) REVERT: D 16 GLU cc_start: 0.8424 (tt0) cc_final: 0.8132 (tt0) REVERT: E 345 GLN cc_start: 0.6830 (mm-40) cc_final: 0.6609 (mm-40) REVERT: E 366 PHE cc_start: 0.8457 (p90) cc_final: 0.7833 (p90) REVERT: E 414 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7249 (mm-30) outliers start: 17 outliers final: 15 residues processed: 144 average time/residue: 0.1280 time to fit residues: 28.1495 Evaluate side-chains 139 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 97 optimal weight: 0.0370 chunk 125 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.125727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.097636 restraints weight = 22872.689| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.06 r_work: 0.3014 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16096 Z= 0.149 Angle : 0.554 8.815 21863 Z= 0.282 Chirality : 0.043 0.263 2459 Planarity : 0.004 0.045 2759 Dihedral : 7.750 105.443 2374 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.11 % Allowed : 13.73 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.20), residues: 1922 helix: 2.54 (0.19), residues: 796 sheet: 0.68 (0.31), residues: 297 loop : -1.34 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 166 TYR 0.022 0.001 TYR C 510 PHE 0.022 0.001 PHE E 337 TRP 0.010 0.001 TRP E 148 HIS 0.004 0.001 HIS E 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (16095) covalent geometry : angle 0.55447 / 0.28 (21863) hydrogen bonds : bond 0.05312 / 3.62 ( 707) hydrogen bonds : angle 3.96620 / 2.94 ( 2028) Misc. bond : bond 0.00018 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3496.79 seconds wall clock time: 60 minutes 35.46 seconds (3635.46 seconds total)