Starting phenix.real_space_refine on Sat May 17 17:19:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c81_16468/05_2025/8c81_16468.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c81_16468/05_2025/8c81_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8c81_16468/05_2025/8c81_16468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c81_16468/05_2025/8c81_16468.map" model { file = "/net/cci-nas-00/data/ceres_data/8c81_16468/05_2025/8c81_16468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c81_16468/05_2025/8c81_16468.cif" } resolution = 3.3 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= 0.027 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.57, per 1000 atoms: 0.67 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: 4.26 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.76 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: 4.96 Time building geometry restraints manager: 4.72 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: 9403 27.69 - 55.37: 424 55.37 - 83.06: 44 83.06 - 110.75: 20 110.75 - 138.43: 10 Dihedral angle restraints: 9901 sinusoidal: 4234 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 9898 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: 5.850 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: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.980 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 16.325 138.435 6251 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.97 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 (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: 0.64 (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 TRP 0.013 0.001 TRP E 346 HIS 0.004 0.001 HIS E 331 PHE 0.015 0.001 PHE C 168 TYR 0.020 0.001 TYR C 510 ARG 0.005 0.000 ARG A 50 Details of bonding type rmsd hydrogen bonds : bond 0.15968 ( 707) hydrogen bonds : angle 5.64964 ( 2028) covalent geometry : bond 0.00356 (16095) covalent geometry : angle 0.60513 (21863) Misc. bond : bond 0.00031 ( 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 : 1.875 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: 0.2684 time to fit residues: 60.7661 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 : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 5.9990 chunk 144 optimal weight: 0.0870 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 173 optimal weight: 8.9990 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3538 r_free = 0.3538 target = 0.126515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.098776 restraints weight = 23218.653| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.05 r_work: 0.3042 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16096 Z= 0.177 Angle : 0.605 9.442 21863 Z= 0.308 Chirality : 0.045 0.242 2459 Planarity : 0.004 0.046 2759 Dihedral : 11.738 127.913 2554 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.70 % Allowed : 6.02 % Favored : 93.28 % 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: 0.66 (0.19), residues: 1922 helix: 2.29 (0.19), residues: 791 sheet: 0.43 (0.31), residues: 294 loop : -1.48 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 110 HIS 0.005 0.001 HIS E 331 PHE 0.019 0.001 PHE D 67 TYR 0.026 0.001 TYR E 318 ARG 0.004 0.000 ARG E 39 Details of bonding type rmsd hydrogen bonds : bond 0.06385 ( 707) hydrogen bonds : angle 4.41938 ( 2028) covalent geometry : bond 0.00431 (16095) covalent geometry : angle 0.60531 (21863) Misc. bond : bond 0.00029 ( 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 141 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 1.752 Fit side-chains revert: symmetry clash REVERT: E 245 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7161 (tm-30) REVERT: E 366 PHE cc_start: 0.8391 (p90) cc_final: 0.7939 (p90) outliers start: 12 outliers final: 8 residues processed: 137 average time/residue: 0.2606 time to fit residues: 54.8742 Evaluate side-chains 131 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain B residue 64 ILE 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 66 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN D 21 ASN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.100460 restraints weight = 23126.953| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.00 r_work: 0.3074 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16096 Z= 0.131 Angle : 0.554 9.119 21863 Z= 0.280 Chirality : 0.043 0.241 2459 Planarity : 0.004 0.045 2759 Dihedral : 10.384 113.305 2554 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.82 % Allowed : 7.36 % Favored : 91.82 % 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: 0.77 (0.20), residues: 1922 helix: 2.36 (0.19), residues: 796 sheet: 0.51 (0.31), residues: 296 loop : -1.43 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 441 HIS 0.004 0.001 HIS E 331 PHE 0.012 0.001 PHE B 256 TYR 0.020 0.001 TYR C 510 ARG 0.003 0.000 ARG E 39 Details of bonding type rmsd hydrogen bonds : bond 0.05323 ( 707) hydrogen bonds : angle 4.21419 ( 2028) covalent geometry : bond 0.00308 (16095) covalent geometry : angle 0.55407 (21863) Misc. bond : bond 0.00011 ( 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 147 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 1.744 Fit