Starting phenix.real_space_refine on Sat Jun 14 07:57:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c81_16468/06_2025/8c81_16468.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c81_16468/06_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_16468/06_2025/8c81_16468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c81_16468/06_2025/8c81_16468.map" model { file = "/net/cci-nas-00/data/ceres_data/8c81_16468/06_2025/8c81_16468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c81_16468/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.60, 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: 4.44 Conformation dependent library (CDL) restraints added in 2.1 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: 1.81 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: 5.26 Time building geometry restraints manager: 4.84 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: 4.570 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: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 38.280 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.440 ------------------------------------------------------------------------------- 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 : 1.691 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: 0.2671 time to fit residues: 60.4839 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 : 1.769 ------------------------------------------------------------------------------- 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 = 0.098775 restraints weight = 23218.426| |-----------------------------------------------------------------------------| 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 : 11.738 127.915 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 4.41932 ( 2028) covalent geometry : bond 0.00431 (16095) covalent geometry : angle 0.60528 (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 : 1.789 Fit side-chains revert: symmetry clash REVERT: E 245 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7159 (tm-30) REVERT: E 366 PHE cc_start: 0.8392 (p90) cc_final: 0.7940 (p90) outliers start: 12 outliers final: 8 residues processed: 137 average time/residue: 0.2943 time to fit residues: 62.5562 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 : 1.778 ------------------------------------------------------------------------------- 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: 2.9990 chunk 108 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.126874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.099063 restraints weight = 23188.404| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.05 r_work: 0.3053 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16096 Z= 0.148 Angle : 0.568 9.207 21863 Z= 0.289 Chirality : 0.043 0.244 2459 Planarity : 0.004 0.045 2759 Dihedral : 10.383 113.280 2554 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.94 % Allowed : 7.66 % Favored : 91.41 % 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: 0.72 (0.20), residues: 1922 helix: 2.35 (0.19), residues: 791 sheet: 0.46 (0.31), residues: 296 loop : -1.46 (0.20), residues: 835 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 0.013 0.001 PHE B 256 TYR 0.023 0.001 TYR E 318 ARG 0.003 0.000 ARG E 39 Details of bonding type rmsd hydrogen bonds : bond 0.05685 ( 707) hydrogen bonds : angle 4.24153 ( 2028) covalent geometry : bond 0.00356 (16095) covalent geometry : angle 0.56816 (21863) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 1.909 Fit side-chains REVERT: A 81 ASP cc_start: 0.8826 (t70) cc_final: 0.8564 (t0) REVERT: E 245 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7168 (tm-30) REVERT: E 366 PHE cc_start: 0.8412 (p90) cc_final: 0.8017 (p90) outliers start: 16 outliers final: 14 residues processed: 141 average time/residue: 0.2661 time to fit residues: 57.8142 Evaluate side-chains 135 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 1.694 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 163 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3531 r_free = 0.3531 target = 0.126045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.098321 restraints weight = 23136.848| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.02 r_work: 0.3040 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16096 Z= 0.152 Angle : 0.566 8.510 21863 Z= 0.288 Chirality : 0.044 0.249 2459 Planarity : 0.004 0.043 2759 Dihedral : 9.673 111.763 2554 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.23 % Allowed : 9.64 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1922 helix: 2.35 (0.19), residues: 796 sheet: 0.40 (0.31), residues: 297 loop : -1.44 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 110 HIS 0.005 0.001 HIS E 331 PHE 0.018 0.001 PHE D 67 TYR 0.023 0.001 TYR E 318 ARG 0.004 0.000 ARG E 39 Details of bonding