Starting phenix.real_space_refine on Sun Aug 24 01:14:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c81_16468/08_2025/8c81_16468.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c81_16468/08_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_16468/08_2025/8c81_16468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c81_16468/08_2025/8c81_16468.map" model { file = "/net/cci-nas-00/data/ceres_data/8c81_16468/08_2025/8c81_16468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c81_16468/08_2025/8c81_16468.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 3.42, per 1000 atoms: 0.22 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: 1.43 Conformation dependent library (CDL) restraints added in 443.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.59 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: 2.89 Time building geometry restraints manager: 1.85 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: 5.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.790 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.830 ------------------------------------------------------------------------------- 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 : 3.93 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 aren 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 covalent geometry : bond 0.00356 (16095) covalent geometry : angle 0.60513 (21863) hydrogen bonds : bond 0.15968 ( 707) hydrogen bonds : angle 5.64964 ( 2028) 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 : 0.553 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: 0.1271 time to fit residues: 28.7723 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 : 0.521 ------------------------------------------------------------------------------- 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... 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 = 0.3518 r_free = 0.3518 target = 0.124751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.097034 restraints weight = 23147.213| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.07 r_work: 0.3019 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16096 Z= 0.215 Angle : 0.637 9.719 21863 Z= 0.326 Chirality : 0.046 0.252 2459 Planarity : 0.004 0.047 2759 Dihedral : 11.974 130.444 2554 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.76 % Allowed : 6.20 % Favored : 93.05 % 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 aren 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 0.001 ARG E 39 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 covalent geometry : bond 0.00532 (16095) covalent geometry : angle 0.63737 (21863) hydrogen bonds : bond 0.07047 ( 707) hydrogen bonds : angle 4.49849 ( 2028) Misc. bond : bond 0.00025 ( 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 : 0.649 Fit side-chains REVERT: E 245 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7195 (tm-30) REVERT: E 366 PHE cc_start: 0.8371 (p90) cc_final: 0.7926 (p90) outliers start: 13 outliers final: 9 residues processed: 135 average time/residue: 0.1314 time to fit residues: 27.0634 Evaluate side-chains 129 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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: 6.9990 chunk 165 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 184 optimal weight: 0.0270 chunk 176 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 187 optimal weight: 0.3980 overall best weight: 0.6240 ------------------------------------------------------------------------------- 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 291 ASN 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 = 0.3579 r_free = 0.3579 target = 0.129837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.102470 restraints weight = 23264.628| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.01 r_work: 0.3103 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16096 Z= 0.107 Angle : 0.531 9.409 21863 Z= 0.267 Chirality : 0.042 0.236 2459 Planarity : 0.004 0.045 2759 Dihedral : 10.137 112.343 2554 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.64 % Allowed : 7.48 % Favored : 91.88 % 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 aren not related in a simple way. whole: 0.80 (0.20), residues: 1922 helix: 2.39 (0.19), residues: 796 sheet: 0.54 (0.31), residues: 297 loop : -1.43 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 39 TYR 0.018 0.001 TYR C 510 PHE 0.011 0.001 PHE B 256 TRP 0.010 0.001 TRP E 441 HIS 0.004 0.001 HIS E 331 Details of bonding type rmsd covalent geometry : bond 0.00237 (16095) covalent geometry : angle 0.53125 (21863) hydrogen bonds : bond 0.04538 ( 707) hydrogen bonds : angle 4.17141 ( 2028) Misc. bond : bond 0.00001 ( 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 145 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.614 Fit side-chains REVERT: A 81 ASP cc_start: 0.8768 (t70) cc_final: 0.8504 (t0) REVERT: D 16 GLU cc_start: 0.8381 (tt0) cc_final: 0.8145 (tt0) REVERT: E 366 PHE cc_start: 0.8349 (p90) cc_final: 0.7940 (p90) outliers start: 11 outliers final: 9 residues processed: 141 average