Starting phenix.real_space_refine on Sun May 3 00:28:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uh6_64156/05_2026/9uh6_64156.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uh6_64156/05_2026/9uh6_64156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uh6_64156/05_2026/9uh6_64156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uh6_64156/05_2026/9uh6_64156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uh6_64156/05_2026/9uh6_64156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uh6_64156/05_2026/9uh6_64156.map" } resolution = 3.1 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= 0.012 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 53 5.16 5 C 5753 2.51 5 N 1604 2.21 5 O 1748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9164 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5190 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 24, 'TRANS': 648} Chain: "B" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1906 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 231} Chain: "F" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1973 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'ADP': 1, 'BTN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'1VU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.42, per 1000 atoms: 0.26 Number of scatterers: 9164 At special positions: 0 Unit cell: (97.75, 100.3, 137.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 53 16.00 P 5 15.00 Mg 1 11.99 O 1748 8.00 N 1604 7.00 C 5753 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: 0.85 Conformation dependent library (CDL) restraints added in 414.0 milliseconds 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 13 sheets defined 40.6% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 71 through 85 removed outlier: 3.789A pdb=" N ALA A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.711A pdb=" N ALA A 98 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER A 99 " --> pdb=" O VAL A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 99' Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 123 through 135 Processing helix chain 'A' and resid 149 through 159 removed outlier: 4.667A pdb=" N GLU A 159 " --> pdb=" O CYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 176 through 187 Processing helix chain 'A' and resid 201 through 212 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 309 through 328 Processing helix chain 'A' and resid 357 through 364 removed outlier: 4.211A pdb=" N THR A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE A 364 " --> pdb=" O VAL A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 458 through 472 Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 502 through 508 removed outlier: 3.572A pdb=" N TYR A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 540 Processing helix chain 'A' and resid 641 through 647 Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 315 through 324 removed outlier: 3.995A pdb=" N ILE B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 328 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 367 through 384 removed outlier: 3.558A pdb=" N VAL B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 384 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 406 removed outlier: 3.944A pdb=" N GLU B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 422 removed outlier: 3.731A pdb=" N HIS B 411 " --> pdb=" O GLY B 407 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 442 removed outlier: 4.114A pdb=" N ASP B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.603A pdb=" N CYS B 448 " --> pdb=" O LYS B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 473 Processing helix chain 'B' and resid 478 through 490 removed outlier: 4.169A pdb=" N ALA B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN B 483 " --> pdb=" O VAL B 479 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 499 removed outlier: 3.621A pdb=" N ARG B 499 " --> pdb=" O PRO B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 509 No H-bonds generated for 'chain 'B' and resid 507 through 509' Processing helix chain 'B' and resid 510 through 522 removed outlier: 4.188A pdb=" N CYS B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'F' and resid 34 through 49 removed outlier: 3.503A pdb=" N GLU F 40 " --> pdb=" O ASN F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 61 removed outlier: 3.519A pdb=" N ARG F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 128 through 132 Processing helix chain 'F' and resid 134 through 152 Processing helix chain 'F' and resid 169 through 187 removed outlier: 4.127A pdb=" N LEU F 173 " --> pdb=" O GLY F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 210 removed outlier: 3.713A pdb=" N ALA F 209 " --> pdb=" O VAL F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 236 Processing