Starting phenix.real_space_refine on Sun May 3 00:25:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zv3_60506/05_2026/8zv3_60506.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zv3_60506/05_2026/8zv3_60506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zv3_60506/05_2026/8zv3_60506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zv3_60506/05_2026/8zv3_60506.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zv3_60506/05_2026/8zv3_60506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zv3_60506/05_2026/8zv3_60506.map" } resolution = 2.77 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= 0.001 sd= 0.015 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 6 5.49 5 Mg 1 5.21 5 S 53 5.16 5 C 5755 2.51 5 N 1604 2.21 5 O 1751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 9170 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: 1975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1975 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {' MG': 1, 'ATP': 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: 2.20, per 1000 atoms: 0.24 Number of scatterers: 9170 At special positions: 0 Unit cell: (96.6, 97.44, 136.92, 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 6 15.00 Mg 1 11.99 O 1751 8.00 N 1604 7.00 C 5755 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: 0.92 Conformation dependent library (CDL) restraints added in 268.0 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: 2180 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 13 sheets defined 40.8% alpha, 23.4% 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 72 through 85 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: 4.183A pdb=" N GLU A 159 " --> pdb=" O CYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 176 removed outlier: 4.256A pdb=" N ASP A 176 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 187 Processing helix chain 'A' and resid 201 through 213 removed outlier: 3.843A pdb=" N GLU A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) 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 366 removed outlier: 4.338A pdb=" N THR A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 4.015A 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 458 through 472 Processing helix chain 'A' and resid 481 through 490 Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 502 through 508 Processing helix chain 'A' and resid 518 through 541 removed outlier: 3.749A pdb=" N GLN A 541 " --> pdb=" O GLN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 648 Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 315 through 324 removed outlier: 3.855A 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: 3.528A pdb=" N PHE B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 407 Processing helix chain 'B' and resid 407 through 422 removed outlier: 3.665A pdb=" N ALA B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 442 removed outlier: 3.760A pdb=" N ASP B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 464 through 473 Processing helix chain 'B' and resid 478 through 491 removed outlier: 4.126A pdb=" N ALA B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 499 removed outlier: 3.618A 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: 3.867A pdb=" N CYS B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 49 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 91 through 95 removed outlier: 4.184A pdb=" N GLY F 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) 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 186 removed outlier: 3.728A pdb=" N LEU F 173 " --> pdb=" O GLY F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 205 through 211 removed outlier: 3.682A 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 240 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 109 through 111 removed outlier: 3.966A pdb=" N ILE A 92 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 138 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 139 " --> pdb=" O VAL A 162 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 229 through 232 Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 284 removed outlier: 6.649A pdb=" N THR A 334 " --> pdb=" O MET A 350 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N MET A 350 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU A 336 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 282 through 284 removed outlier: 5.247A pdb=" N HIS A 269 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER A 291 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL A 300 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN A 293 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS A 298 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 14.563A pdb=" N GLN A 297 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 11.028A pdb=" N TYR A 401 " --> pdb=" O GLN A 297 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL A 299 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 415 through 416 removed outlier: 3.525A 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: 6.523A pdb=" N SER A 626 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG A 619 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN A 624 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 661 through 663 Processing sheet with id=AA9, first strand: chain 'A' and resid 696 through 700 removed outlier: 4.323A pdb=" N CYS A 688 " --> pdb=" O MET A 699 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ILE A 687 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL A 673 