type rmsd hydrogen bonds : bond 0.05716 ( 707) hydrogen bonds : angle 4.17933 ( 2028) covalent geometry : bond 0.00369 (16095) covalent geometry : angle 0.56600 (21863) Misc. bond : bond 0.00014 ( 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 149 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.745 Fit side-chains REVERT: A 81 ASP cc_start: 0.8780 (t70) cc_final: 0.8483 (t0) REVERT: E 245 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7207 (tm-30) REVERT: E 366 PHE cc_start: 0.8439 (p90) cc_final: 0.7985 (p90) REVERT: E 414 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7836 (mm-30) outliers start: 21 outliers final: 18 residues processed: 143 average time/residue: 0.2682 time to fit residues: 58.3735 Evaluate side-chains 139 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 161 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 0.0270 chunk 40 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.120869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.092744 restraints weight = 23369.790| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.08 r_work: 0.2934 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16096 Z= 0.249 Angle : 0.649 8.650 21863 Z= 0.337 Chirality : 0.047 0.254 2459 Planarity : 0.004 0.045 2759 Dihedral : 9.913 112.108 2554 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.52 % Allowed : 11.05 % Favored : 87.43 % 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: 0.43 (0.19), residues: 1922 helix: 2.15 (0.19), residues: 798 sheet: 0.07 (0.30), residues: 292 loop : -1.58 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 110 HIS 0.007 0.001 HIS C 203 PHE 0.018 0.002 PHE B 364 TYR 0.032 0.002 TYR E 318 ARG 0.004 0.000 ARG E 39 Details of bonding type rmsd hydrogen bonds : bond 0.07551 ( 707) hydrogen bonds : angle 4.39272 ( 2028) covalent geometry : bond 0.00627 (16095) covalent geometry : angle 0.64913 (21863) Misc. bond : bond 0.00033 ( 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 150 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 2.497 Fit side-chains REVERT: E 245 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7478 (tm-30) REVERT: E 366 PHE cc_start: 0.8493 (p90) cc_final: 0.8046 (p90) REVERT: E 414 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7830 (mm-30) outliers start: 26 outliers final: 21 residues processed: 143 average time/residue: 0.3351 time to fit residues: 72.3687 Evaluate side-chains 138 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 2.162 ------------------------------------------------------------------------------- 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 40 VAL 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 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: 0.9990 chunk 176 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 153 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 1 optimal weight: 0.2980 chunk 63 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 C 291 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.098821 restraints weight = 23045.038| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.05 r_work: 0.3032 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16096 Z= 0.112 Angle : 0.530 9.199 21863 Z= 0.269 Chirality : 0.042 0.246 2459 Planarity : 0.004 0.047 2759 Dihedral : 9.115 107.484 2554 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.82 % Allowed : 12.04 % Favored : 87.14 % 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: 0.71 (0.20), residues: 1922 helix: 2.34 (0.19), residues: 795 sheet: 0.38 (0.30), residues: 302 loop : -1.45 (0.20), residues: 825 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 0.019 0.001 PHE D 67 TYR 0.019 0.001 TYR C 510 ARG 0.004 0.000 ARG E 39 Details of bonding type rmsd hydrogen bonds : bond 0.04642 ( 707) hydrogen bonds : angle 4.09544 ( 2028) covalent geometry : bond 0.00252 (16095) covalent geometry : angle 0.52953 (21863) Misc. bond : bond 0.00006 ( 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 142 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.812 Fit side-chains REVERT: A 81 ASP cc_start: 0.8825 (t70) cc_final: 0.8550 (t0) REVERT: E 245 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7405 (tm-30) REVERT: E 366 PHE cc_start: 0.8465 (p90) cc_final: 0.7952 (p90) REVERT: E 414 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7821 (mm-30) outliers start: 14 outliers final: 12 residues processed: 138 average time/residue: 0.2939 time to fit residues: 61.5747 Evaluate side-chains 134 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 1.775 ------------------------------------------------------------------------------- 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 283 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 106 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 155 optimal weight: 0.0980 chunk 134 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 190 optimal weight: 0.0020 chunk 110 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.129285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.101279 restraints weight = 22998.441| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.07 r_work: 0.3068 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1402 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= 0.099 Angle : 0.504 9.614 21863 Z= 0.254 Chirality : 0.042 0.316 2459 Planarity : 0.004 0.044 2759 Dihedral : 8.071 103.196 2554 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.05 % Allowed : 12.