side-chains REVERT: A 81 ASP cc_start: 0.8803 (t70) cc_final: 0.8544 (t0) REVERT: D 16 GLU cc_start: 0.8403 (tt0) cc_final: 0.8161 (tt0) REVERT: E 366 PHE cc_start: 0.8378 (p90) cc_final: 0.7948 (p90) outliers start: 14 outliers final: 12 residues processed: 143 average time/residue: 0.2579 time to fit residues: 56.5737 Evaluate side-chains 131 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 190 CYS 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 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 38 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.0770 chunk 164 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 ASN ** E 355 HIS ** 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 = 0.3557 r_free = 0.3557 target = 0.128168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.100789 restraints weight = 23084.786| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.96 r_work: 0.3078 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16096 Z= 0.124 Angle : 0.541 8.423 21863 Z= 0.273 Chirality : 0.043 0.245 2459 Planarity : 0.004 0.043 2759 Dihedral : 9.541 111.488 2554 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.94 % Allowed : 9.59 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1922 helix: 2.43 (0.19), residues: 795 sheet: 0.49 (0.31), residues: 300 loop : -1.37 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 188 HIS 0.004 0.001 HIS E 331 PHE 0.018 0.001 PHE D 67 TYR 0.020 0.001 TYR C 510 ARG 0.004 0.000 ARG E 39 Details of bonding type rmsd hydrogen bonds : bond 0.05023 ( 707) hydrogen bonds : angle 4.10718 ( 2028) covalent geometry : bond 0.00291 (16095) covalent geometry : angle 0.54122 (21863) Misc. bond : bond 0.00011 ( 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 139 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 1.898 Fit side-chains REVERT: A 81 ASP cc_start: 0.8770 (t70) cc_final: 0.8479 (t0) REVERT: D 16 GLU cc_start: 0.8391 (tt0) cc_final: 0.8089 (tt0) REVERT: E 366 PHE cc_start: 0.8382 (p90) cc_final: 0.7770 (p90) REVERT: E 414 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7351 (mm-30) outliers start: 16 outliers final: 13 residues processed: 135 average time/residue: 0.2685 time to fit residues: 56.2474 Evaluate side-chains 136 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 190 CYS 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 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 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 91 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN C 67 ASN C 291 ASN E 355 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.123245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.095041 restraints weight = 23216.938| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.09 r_work: 0.2974 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16096 Z= 0.196 Angle : 0.596 8.591 21863 Z= 0.307 Chirality : 0.045 0.254 2459 Planarity : 0.004 0.043 2759 Dihedral : 9.594 111.648 2554 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.46 % Allowed : 10.46 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.65 (0.20), residues: 1922 helix: 2.29 (0.19), residues: 799 sheet: 0.21 (0.30), residues: 294 loop : -1.42 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 110 HIS 0.005 0.001 HIS C 203 PHE 0.015 0.001 PHE B 364 TYR 0.027 0.002 TYR E 318 ARG 0.004 0.000 ARG E 39 Details of bonding type rmsd hydrogen bonds : bond 0.06557 ( 707) hydrogen bonds : angle 4.23297 ( 2028) covalent geometry : bond 0.00486 (16095) covalent geometry : angle 0.59625 (21863) Misc. bond : bond 0.00018 ( 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 151 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.848 Fit side-chains REVERT: A 81 ASP cc_start: 0.8872 (t70) cc_final: 0.8574 (t0) REVERT: B 127 MET cc_start: 0.8495 (mtp) cc_final: 0.8167 (mtp) REVERT: E 245 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7417 (tm-30) REVERT: E 366 PHE cc_start: 0.8369 (p90) cc_final: 0.7958 (p90) REVERT: E 414 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7776 (mm-30) outliers start: 25 outliers final: 21 residues processed: 143 average time/residue: 0.2757 time to fit residues: 59.6764 Evaluate side-chains 142 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.886 ------------------------------------------------------------------------------- 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 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 181 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 ASN C 291 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.124657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.096586 restraints weight = 23132.681| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.05 r_work: 0.3000 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16096 Z= 0.151 Angle : 0.557 8.811 21863 Z= 0.285 Chirality : 0.044 0.251 2459 Planarity : 0.004 0.042 2759 Dihedral : 9.249 109.345 2554 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.29 % Allowed : 11.05 % Favored : 87.67 % 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: 0.70 (0.20), residues: 1922 helix: 2.35 (0.19), residues: 796 sheet: 0.29 (0.31), residues: 287 loop : -1.42 