time/residue: 0.1165 time to fit residues: 25.1684 Evaluate side-chains 126 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain C residue 260 SER 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 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: 0.9980 chunk 139 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3531 r_free = 0.3531 target = 0.125801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.098238 restraints weight = 23160.269| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.00 r_work: 0.3037 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1128 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= 0.173 Angle : 0.579 8.394 21863 Z= 0.295 Chirality : 0.044 0.251 2459 Planarity : 0.004 0.044 2759 Dihedral : 9.712 112.180 2554 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.05 % Allowed : 9.88 % Favored : 89.07 % 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 aren not related in a simple way. whole: 0.75 (0.20), residues: 1922 helix: 2.35 (0.19), residues: 797 sheet: 0.36 (0.30), residues: 306 loop : -1.40 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 39 TYR 0.024 0.001 TYR E 318 PHE 0.018 0.001 PHE D 67 TRP 0.009 0.001 TRP A 110 HIS 0.005 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00426 (16095) covalent geometry : angle 0.57869 (21863) hydrogen bonds : bond 0.06014 ( 707) hydrogen bonds : angle 4.19084 ( 2028) Misc. bond : bond 0.00023 ( 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 144 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.514 Fit side-chains REVERT: A 81 ASP cc_start: 0.8788 (t70) cc_final: 0.8496 (t0) REVERT: E 245 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7198 (tm-30) REVERT: E 366 PHE cc_start: 0.8428 (p90) cc_final: 0.7876 (p90) REVERT: E 414 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7751 (mm-30) outliers start: 18 outliers final: 17 residues processed: 138 average time/residue: 0.1232 time to fit residues: 25.7706 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 : 0.609 ------------------------------------------------------------------------------- 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 40 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 188 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 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: 2.9990 chunk 38 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 295 HIS C 67 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 = 0.3445 r_free = 0.3445 target = 0.120503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.092538 restraints weight = 23304.708| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.03 r_work: 0.2939 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 16096 Z= 0.261 Angle : 0.662 8.724 21863 Z= 0.344 Chirality : 0.047 0.253 2459 Planarity : 0.004 0.046 2759 Dihedral : 10.005 112.184 2554 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.64 % Allowed : 10.87 % Favored : 87.49 % 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 aren not related in a simple way. whole: 0.39 (0.19), residues: 1922 helix: 2.13 (0.19), residues: 797 sheet: 0.04 (0.30), residues: 294 loop : -1.61 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 256 TYR 0.033 0.002 TYR E 318 PHE 0.018 0.002 PHE B 364 TRP 0.010 0.001 TRP A 110 HIS 0.007 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00655 (16095) covalent geometry : angle 0.66228 (21863) hydrogen bonds : bond 0.07769 ( 707) hydrogen bonds : angle 4.42071 ( 2028) Misc. bond : bond 0.00032 ( 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: 28 poor density : 123 time to evaluate : 0.721 Fit side-chains REVERT: E 245 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7406 (tm-30) REVERT: E 366 PHE cc_start: 0.8493 (p90) cc_final: 0.8049 (p90) REVERT: E 414 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7854 (mm-30) outliers start: 28 outliers final: 24 residues processed: 144 average time/residue: 0.1325 time to fit residues: 28.7314 Evaluate side-chains 140 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 205 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain C residue 8 THR 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: 0.3980 chunk 132 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 168 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.126053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.098087 restraints weight = 22951.375| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.05 r_work: 0.3024 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1322 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= 0.113 Angle : 0.535 8.823 21863 Z= 0.273 Chirality : 0.042 0.248 2459 Planarity : 0.004 0.048 2759 Dihedral : 9.266 107.740 2554 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.99 % Allowed : 12.04 % Favored : 86.97 % 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 aren not related in a simple way. whole: 0.66 (0.20), residues: 1922 helix: 2.31 (0.19), residues: 795 sheet: 0.32 (0.31), residues: 301 loop : -1.48 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 39 TYR 0.019 