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.20), residues: 1922 helix: 2.50 (0.19), residues: 796 sheet: 0.57 (0.31), residues: 301 loop : -1.37 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 188 HIS 0.004 0.000 HIS E 331 PHE 0.031 0.001 PHE E 337 TYR 0.016 0.001 TYR C 510 ARG 0.005 0.000 ARG E 39 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 707) hydrogen bonds : angle 3.92765 ( 2028) covalent geometry : bond 0.00218 (16095) covalent geometry : angle 0.50414 (21863) Misc. bond : bond 0.00013 ( 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 149 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.900 Fit side-chains REVERT: A 81 ASP cc_start: 0.8816 (t70) cc_final: 0.8540 (t0) REVERT: A 126 MET cc_start: 0.9050 (ttm) cc_final: 0.8774 (ttm) REVERT: B 127 MET cc_start: 0.8277 (mtp) cc_final: 0.7975 (mtp) REVERT: D 16 GLU cc_start: 0.8474 (tt0) cc_final: 0.8195 (tt0) REVERT: E 116 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8797 (mm-30) REVERT: E 366 PHE cc_start: 0.8395 (p90) cc_final: 0.7816 (p90) REVERT: E 414 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7432 (mm-30) outliers start: 18 outliers final: 16 residues processed: 143 average time/residue: 0.2764 time to fit residues: 60.4279 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 : 1.838 ------------------------------------------------------------------------------- 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 C residue 289 LYS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 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 37 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.127894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.099743 restraints weight = 22936.765| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.07 r_work: 0.3041 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16096 Z= 0.115 Angle : 0.519 8.944 21863 Z= 0.262 Chirality : 0.042 0.262 2459 Planarity : 0.004 0.044 2759 Dihedral : 8.078 101.120 2554 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.17 % Allowed : 12.74 % 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 (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: 0.97 (0.20), residues: 1922 helix: 2.53 (0.19), residues: 796 sheet: 0.69 (0.31), residues: 297 loop : -1.36 (0.20), residues: 829 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 0.023 0.001 PHE E 337 TYR 0.019 0.001 TYR C 510 ARG 0.004 0.000 ARG E 39 Details of bonding type rmsd hydrogen bonds : bond 0.04537 ( 707) hydrogen bonds : angle 3.92712 ( 2028) covalent geometry : bond 0.00268 (16095) covalent geometry : angle 0.51860 (21863) Misc. bond : bond 0.00010 ( 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 143 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.872 Fit side-chains REVERT: A 81 ASP cc_start: 0.8833 (t70) cc_final: 0.8550 (t0) REVERT: A 126 MET cc_start: 0.9068 (ttm) cc_final: 0.8785 (ttm) REVERT: B 274 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: D 16 GLU cc_start: 0.8522 (tt0) cc_final: 0.8245 (tt0) REVERT: D 51 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8639 (mtp) REVERT: E 366 PHE cc_start: 0.8440 (p90) cc_final: 0.8023 (p90) outliers start: 20 outliers final: 17 residues processed: 135 average time/residue: 0.2800 time to fit residues: 57.8914 Evaluate side-chains 139 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.646 ------------------------------------------------------------------------------- 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 C residue 289 LYS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 51 MET 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: 3.