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 110 HIS 0.004 0.001 HIS E 331 PHE 0.019 0.001 PHE D 67 TYR 0.022 0.001 TYR C 510 ARG 0.003 0.000 ARG E 39 Details of bonding type rmsd hydrogen bonds : bond 0.05645 ( 707) hydrogen bonds : angle 4.13874 ( 2028) covalent geometry : bond 0.00366 (16095) covalent geometry : angle 0.55655 (21863) Misc. bond : bond 0.00009 ( 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: 22 poor density : 121 time to evaluate : 1.955 Fit side-chains REVERT: A 81 ASP cc_start: 0.8841 (t70) cc_final: 0.8563 (t0) REVERT: B 127 MET cc_start: 0.8429 (mtp) cc_final: 0.8055 (mtp) REVERT: E 245 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7410 (tm-30) REVERT: E 366 PHE cc_start: 0.8370 (p90) cc_final: 0.7926 (p90) REVERT: E 414 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7762 (mm-30) outliers start: 22 outliers final: 18 residues processed: 136 average time/residue: 0.2909 time to fit residues: 59.9128 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 : 1.888 ------------------------------------------------------------------------------- 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 40 VAL Chi-restraints excluded: chain C residue 129 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 106 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 190 optimal weight: 0.9990 chunk 110 optimal weight: 0.0570 chunk 130 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN C 291 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.128535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.100682 restraints weight = 22929.646| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.05 r_work: 0.3051 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1336 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= 0.105 Angle : 0.510 9.072 21863 Z= 0.256 Chirality : 0.042 0.397 2459 Planarity : 0.004 0.040 2759 Dihedral : 8.219 105.243 2554 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.11 % Allowed : 11.51 % Favored : 87.38 % 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: 0.89 (0.20), residues: 1922 helix: 2.47 (0.19), residues: 797 sheet: 0.55 (0.31), residues: 298 loop : -1.37 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 188 HIS 0.004 0.001 HIS E 331 PHE 0.011 0.001 PHE B 256 TYR 0.018 0.001 TYR C 510 ARG 0.004 0.000 ARG A 50 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 707) hydrogen bonds : angle 3.97610 ( 2028) covalent geometry : bond 0.00238 (16095) covalent geometry : angle 0.51002 (21863) Misc. bond : bond 0.00005 ( 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 147 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.725 Fit side-chains REVERT: A 81 ASP cc_start: 0.8809 (t70) cc_final: 0.8561 (t0) REVERT: D 16 GLU cc_start: 0.8497 (tt0) cc_final: 0.8225 (tt0) REVERT: E 366 PHE cc_start: 0.8432 (p90) cc_final: 0.8049 (p90) outliers start: 19 outliers final: 17 residues processed: 141 average time/residue: 0.2689 time to fit residues: 57.8410 Evaluate side-chains 137 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 1.899 ------------------------------------------------------------------------------- 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 B residue 375 GLN 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 D residue 65 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 37 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.122498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.094173 restraints weight = 23024.478| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.09 r_work: 0.2962 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1434 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= 0.210 Angle : 0.612 8.255 21863 Z= 0.316 Chirality : 0.046 0.313 2459 Planarity : 0.004 0.041 2759 Dihedral : 8.603 108.216 2554 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.17 % Allowed : 12.45 % 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: 0.64 (0.20), residues: 1922 helix: 2.30 (0.19), residues: 801 sheet: 0.33 (0.31), residues: 284 loop : -1.50 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 110 HIS 0.006 0.001 HIS C 203 PHE 0.027 0.002 PHE E 337 TYR 0.025 0.002 TYR E 318 ARG 0.004 0.000 ARG E 39 Details of bonding type rmsd hydrogen bonds : bond 0.06830 ( 707) hydrogen bonds : angle 4.20804 ( 2028) covalent geometry : bond 0.00522 (16095) covalent geometry : angle 0.61179 (21863) Misc. bond : bond 0.00030 ( 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 145 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 1.886 Fit side-chains REVERT: A 81 ASP cc_start: 0.8870 (t70) cc_final: 0.8574 (t0) REVERT: E 245 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7415 (tm-30) REVERT: E 366 PHE cc_start: 0.8501 (p90) cc_final: 0.8155 (p90) outliers start: 20 outliers final: 18 residues processed: 138 average time/residue: 0.2853 time to fit residues: 59.4245 Evaluate side-chains 140 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.852 ------------------------------------------------------------------------------- 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 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 D residue 65 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 