helix chain 'F' and resid 241 through 246 Processing helix chain 'F' and resid 246 through 253 Processing helix chain 'F' and resid 263 through 276 Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 111 removed outlier: 7.185A pdb=" N THR A 89 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N VAL A 110 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA A 91 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE A 66 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ILE A 92 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL A 68 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS A 65 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N HIS A 140 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU A 67 " --> pdb=" O HIS A 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 282 through 289 removed outlier: 4.512A pdb=" N GLN A 273 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU A 287 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLU A 271 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLU A 289 " --> pdb=" O HIS A 269 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N HIS A 269 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR A 334 " --> pdb=" O MET A 350 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N MET A 350 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 336 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA4, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AA5, first strand: chain 'A' and resid 415 through 416 removed outlier: 3.546A pdb=" N GLY A 415 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 419 through 421 Processing sheet with id=AA7, first strand: chain 'A' and resid 558 through 565 removed outlier: 6.595A pdb=" N SER A 626 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG A 619 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN A 624 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 669 through 673 removed outlier: 4.001A pdb=" N VAL A 669 " --> pdb=" O GLU A 691 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 671 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N VAL A 689 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A 673 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 10.272A pdb=" N ILE A 687 " --> pdb=" O VAL A 673 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 707 through 710 removed outlier: 4.292A pdb=" N SER A 709 " --> pdb=" O GLU A 726 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 330 through 331 removed outlier: 8.456A pdb=" N ILE B 389 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY B 353 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N PHE B 391 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 355 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ASP B 393 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ASN B 357 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N VAL B 394 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LYS B 433 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU B 459 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG B 432 " --> pdb=" O GLU B 459 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ALA B 461 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA B 434 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 330 through 331 removed outlier: 8.456A pdb=" N ILE B 389 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY B 353 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N PHE B 391 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 355 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ASP B 393 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ASN B 357 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N VAL B 394 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LYS B 433 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR B 451 " --> pdb=" O LYS B 426 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP B 504 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 454 " --> pdb=" O ASP B 504 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 80 through 81 removed outlier: 3.538A pdb=" N ARG F 111 " --> pdb=" O VAL F 80 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N ILE F 156 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR F 120 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LEU F 158 " --> pdb=" O TYR F 120 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE F 122 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL F 155 " --> pdb=" O ILE F 193 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU F 195 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY F 157 " --> pdb=" O LEU F 195 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE F 213 " --> pdb=" O GLN F 192 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL F 217 " --> pdb=" O ILE F 