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL A 689 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 680 through 681 Processing sheet with id=AB2, first strand: chain 'B' and resid 330 through 332 removed outlier: 4.578A pdb=" N VAL B 342 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ILE B 389 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLY B 353 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE B 391 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 355 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASP B 393 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASN B 357 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N VAL B 394 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS B 433 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU B 459 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG B 432 " --> pdb=" O GLU B 459 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ALA B 461 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA B 434 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 330 through 332 removed outlier: 4.578A pdb=" N VAL B 342 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ILE B 389 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLY B 353 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE B 391 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 355 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASP B 393 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASN B 357 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N VAL B 394 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS B 433 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS B 426 " --> pdb=" O THR B 451 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N TYR B 453 " --> pdb=" O LYS B 426 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR B 428 " --> pdb=" O TYR B 453 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP B 504 " --> pdb=" O ASN B 452 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 80 through 82 removed outlier: 4.552A pdb=" N THR F 109 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ILE F 156 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR F 120 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU F 158 " --> pdb=" O TYR F 120 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE F 122 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ASP F 160 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLN F 124 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL F 155 " --> pdb=" O ILE F 193 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LEU F 195 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLY F 157 " --> pdb=" O LEU F 195 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET F 197 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ASN F 159 " --> pdb=" O MET F 197 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE F 213 " --> pdb=" O GLN F 192 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY F 198 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG F 259 " --> pdb=" O THR F 214 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1245 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: 1.56 Time building geometry restraints manager: 1.14 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: 1558 1.28 - 1.42: 2260 1.42 - 1.56: 5417 1.56 - 1.70: 18 1.70 - 1.84: 85 Bond restraints: 9338 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 9.18e+02 bond pdb=" O14 1VU F5601 " pdb=" P2 1VU F5601 " ideal model delta sigma weight residual 1.682 1.469 0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C16 1VU F5601 " pdb=" C22 1VU F5601 " ideal model delta sigma weight residual 1.560 1.359 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C3 BTN A 801 " pdb=" O3 BTN A 801 " ideal model delta sigma weight residual 1.220 1.410 -0.190 2.00e-02 2.50e+03 9.02e+01 bond pdb=" C16 1VU F5601 " pdb=" O11 1VU F5601 " ideal model delta sigma weight residual 1.425 1.594 -0.169 2.00e-02 2.50e+03 7.14e+01 ... (remaining 9333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.15: 12636 11.15 - 22.29: 6 22.29 - 33.44: 3 33.44 - 44.59: 0 44.59 - 55.73: 1 Bond angle restraints: 12646 Sorted by residual: angle pdb=" O14 1VU F5601 " pdb=" P2 1VU F5601 " pdb=" O15 1VU F5601 " ideal model delta sigma weight residual 53.72 109.45 -55.73 3.00e+00 1.11e-01 3.45e+02 angle pdb=" O8 1VU F5601 " pdb=" P1 1VU F5601 " pdb=" O9 1VU F5601 " ideal model delta sigma weight residual 140.21 108.92 31.29 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 78.74 109.24 -30.50 3.00e+00 1.11e-01 1.03e+02 angle pdb=" O10 1VU F5601 " pdb=" P1 1VU F5601 " pdb=" O7 1VU F5601 " ideal model delta sigma weight residual 85.76 109.72 -23.96 3.00e+00 1.11e-01 6.38e+01 angle pdb=" O14 1VU F5601 " pdb=" P2 1VU F5601 " pdb=" O16 1VU F5601 " ideal model delta sigma weight residual 128.28 108.87 19.41 3.00e+00 1.11e-01 4.18e+01 ... (remaining 12641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.01: 5604 33.01 - 66.02: 107 66.02 - 99.03: 6 99.03 - 132.04: 1 132.04 - 165.05: 4 Dihedral angle restraints: 5722 sinusoidal: 2335 harmonic: 3387 Sorted by residual: 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 41.17 -165.05 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C 1VU F5601 " pdb=" C1 1VU F5601 " pdb=" C2 1VU F5601 " pdb=" S 1VU F5601 " ideal model delta sinusoidal sigma weight residual 57.40 -138.90 -163.70 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C15 1VU F5601 " pdb=" C23 1VU F5601 " pdb=" O13 1VU F5601 " pdb=" P2 1VU F5601 " ideal model delta sinusoidal sigma