72 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 68 optimal weight: 0.1980 chunk 143 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 128 optimal weight: 0.3980 chunk 111 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN C 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.127219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.099186 restraints weight = 22976.277| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.04 r_work: 0.3035 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1393 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= 0.105 Angle : 0.521 9.079 21863 Z= 0.264 Chirality : 0.042 0.260 2459 Planarity : 0.004 0.046 2759 Dihedral : 8.196 103.049 2554 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.99 % Allowed : 12.45 % Favored : 86.56 % 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: 0.86 (0.20), residues: 1922 helix: 2.48 (0.19), residues: 795 sheet: 0.56 (0.31), residues: 297 loop : -1.42 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 188 HIS 0.004 0.001 HIS E 331 PHE 0.026 0.001 PHE E 337 TYR 0.019 0.001 TYR C 510 ARG 0.004 0.000 ARG A 50 Details of bonding type rmsd hydrogen bonds : bond 0.04512 ( 707) hydrogen bonds : angle 4.01089 ( 2028) covalent geometry : bond 0.00232 (16095) covalent geometry : angle 0.52066 (21863) Misc. bond : bond 0.00001 ( 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 139 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 2.234 Fit side-chains REVERT: A 81 ASP cc_start: 0.8843 (t70) cc_final: 0.8575 (t0) REVERT: D 16 GLU cc_start: 0.8534 (tt0) cc_final: 0.8257 (tt0) REVERT: E 366 PHE cc_start: 0.8398 (p90) cc_final: 0.7897 (p90) outliers start: 17 outliers final: 15 residues processed: 135 average time/residue: 0.2792 time to fit residues: 56.5363 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 : 1.763 ------------------------------------------------------------------------------- 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 187 SER 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 154 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.123409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.095222 restraints weight = 23214.393| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.10 r_work: 0.2969 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16096 Z= 0.187 Angle : 0.588 8.676 21863 Z= 0.302 Chirality : 0.045 0.309 2459 Planarity : 0.004 0.047 2759 Dihedral : 8.487 105.422 2554 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.11 % Allowed : 12.33 % Favored : 86.56 % 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: 0.68 (0.20), residues: 1922 helix: 2.36 (0.19), residues: 798 sheet: 0.35 (0.31), residues: 284 loop : -1.49 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 110 HIS 0.005 0.001 HIS C 203 PHE 0.024 0.001 PHE E 337 TYR 0.023 0.001 TYR C 510 ARG 0.004 0.000 ARG E 39 Details of bonding type rmsd hydrogen bonds : bond 0.06273 ( 707) hydrogen bonds : angle 4.14803 ( 2028) covalent geometry : bond 0.00464 (16095) covalent geometry : angle 0.58756 (21863) Misc. bond : bond 0.00026 ( 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 144 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.963 Fit side-chains REVERT: A 81 ASP cc_start: 0.8857 (t70) cc_final: 0.8570 (t0) REVERT: E 245 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7383 (tm-30) REVERT: E 366 PHE cc_start: 0.8440 (p90) cc_final: 0.8084 (p90) REVERT: E 483 ARG cc_start: 0.8230 (ttm170) cc_final: 0.7888 (ttm170) outliers start: 19 outliers final: 18 residues processed: 138 average time/residue: 0.2850 time to fit residues: 59.1893 Evaluate side-chains 140 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.931 ------------------------------------------------------------------------------- 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 187 SER Chi-restraints excluded: chain C residue 188 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 78 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 183 optimal weight: 0.0980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.124326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.096233 restraints weight = 23017.310| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.06 r_work: 0.2993 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16096 Z= 0.153 Angle : 0.560 8.749 21863 Z= 0.286 Chirality : 0.044 0.279 2459 Planarity : 0.004 0.047 2759 Dihedral : 8.408 103.630 2554 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.11 % Allowed : 12.39 % Favored : 86.50 % 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 (0.20), residues: 1922 helix: 2.38 (0.19), residues: 797 sheet: 0.44 (0.30), residues: 305 loop : -1.52 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 110 HIS 0.004 0.001 HIS E 368 PHE 0.024 0.001 PHE E 337 TYR 0.021 0.001 TYR C 510 ARG 0.004 0.000 ARG E 39 Details of bonding type rmsd hydrogen bonds : bond 0.05659 ( 707) hydrogen bonds : angle 4.10153 ( 2028) covalent geometry : bond 0.00372 (16095) covalent geometry : angle 0.55997 (21863) Misc. bond : bond 0.00016 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7728.55 seconds wall clock time: 135 minutes 2.72 seconds (8102.72 seconds total)