196 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG F 259 " --> pdb=" O THR F 214 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 199 through 201 403 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1560 1.28 - 1.42: 2260 1.42 - 1.56: 5407 1.56 - 1.70: 20 1.70 - 1.84: 85 Bond restraints: 9332 Sorted by residual: bond pdb=" O10 1VU F5601 " pdb=" P1 1VU F5601 " ideal model delta sigma weight residual 2.250 1.644 0.606 2.00e-02 2.50e+03 9.19e+02 bond pdb=" C2 BTN A 801 " pdb=" S1 BTN A 801 " ideal model delta sigma weight residual 1.824 1.437 0.387 2.00e-02 2.50e+03 3.75e+02 bond pdb=" C2' ADP A 802 " pdb=" C3' ADP A 802 " ideal model delta sigma weight residual 1.524 1.246 0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" O14 1VU F5601 " pdb=" P2 1VU F5601 " ideal model delta sigma weight residual 1.682 1.467 0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C16 1VU F5601 " pdb=" C22 1VU F5601 " ideal model delta sigma weight residual 1.560 1.362 0.198 2.00e-02 2.50e+03 9.77e+01 ... (remaining 9327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.20: 12620 11.20 - 22.39: 9 22.39 - 33.59: 5 33.59 - 44.78: 0 44.78 - 55.98: 1 Bond angle restraints: 12635 Sorted by residual: angle pdb=" O14 1VU F5601 " pdb=" P2 1VU F5601 " pdb=" O15 1VU F5601 " ideal model delta sigma weight residual 53.72 109.70 -55.98 3.00e+00 1.11e-01 3.48e+02 angle pdb=" O8 1VU F5601 " pdb=" P1 1VU F5601 " pdb=" O9 1VU F5601 " ideal model delta sigma weight residual 140.21 108.93 31.28 3.00e+00 1.11e-01 1.09e+02 angle pdb=" O10 1VU F5601 " pdb=" P1 1VU F5601 " pdb=" O9 1VU F5601 " ideal model delta sigma weight residual 78.74 109.32 -30.58 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C1' ADP A 802 " pdb=" N9 ADP A 802 " pdb=" C4 ADP A 802 " ideal model delta sigma weight residual 126.00 153.96 -27.96 3.00e+00 1.11e-01 8.69e+01 angle pdb=" C1' ADP A 802 " pdb=" N9 ADP A 802 " pdb=" C8 ADP A 802 " ideal model delta sigma weight residual 126.00 98.47 27.53 3.00e+00 1.11e-01 8.42e+01 ... (remaining 12630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 5559 34.97 - 69.95: 114 69.95 - 104.92: 16 104.92 - 139.89: 1 139.89 - 174.87: 5 Dihedral angle restraints: 5695 sinusoidal: 2312 harmonic: 3383 Sorted by residual: dihedral pdb=" C5' ADP A 802 " pdb=" O5' ADP A 802 " pdb=" PA ADP A 802 " pdb=" O2A ADP A 802 " ideal model delta sinusoidal sigma weight residual -60.00 75.98 -135.98 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" O1B ADP A 802 " pdb=" O3A ADP A 802 " pdb=" PB ADP A 802 " pdb=" PA ADP A 802 " ideal model delta sinusoidal sigma weight residual -60.00 34.59 -94.59 1 2.00e+01 2.50e-03 2.59e+01 dihedral pdb=" C 1VU F5601 " pdb=" C1 1VU F5601 " pdb=" C2 1VU F5601 " pdb=" O 1VU F5601 " ideal model delta sinusoidal sigma weight residual -123.88 50.99 -174.87 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1408 0.121 - 0.243: 19 0.243 - 0.364: 0 0.364 - 0.486: 0 0.486 - 0.607: 1 Chirality restraints: 1428 Sorted by residual: chirality pdb=" C22 1VU F5601 " pdb=" C16 1VU F5601 " pdb=" C23 1VU F5601 " pdb=" O12 1VU F5601 " both_signs ideal model delta sigma weight residual False -2.99 -2.38 -0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" CB ILE B 537 " pdb=" CA ILE B 537 " pdb=" CG1 ILE B 537 " pdb=" CG2 ILE B 537 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C16 1VU F5601 " pdb=" C22 1VU F5601 " pdb=" N2 1VU F5601 " pdb=" O11 1VU F5601 " both_signs ideal model delta sigma weight residual False 2.69 2.47 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1425 not shown) Planarity restraints: 1639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 394 " 0.019 2.00e-02 2.50e+03 1.89e-02 8.93e+00 pdb=" CG TRP A 394 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 394 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 394 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 394 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 394 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 394 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 394 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 394 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 394 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 537 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO B 538 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 538 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 538 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 473 " 0.013 2.00e-02 2.50e+03 1.13e-02 2.54e+00 pdb=" CG TYR A 473 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 473 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 473 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 473 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 473 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 473 