0.001 TYR C 510 PHE 0.019 0.001 PHE D 67 TRP 0.011 0.001 TRP A 188 HIS 0.005 0.001 HIS E 331 Details of bonding type rmsd covalent geometry : bond 0.00254 (16095) covalent geometry : angle 0.53499 (21863) hydrogen bonds : bond 0.04918 ( 707) hydrogen bonds : angle 4.12057 ( 2028) Misc. bond : bond 0.00004 ( 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 144 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.584 Fit side-chains REVERT: A 81 ASP cc_start: 0.8801 (t70) cc_final: 0.8531 (t0) REVERT: B 127 MET cc_start: 0.8408 (mtp) cc_final: 0.8038 (mtp) REVERT: E 245 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7448 (tm-30) REVERT: E 366 PHE cc_start: 0.8466 (p90) cc_final: 0.7956 (p90) REVERT: E 414 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7790 (mm-30) outliers start: 17 outliers final: 15 residues processed: 139 average time/residue: 0.1184 time to fit residues: 24.5353 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 : 0.706 ------------------------------------------------------------------------------- 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 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=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: 0.9990 chunk 184 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 49 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.126681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.098923 restraints weight = 22791.794| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.02 r_work: 0.3032 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16096 Z= 0.117 Angle : 0.529 9.201 21863 Z= 0.268 Chirality : 0.043 0.410 2459 Planarity : 0.004 0.045 2759 Dihedral : 8.374 105.216 2554 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.11 % Allowed : 12.45 % Favored : 86.44 % 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 aren not related in a simple way. whole: 0.82 (0.20), residues: 1922 helix: 2.43 (0.19), residues: 795 sheet: 0.46 (0.31), residues: 305 loop : -1.42 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 39 TYR 0.019 0.001 TYR C 510 PHE 0.036 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 covalent geometry : bond 0.00270 (16095) covalent geometry : angle 0.52905 (21863) hydrogen bonds : bond 0.04791 ( 707) hydrogen bonds : angle 4.00667 ( 2028) Misc. bond : bond 0.00017 ( 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 146 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.526 Fit side-chains REVERT: A 81 ASP cc_start: 0.8809 (t70) cc_final: 0.8549 (t0) REVERT: B 127 MET cc_start: 0.8310 (mtp) cc_final: 0.7909 (mtp) REVERT: D 16 GLU cc_start: 0.8515 (tt0) cc_final: 0.8217 (tt0) REVERT: E 245 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7398 (tm-30) REVERT: E 366 PHE cc_start: 0.8431 (p90) cc_final: 0.8020 (p90) outliers start: 19 outliers final: 18 residues processed: 139 average time/residue: 0.1172 time to fit residues: 24.6459 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 : 0.424 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 27 optimal weight: 0.0170 chunk 98 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.127802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.099984 restraints weight = 23047.513| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.03 r_work: 0.3048 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16096 Z= 0.107 Angle : 0.514 8.852 21863 Z= 0.259 Chirality : 0.042 0.245 2459 Planarity : 0.004 0.045 2759 Dihedral : 8.160 101.811 2554 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.29 % Allowed : 12.62 % Favored : 86.09 % 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 aren not related in a simple way. whole: 0.88 (0.20), residues: 1922 helix: 2.49 (0.19), residues: 795 sheet: 0.57 (0.31), residues: 299 loop : -1.41 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 39 TYR 0.019 0.001 TYR C 510 PHE 0.024 0.001 PHE E 337 TRP 0.009 0.001 TRP A 188 HIS 0.004 0.001 HIS E 331 Details of bonding type rmsd covalent geometry : bond 0.00242 (16095) covalent geometry : angle 0.51399 (21863) hydrogen bonds : bond 0.04397 ( 707) hydrogen bonds : angle 3.95541 ( 2028) Misc. bond : bond 0.00009 ( 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: 22 poor density : 123 time to evaluate : 0.409 Fit side-chains REVERT: A 81 ASP cc_start: 0.8810 (t70) cc_final: 0.8548 (t0) REVERT: A 126 MET cc_start: 0.9051 (ttm) cc_final: 0.8762 (ttm) REVERT: B 274 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: D 16 GLU cc_start: 0.8475 (tt0) cc_final: 0.8179 (tt0) REVERT: E 170 HIS cc_start: 0.7419 (OUTLIER) cc_final: 0.7217 (t70) REVERT: E 366 PHE cc_start: 0.8404 (p90) cc_final: 0.7962 (p90) outliers start: 22 outliers final: 16 residues processed: 137 average time/residue: 0.1204 time to fit residues: 25.2127 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 : 0.573 ------------------------------------------------------------------------------- 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 274 GLN 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 170 HIS 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 126 optimal weight: 0.8980 chunk 173 optimal weight: 7.9990 chunk 68 optimal weight: 0.0470 chunk 114 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 165 optimal weight: 0.0570 chunk 71 optimal weight: 2.