weight residual 86.09 -56.36 142.45 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 5719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1405 0.113 - 0.225: 23 0.225 - 0.338: 1 0.338 - 0.450: 0 0.450 - 0.563: 1 Chirality restraints: 1430 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 -2.43 -0.56 2.00e-01 2.50e+01 7.92e+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 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C2 BTN A 801 " pdb=" C4 BTN A 801 " pdb=" C7 BTN A 801 " pdb=" S1 BTN A 801 " both_signs ideal model delta sigma weight residual False 3.08 2.88 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1427 not shown) Planarity restraints: 1639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTN A 801 " -0.004 2.00e-02 2.50e+03 1.75e-02 4.58e+00 pdb=" C4 BTN A 801 " -0.017 2.00e-02 2.50e+03 pdb=" C5 BTN A 801 " 0.029 2.00e-02 2.50e+03 pdb=" N1 BTN A 801 " -0.024 2.00e-02 2.50e+03 pdb=" N2 BTN A 801 " 0.008 2.00e-02 2.50e+03 pdb=" O3 BTN A 801 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 473 " 0.017 2.00e-02 2.50e+03 1.41e-02 3.95e+00 pdb=" CG TYR A 473 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 473 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 473 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 473 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 473 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 473 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 473 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 178 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C ASP F 178 " 0.023 2.00e-02 2.50e+03 pdb=" O ASP F 178 " -0.009 2.00e-02 2.50e+03 pdb=" N ILE F 179 " -0.008 2.00e-02 2.50e+03 ... (remaining 1636 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 135 2.66 - 3.22: 8512 3.22 - 3.78: 13919 3.78 - 4.34: 19549 4.34 - 4.90: 32388 Nonbonded interactions: 74503 Sorted by model distance: nonbonded pdb=" OE2 GLU A 336 " pdb="MG MG A 803 " model vdw 2.100 2.170 nonbonded pdb=" O LYS A 132 " pdb=" NH1 ARG A 135 " model vdw 2.183 3.120 nonbonded pdb=" OE2 GLU A 73 " pdb=" OH TYR A 143 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR B 435 " pdb=" OE2 GLU B 459 " model vdw 2.296 3.040 nonbonded pdb=" O LYS F 248 " pdb=" OG1 THR F 252 " model vdw 2.310 3.040 ... (remaining 74498 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: 3.890 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.150 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 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:5.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 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 : 0.009 0.606 9339 Z= 0.480 Angle : 0.956 55.734 12646 Z= 0.384 Chirality : 0.046 0.563 1430 Planarity : 0.004 0.038 1639 Dihedral : 14.031 165.050 3542 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 1.02 (0.26), residues: 423 sheet: 0.99 (0.35), residues: 236 loop : -0.71 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 243 TYR 0.034 0.001 TYR A 473 PHE 0.012 0.001 PHE A 242 TRP 0.020 0.002 TRP A 394 HIS 0.004 0.001 HIS B 446 Details of bonding type rmsd covalent geometry : bond 0.00931 ( 9338) covalent geometry : angle 0.95615 (12646) hydrogen bonds : bond 0.14618 ( 429) hydrogen bonds : angle 6.27608 ( 1245) Misc. bond : bond 0.12524 ( 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 128 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 470 GLU cc_start: 0.8223 (mp0) cc_final: 0.7982 (mp0) REVERT: B 489 LYS cc_start: 0.9038 (ttmt) cc_final: 0.8748 (ttpp) REVERT: F 236 ASN cc_start: 0.8979 (t0) cc_final: 0.8676 (t0) outliers start: 0 outliers final: 1 residues processed: 128 average time/residue: 0.7015 time to fit residues: 94.4067 Evaluate side-chains 89 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 229 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.0980 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 40.0000 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 344 ASN A 351 ASN F 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.125902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.078013 restraints weight = 15319.474| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.77 r_work: 0.2733 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9339 Z= 0.151 Angle : 0.564 9.613 12646 Z= 0.289 Chirality : 0.045 0.138 1430 Planarity : 0.004 0.044 1639 Dihedral : 12.260 140.617 1395 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.02 % Allowed : 8.07 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.25), residues: 1175 helix: 1.34 (0.25), residues: 434 sheet: 1.10 (0.35), residues: 222 loop : -0.74 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 154 TYR 0.009 0.001 TYR F 206 PHE 0.020 0.001 PHE A 307 TRP 0.009 0.001 TRP A 233 HIS 0.005 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9338) covalent geometry : angle 0.56422 (12646) hydrogen bonds : bond 0.04304 ( 429) hydrogen bonds : angle 4.79014 ( 1245) Misc. bond : bond 0.00011 ( 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 103 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.7947 (tpt) cc_final: 0.7724 (tpt) REVERT: B 308 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8506 (mm) REVERT: B 470 GLU cc_start: 0.8227 (mp0) cc_final: 0.7840 (mp0) REVERT: F 38 ARG cc_start: 0.3605 (tmt170) cc_final: 0.3269 (tmt170) outliers start: 10 outliers final: 8 residues processed: 97 average time/residue: 0.7057 time to fit residues: 72.0399 Evaluate side-chains 88 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 518 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 112 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 64 optimal weight: 50.