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 473 " 0.001 2.00e-02 2.50e+03 ... (remaining 1636 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 142 2.67 - 3.23: 8516 3.23 - 3.78: 13340 3.78 - 4.34: 18213 4.34 - 4.90: 30515 Nonbonded interactions: 70726 Sorted by model distance: nonbonded pdb=" O3B ADP A 802 " pdb="MG MG A 803 " model vdw 2.109 2.170 nonbonded pdb=" O2A ADP A 802 " pdb="MG MG A 803 " model vdw 2.119 2.170 nonbonded pdb=" OE1 GLU A 349 " pdb="MG MG A 803 " model vdw 2.158 2.170 nonbonded pdb=" O ASP A 235 " pdb=" OG1 THR A 238 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASP B 504 " pdb=" N ILE B 505 " model vdw 2.239 3.120 ... (remaining 70721 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: 5.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.770 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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 : 0.012 0.606 9333 Z= 0.591 Angle : 1.075 55.976 12635 Z= 0.415 Chirality : 0.048 0.607 1428 Planarity : 0.003 0.062 1639 Dihedral : 15.928 174.865 3519 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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 are not related in a simple way. whole: 0.24 (0.25), residues: 1175 helix: 1.08 (0.27), residues: 410 sheet: 1.08 (0.37), residues: 206 loop : -0.91 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 486 TYR 0.027 0.001 TYR A 473 PHE 0.012 0.001 PHE A 163 TRP 0.050 0.002 TRP A 394 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.01155 ( 9332) covalent geometry : angle 1.07537 (12635) hydrogen bonds : bond 0.14608 ( 388) hydrogen bonds : angle 5.82839 ( 1128) Misc. bond : bond 0.12946 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 265 ASP cc_start: 0.8462 (p0) cc_final: 0.8164 (p0) REVERT: B 459 GLU cc_start: 0.8194 (pp20) cc_final: 0.7397 (pp20) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0968 time to fit residues: 17.2216 Evaluate side-chains 108 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.0870 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS B 452 ASN F 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.140364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.086144 restraints weight = 15469.298| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.29 r_work: 0.2869 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9333 Z= 0.162 Angle : 0.582 6.994 12635 Z= 0.292 Chirality : 0.045 0.197 1428 Planarity : 0.004 0.061 1639 Dihedral : 13.112 161.479 1370 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.61 % Allowed : 6.84 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.25), residues: 1175 helix: 1.18 (0.26), residues: 421 sheet: 1.06 (0.37), residues: 211 loop : -0.90 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 432 TYR 0.012 0.001 TYR A 473 PHE 0.014 0.001 PHE F 102 TRP 0.023 0.001 TRP A 394 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9332) covalent geometry : angle 0.58161 (12635) hydrogen bonds : bond 0.04431 ( 388) hydrogen bonds : angle 4.52786 ( 1128) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.389 Fit side-chains REVERT: A 128 MET cc_start: 0.8908 (mmm) cc_final: 0.8608 (mmm) REVERT: A 265 ASP cc_start: 0.8630 (p0) cc_final: 0.8322 (p0) REVERT: A 691 GLU cc_start: 0.7314 (pm20) cc_final: 0.6856 (pm20) REVERT: B 459 GLU cc_start: 0.8247 (pp20) cc_final: 0.7188 (pp20) REVERT: B 463 MET cc_start: 0.8695 (mtt) cc_final: 0.8419 (mmt) REVERT: B 504 ASP cc_start: 0.7620 (t0) cc_final: 0.7378 (t0) REVERT: F 232 LYS cc_start: 0.8886 (tppt) cc_final: 0.8546 (tppt) outliers start: 6 outliers final: 4 residues processed: 115 average time/residue: 0.0960 time to fit residues: 15.6719 Evaluate side-chains 107 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain F residue 144 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 87 optimal weight: 0.4980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 ASN F 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.139734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.085511 restraints weight = 15438.124| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.28 r_work: 0.2857 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9333 Z= 0.166 Angle : 0.559 6.939 12635 Z= 0.283 Chirality : 0.045 0.202 1428 Planarity : 0.004 0.062 1639 Dihedral : 12.201 160.872 1370 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.33 % Allowed : 9.60 % 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 are not related in a simple way. whole: 0.33 (0.25), residues: 1175 helix: 1.16 (0.26), residues: 428 sheet: 1.06 (0.37), residues: 209 loop : -0.90 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 268 TYR 0.010 0.001 TYR A 473 PHE 0.013 0.001 PHE A 163 TRP 0.015 0.001 TRP A 394 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9332) covalent geometry : angle 0.55907 (12635) hydrogen bonds : bond 0.04278 ( 388) hydrogen bonds : angle 4.34202 ( 1128) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.373 Fit side-chains REVERT: A 128 MET cc_start: 0.9109 (mmm) cc_final: 0.8683 (mmm) REVERT: A 217 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8344 (pmm) REVERT: A 265 ASP cc_start: 0.8692 (p0) cc_final: 0.8405 (p0) REVERT: A 691 GLU cc_start: 0.7361 (pm20) cc_final: 0.6872 (pm20) REVERT: A 695 MET cc_start: 0.6520 (mmt) cc_final: 0.6179 (mmt) REVERT: B 308 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8818 (mm) REVERT: B 459 GLU cc_start: 0.8309 (pp20) cc_final: 0.7338 (pp20) REVERT: B 463 MET cc_start: 0.8725 (mtt) cc_final: 0.8443 (mmt) REVERT: B 504 ASP cc_start: 0.7899 (t0) cc_final: 0.7635 (t0) REVERT: B 518 ASP cc_start: 0.8822 (m-30) cc_final: 0.8611 (t0) outliers start: 13 outliers final: 9 residues processed: 112 average time/residue: 0.0932 time to fit residues: 15.1313 Evaluate side-chains 112 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain F residue 144 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 113 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 86 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 HIS F 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.140369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.085530 restraints weight = 15722.238| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.37 r_work: 0.2855 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9333 Z= 0.151 Angle : 0.554 6.728 12635 Z= 0.280 Chirality : 0.044 0.211 1428 Planarity : 0.004 0.064 1639 Dihedral : 11.307 156.364 1370 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.23 % Allowed : 10.62 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.25), residues: 1175 helix: 1.20 (0.26), residues: 428 sheet: 1.11 (0.37), residues: 209 loop : -0.90 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 268 TYR 0.012 0.001 TYR B 417 PHE 0.015 0.001 PHE F 102 TRP 0.011 0.001 TRP A 394 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9332) covalent geometry : angle 0.55362 (12635) hydrogen bonds : bond 0.03994 ( 388) hydrogen bonds : angle 4.23143 ( 1128) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.372 Fit side-chains REVERT: A 128 MET cc_start: 0.9251 (mmm) cc_final: 0.8867 (mmm) REVERT: A 217 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8373 (pmm) REVERT: A 265 ASP cc_start: 0.8719 (p0) cc_final: 0.8417 (p0) REVERT: A 666 MET cc_start: 0.6422 (pmm) cc_final: 0.6211 (pmm) REVERT: A 691 GLU cc_start: 0.7360 (pm20) cc_final: 0.6913 (pm20) REVERT: B 308 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8820 (mm) REVERT: B 459 GLU cc_start: 0.8297 (pp20) cc_final: 0.7284 (pp20) REVERT: B 463 MET cc_start: 0.8725 (mtt) cc_final: 0.8463 (mmt) REVERT: B 504 ASP cc_start: 0.7960 (t0) cc_final: 0.7696 (t0) REVERT: B 518 ASP cc_start: 0.8824 (m-30) cc_final: 0.8602 (t0) outliers start: 12 outliers final: 8 residues processed: 111 average time/residue: 0.0932 time to fit residues: 14.9125 Evaluate side-chains 110 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain F residue 144 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.2980 chunk 16 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 40.0000 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.137500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.082813 restraints weight = 15562.729| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.28 r_work: 0.2807 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 9333 Z= 0.281 Angle : 0.632 7.453 12635 Z= 0.323 Chirality : 0.047 0.219 1428 Planarity : 0.004 0.064 1639 Dihedral : 10.896 151.870 1370 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.33 % Allowed : 11.64 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.25), residues: 1175 helix: 1.15 (0.26), residues: 414 sheet: 0.92 (0.36), residues: 215 loop : -1.03 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 165 TYR 0.011 0.001 TYR F 206 PHE 0.017 0.002 PHE A 163 TRP 0.012 0.002 TRP A 394 HIS 0.008 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00679 ( 9332) covalent geometry : angle 0.63217 (12635) hydrogen bonds : bond 0.05329 ( 388) hydrogen bonds : angle 4.47648 ( 1128) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.349 Fit side-chains REVERT: A 265 ASP cc_start: 0.8828 (p0) cc_final: 0.8524 (p0) REVERT: A 691 GLU cc_start: 0.7448 (pm20) cc_final: 0.6972 (pm20) REVERT: A 695 MET cc_start: 0.6840 (mmt) cc_final: 0.6376 (mmt) REVERT: B 308 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8866 (mm) REVERT: B 328 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8724 (mt-10) REVERT: B 459 GLU cc_start: 0.8358 (pp20) cc_final: 0.7342 (pp20) REVERT: B 504 ASP cc_start: 0.8007 (t0) cc_final: 0.7798 (t0) outliers start: 13 outliers final: 9 residues processed: 