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.129420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.101423 restraints weight = 23050.978| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.06 r_work: 0.3074 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1514 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= 0.097 Angle : 0.499 8.903 21863 Z= 0.251 Chirality : 0.041 0.260 2459 Planarity : 0.004 0.044 2759 Dihedral : 7.925 95.966 2554 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.17 % Allowed : 12.92 % 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 aren not related in a simple way. whole: 0.99 (0.20), residues: 1922 helix: 2.57 (0.19), residues: 795 sheet: 0.64 (0.31), residues: 301 loop : -1.34 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 39 TYR 0.017 0.001 TYR C 510 PHE 0.021 0.001 PHE E 337 TRP 0.012 0.001 TRP E 346 HIS 0.005 0.000 HIS E 368 Details of bonding type rmsd covalent geometry : bond 0.00215 (16095) covalent geometry : angle 0.49850 (21863) hydrogen bonds : bond 0.03935 ( 707) hydrogen bonds : angle 3.89238 ( 2028) Misc. bond : bond 0.00007 ( 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 153 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.556 Fit side-chains REVERT: A 81 ASP cc_start: 0.8838 (t70) cc_final: 0.8561 (t0) REVERT: D 16 GLU cc_start: 0.8448 (tt0) cc_final: 0.8154 (tt0) REVERT: E 116 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8801 (mm-30) REVERT: E 345 GLN cc_start: 0.6805 (mm-40) cc_final: 0.6595 (mm-40) REVERT: E 366 PHE cc_start: 0.8396 (p90) cc_final: 0.7860 (p90) outliers start: 20 outliers final: 17 residues processed: 145 average time/residue: 0.1181 time to fit residues: 26.1126 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 : 0.528 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 104 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 126 optimal weight: 0.0010 chunk 83 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 187 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.8988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.127442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.099588 restraints weight = 22870.986| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.06 r_work: 0.3042 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1491 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= 0.119 Angle : 0.524 8.682 21863 Z= 0.265 Chirality : 0.042 0.244 2459 Planarity : 0.004 0.044 2759 Dihedral : 7.987 93.925 2554 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.94 % Allowed : 13.38 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.20), residues: 1922 helix: 2.54 (0.19), residues: 797 sheet: 0.64 (0.31), residues: 299 loop : -1.33 (0.21), residues: 826 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 0.022 0.001 PHE D 67 TRP 0.009 0.001 TRP A 110 HIS 0.004 0.001 HIS E 368 Details of bonding type rmsd covalent geometry : bond 0.00279 (16095) covalent geometry : angle 0.52409 (21863) hydrogen bonds : bond 0.04652 ( 707) hydrogen bonds : angle 3.91401 ( 2028) Misc. bond : bond 0.00016 ( 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 141 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.655 Fit side-chains REVERT: A 81 ASP cc_start: 0.8870 (t70) cc_final: 0.8577 (t0) REVERT: D 16 GLU cc_start: 0.8499 (tt0) cc_final: 0.8218 (tt0) REVERT: E 366 PHE cc_start: 0.8440 (p90) cc_final: 0.7917 (p90) outliers start: 16 outliers final: 16 residues processed: 136 average time/residue: 0.1152 time to fit residues: 24.0053 Evaluate side-chains 138 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 97 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 167 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.122818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.094497 restraints weight = 22990.603| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.08 r_work: 0.2965 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16096 Z= 0.208 Angle : 0.610 8.753 21863 Z= 0.314 Chirality : 0.046 0.311 2459 Planarity : 0.004 0.046 2759 Dihedral : 8.506 100.239 2554 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.11 % Allowed : 13.50 % Favored : 85.39 % 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 aren not related in a simple way. whole: 0.73 (0.20), residues: 1922 helix: 2.37 (0.19), residues: 798 sheet: 0.33 (0.31), residues: 293 loop : -1.43 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 348 TYR 0.024 0.002 TYR E 318 PHE 0.025 0.002 PHE E 337 TRP 0.010 0.001 TRP A 110 HIS 0.006 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00519 (16095) covalent geometry : angle 0.61027 (21863) hydrogen bonds : bond 0.06697 ( 707) hydrogen bonds : angle 4.16042 ( 2028) Misc. bond : bond 0.00029 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3686.33 seconds wall clock time: 63 minutes 49.84 seconds (3829.84 seconds total)