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 143 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 87 optimal weight: 0.3980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.123961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.095884 restraints weight = 23042.644| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.04 r_work: 0.2991 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16096 Z= 0.171 Angle : 0.570 8.615 21863 Z= 0.293 Chirality : 0.044 0.305 2459 Planarity : 0.004 0.045 2759 Dihedral : 8.374 101.674 2554 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.40 % Allowed : 13.03 % Favored : 85.56 % 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: 0.79 (0.20), residues: 1922 helix: 2.42 (0.19), residues: 798 sheet: 0.45 (0.31), residues: 288 loop : -1.43 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 110 HIS 0.005 0.001 HIS E 368 PHE 0.021 0.001 PHE E 337 TYR 0.023 0.001 TYR C 510 ARG 0.005 0.000 ARG E 39 Details of bonding type rmsd hydrogen bonds : bond 0.05996 ( 707) hydrogen bonds : angle 4.08239 ( 2028) covalent geometry : bond 0.00422 (16095) covalent geometry : angle 0.57013 (21863) Misc. bond : bond 0.00024 ( 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 146 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.955 Fit side-chains REVERT: A 81 ASP cc_start: 0.8861 (t70) cc_final: 0.8569 (t0) REVERT: E 245 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7367 (tm-30) REVERT: E 366 PHE cc_start: 0.8476 (p90) cc_final: 0.8023 (p90) outliers start: 24 outliers final: 19 residues processed: 136 average time/residue: 0.3255 time to fit residues: 67.6055 Evaluate side-chains 139 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 2.308 ------------------------------------------------------------------------------- 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 C residue 466 MET Chi-restraints excluded: chain D residue 9 VAL 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 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 154 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 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 = 0.3504 r_free = 0.3504 target = 0.125292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.097126 restraints weight = 23218.466| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.08 r_work: 0.3007 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 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 : 0.003 0.030 16096 Z= 0.141 Angle : 0.549 8.638 21863 Z= 0.279 Chirality : 0.043 0.270 2459 Planarity : 0.004 0.045 2759 Dihedral : 8.288 99.441 2554 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.05 % Allowed : 13.03 % 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 (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: 0.78 (0.20), residues: 1922 helix: 2.42 (0.19), residues: 797 sheet: 0.41 (0.31), residues: 288 loop : -1.43 (0.20), residues: 837 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 0.021 0.001 PHE D 67 TYR 0.021 0.001 TYR C 510 ARG 0.004 0.000 ARG E 39 Details of bonding type rmsd hydrogen bonds : bond 0.05334 ( 707) hydrogen bonds : angle 4.04085 ( 2028) covalent geometry : bond 0.00338 (16095) covalent geometry : angle 0.54875 (21863) Misc. bond : bond 0.00013 ( 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 140 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.681 Fit side-chains REVERT: A 81 ASP cc_start: 0.8867 (t70) cc_final: 0.8584 (t0) REVERT: B 127 MET cc_start: 0.8354 (mtp) cc_final: 0.8133 (mtp) REVERT: E 245 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7354 (tm-30) REVERT: E 366 PHE cc_start: 0.8471 (p90) cc_final: 0.7998 (p90) outliers start: 18 outliers final: 17 residues processed: 135 average time/residue: 0.4047 time to fit residues: 83.4169 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 : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 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: 0.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 150 optimal weight: 0.0670 chunk 178 optimal weight: 6.9990 chunk 4 optimal weight: 0.0370 chunk 148 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 183 optimal weight: 0.2980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.130700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.102226 restraints weight = 22928.320| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.02 r_work: 0.3092 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16096 Z= 0.090 Angle : 0.497 8.813 21863 Z= 0.248 Chirality : 0.041 0.240 2459 Planarity : 0.004 0.044 2759 Dihedral : 7.836 91.903 2554 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.99 % Allowed : 13.03 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.20), residues: 1922 helix: 2.59 (0.19), residues: 793 sheet: 0.71 (0.31), residues: 292 loop : -1.32 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 188 HIS 0.003 0.000 HIS E 368 PHE 0.020 0.001 PHE E 337 TYR 0.013 0.001 TYR C 510 ARG 0.004 0.000 ARG E 39 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 707) hydrogen bonds : angle 3.88854 ( 2028) covalent geometry : bond 0.00193 (16095) covalent geometry : angle 0.49733 (21863) Misc. bond : bond 0.00003 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8823.69 seconds wall clock time: 155 minutes 3.56 seconds (9303.56 seconds total)