115 average time/residue: 0.0932 time to fit residues: 15.3342 Evaluate side-chains 112 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain F residue 144 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 87 optimal weight: 0.0670 chunk 83 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 ASN F 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.140383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.086127 restraints weight = 15664.038| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.28 r_work: 0.2866 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9333 Z= 0.120 Angle : 0.555 7.650 12635 Z= 0.277 Chirality : 0.044 0.187 1428 Planarity : 0.004 0.067 1639 Dihedral : 10.388 149.243 1370 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.33 % Allowed : 11.95 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.25), residues: 1175 helix: 1.29 (0.27), residues: 421 sheet: 1.12 (0.37), residues: 207 loop : -0.93 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 486 TYR 0.009 0.001 TYR F 176 PHE 0.013 0.001 PHE F 102 TRP 0.008 0.001 TRP A 394 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9332) covalent geometry : angle 0.55467 (12635) hydrogen bonds : bond 0.03581 ( 388) hydrogen bonds : angle 4.15464 ( 1128) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.348 Fit side-chains REVERT: A 265 ASP cc_start: 0.8812 (p0) cc_final: 0.8537 (p0) REVERT: A 691 GLU cc_start: 0.7430 (pm20) cc_final: 0.7001 (pm20) REVERT: A 695 MET cc_start: 0.6578 (mmt) cc_final: 0.6287 (mmt) REVERT: B 308 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8846 (mm) REVERT: B 459 GLU cc_start: 0.8317 (pp20) cc_final: 0.7276 (pp20) REVERT: B 504 ASP cc_start: 0.7935 (t0) cc_final: 0.7709 (t0) REVERT: F 232 LYS cc_start: 0.8895 (tppt) cc_final: 0.8625 (tppt) REVERT: F 243 GLU cc_start: 0.9126 (pm20) cc_final: 0.8657 (pm20) outliers start: 13 outliers final: 10 residues processed: 116 average time/residue: 0.0899 time to fit residues: 14.9376 Evaluate side-chains 113 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain F residue 144 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 ASN F 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.138797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.084367 restraints weight = 15655.545| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.27 r_work: 0.2833 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9333 Z= 0.204 Angle : 0.592 8.673 12635 Z= 0.298 Chirality : 0.045 0.232 1428 Planarity : 0.004 0.066 1639 Dihedral : 10.171 146.718 1370 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.84 % Allowed : 11.85 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.25), residues: 1175 helix: 1.26 (0.27), residues: 414 sheet: 1.02 (0.36), residues: 209 loop : -0.96 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 165 TYR 0.011 0.001 TYR F 176 PHE 0.015 0.001 PHE A 163 TRP 0.008 0.001 TRP A 394 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 9332) covalent geometry : angle 0.59198 (12635) hydrogen bonds : bond 0.04519 ( 388) hydrogen bonds : angle 4.27926 ( 1128) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 265 ASP cc_start: 0.8872 (p0) cc_final: 0.8574 (p0) REVERT: A 691 GLU cc_start: 0.7440 (pm20) cc_final: 0.6982 (pm20) REVERT: A 695 MET cc_start: 0.6628 (mmt) cc_final: 0.6376 (mmt) REVERT: B 308 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8865 (mm) REVERT: B 459 GLU cc_start: 0.8336 (pp20) cc_final: 0.7273 (pp20) REVERT: B 504 ASP cc_start: 0.8015 (t0) cc_final: 0.7806 (t0) outliers start: 18 outliers final: 14 residues processed: 112 average time/residue: 0.0956 time to fit residues: 15.1552 Evaluate side-chains 113 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 144 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 32 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 106 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: B 452 ASN F 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.140432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.085830 restraints weight = 15514.139| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.32 r_work: 0.2868 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9333 Z= 0.124 Angle : 0.558 9.935 12635 Z= 0.278 Chirality : 0.043 0.217 1428 Planarity : 0.004 0.069 1639 Dihedral : 9.903 144.087 1370 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.94 % Allowed : 12.05 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1175 helix: 1.33 (0.27), residues: 421 sheet: 1.11 (0.37), residues: 207 loop : -0.88 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 154 TYR 0.007 0.001 TYR F 176 PHE 0.013 0.001 PHE F 102 TRP 0.007 0.001 TRP A 394 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9332) covalent geometry : angle 0.55768 (12635) hydrogen bonds : bond 0.03542 ( 388) hydrogen bonds : angle 4.10335 ( 1128) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 265 ASP cc_start: 0.8870 (p0) cc_final: 0.8582 (p0) REVERT: B 459 GLU cc_start: 0.8307 (pp20) cc_final: 0.7231 (pp20) REVERT: B 504 ASP cc_start: 0.7963 (t0) cc_final: 0.7731 (t0) outliers start: 19 outliers final: 16 residues processed: 117 average time/residue: 0.0883 time to fit residues: 15.0207 Evaluate side-chains 117 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 144 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 87 optimal weight: 0.2980 chunk 80 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.140159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.085462 restraints weight = 15604.759| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.34 r_work: 0.2855 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9333 Z= 0.145 Angle : 0.579 10.928 12635 Z= 0.287 Chirality : 0.044 0.232 1428 Planarity : 0.004 0.067 1639 Dihedral : 9.822 142.406 1370 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.84 % Allowed : 12.26 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.25), residues: 1175 helix: 1.31 (0.26), residues: 421 sheet: 1.03 (0.37), residues: 209 loop : -0.86 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 154 TYR 0.014 0.001 TYR B 417 PHE 0.014 0.001 PHE F 102 TRP 0.007 0.001 TRP A 394 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9332) covalent geometry : angle 0.57900 (12635) hydrogen bonds : bond 0.03863 ( 388) hydrogen bonds : angle 4.12349 ( 1128) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.355 Fit side-chains REVERT: A 73 GLU cc_start: 0.8528 (pm20) cc_final: 0.8322 (pm20) REVERT: A 265 ASP cc_start: 0.8898 (p0) cc_final: 0.8597 (p0) REVERT: B 459 GLU cc_start: 0.8313 (pp20) cc_final: 0.7226 (pp20) REVERT: B 504 ASP cc_start: 0.7969 (t0) cc_final: 0.7738 (t0) outliers start: 18 outliers final: 16 residues processed: 119 average time/residue: 0.0840 time to fit residues: 14.5973 Evaluate side-chains 116 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 144 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.140483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.085827 restraints weight = 15570.922| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.34 r_work: 0.2868 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9333 Z= 0.129 Angle : 0.581 10.931 12635 Z= 0.287 Chirality : 0.044 0.228 1428 Planarity : 0.004 0.068 1639 Dihedral : 9.724 140.489 1370 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.74 % Allowed : 13.18 % Favored : 85.09 % 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 are not related in a simple way. whole: 0.46 (0.25), residues: 1175 helix: 1.37 (0.27), residues: 421 sheet: 1.08 (0.37), residues: 207 loop : -0.86 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 154 TYR 0.008 0.001 TYR F 176 PHE 0.013 0.001 PHE F 102 TRP 0.007 0.001 TRP A 394 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9332) covalent geometry : angle 0.58103 (12635) hydrogen bonds : bond 0.03564 ( 388) hydrogen bonds : angle 4.06567 ( 1128) Misc. bond : bond 0.00010 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.396 Fit side-chains REVERT: A 265 ASP cc_start: 0.8899 (p0) cc_final: 0.8598 (p0) REVERT: B 459 GLU cc_start: 0.8324 (pp20) cc_final: 0.7246 (pp20) REVERT: B 504 ASP cc_start: 0.7889 (t0) cc_final: 0.7650 (t0) outliers start: 17 outliers final: 16 residues processed: 117 average time/residue: 0.0937 time to fit residues: 15.9230 Evaluate side-chains 115 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 144 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 13 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 452 ASN ** 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 = 0.3868 r_free = 0.3868 target = 0.139559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.085478 restraints weight = 15430.080| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.25 r_work: 0.2859 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9333 Z= 0.154 Angle : 0.596 10.915 12635 Z= 0.295 Chirality : 0.044 0.230 1428 Planarity : 0.004 0.068 1639 Dihedral : 9.670 138.619 1370 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.94 % Allowed : 13.07 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1175 helix: 1.36 (0.27), residues: 421 sheet: 0.98 (0.37), residues: 209 loop : -0.86 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 154 TYR 0.010 0.001 TYR F 176 PHE 0.014 0.001 PHE A 163 TRP 0.007 0.001 TRP A 394 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9332) covalent geometry : angle 0.59642 (12635) hydrogen bonds : bond 0.03910 ( 388) hydrogen bonds : angle 4.11515 ( 1128) Misc. bond : bond 0.00010 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2688.25 seconds wall clock time: 46 minutes 38.04 seconds (2798.04 seconds total)