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.123735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.073077 restraints weight = 15292.287| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.39 r_work: 0.2699 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9339 Z= 0.230 Angle : 0.578 9.707 12646 Z= 0.299 Chirality : 0.046 0.138 1430 Planarity : 0.004 0.038 1639 Dihedral : 10.702 118.617 1393 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.43 % Allowed : 9.60 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.25), residues: 1175 helix: 1.37 (0.25), residues: 434 sheet: 1.20 (0.34), residues: 216 loop : -0.78 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 154 TYR 0.011 0.001 TYR F 206 PHE 0.016 0.002 PHE F 122 TRP 0.008 0.002 TRP B 531 HIS 0.007 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 9338) covalent geometry : angle 0.57837 (12646) hydrogen bonds : bond 0.04841 ( 429) hydrogen bonds : angle 4.71876 ( 1245) Misc. bond : bond 0.00062 ( 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 94 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: B 308 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8470 (mm) REVERT: B 470 GLU cc_start: 0.8370 (mp0) cc_final: 0.8000 (mp0) outliers start: 14 outliers final: 7 residues processed: 88 average time/residue: 0.6742 time to fit residues: 62.8948 Evaluate side-chains 82 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain F residue 239 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 104 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.124012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.073139 restraints weight = 15443.432| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.42 r_work: 0.2694 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9339 Z= 0.204 Angle : 0.561 10.974 12646 Z= 0.288 Chirality : 0.045 0.139 1430 Planarity : 0.004 0.037 1639 Dihedral : 9.928 112.937 1393 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.84 % Allowed : 10.62 % Favored : 87.54 % 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: 0.59 (0.25), residues: 1175 helix: 1.44 (0.25), residues: 434 sheet: 0.95 (0.33), residues: 233 loop : -0.79 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 154 TYR 0.012 0.001 TYR F 206 PHE 0.014 0.002 PHE F 122 TRP 0.007 0.001 TRP B 531 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 9338) covalent geometry : angle 0.56129 (12646) hydrogen bonds : bond 0.04438 ( 429) hydrogen bonds : angle 4.61685 ( 1245) Misc. bond : bond 0.00238 ( 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 94 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 308 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8439 (mm) REVERT: B 470 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: B 489 LYS cc_start: 0.8951 (ttmt) cc_final: 0.8730 (ttmt) REVERT: F 54 ARG cc_start: 0.7839 (mtt90) cc_final: 0.7635 (mtp85) outliers start: 18 outliers final: 8 residues processed: 89 average time/residue: 0.6562 time to fit residues: 62.0645 Evaluate side-chains 87 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain F residue 235 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.0370 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 50.0000 chunk 71 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.125601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.077678 restraints weight = 15319.776| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.55 r_work: 0.2735 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9339 Z= 0.113 Angle : 0.521 11.030 12646 Z= 0.266 Chirality : 0.043 0.136 1430 Planarity : 0.003 0.033 1639 Dihedral : 9.137 105.327 1393 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.63 % Allowed : 11.13 % Favored : 87.23 % 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: 0.67 (0.25), residues: 1175 helix: 1.57 (0.26), residues: 435 sheet: 0.89 (0.34), residues: 227 loop : -0.74 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 243 TYR 0.022 0.001 TYR B 417 PHE 0.010 0.001 PHE A 152 TRP 0.005 0.001 TRP A 233 HIS 0.005 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9338) covalent geometry : angle 0.52139 (12646) hydrogen bonds : bond 0.03547 ( 429) hydrogen bonds : angle 4.43629 ( 1245) Misc. bond : bond 0.00100 ( 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 98 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 308 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8536 (mm) REVERT: B 470 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: B 485 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8222 (tm-30) REVERT: B 489 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8587 (ttmt) REVERT: B 490 PHE cc_start: 0.8587 (m-80) cc_final: 0.8340 (m-80) outliers start: 16 outliers final: 7 residues processed: 94 average time/residue: 0.6916 time to fit residues: 68.7813 Evaluate side-chains 91 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain F residue 239 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 0.0470 chunk 62 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 chunk 105 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.126839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.079084 restraints weight = 15330.301| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.81 r_work: 0.2750 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9339 Z= 0.098 Angle : 0.542 11.638 12646 Z= 0.270 Chirality : 0.043 0.136 1430 Planarity : 0.004 0.051 1639 Dihedral : 8.724 103.051 1393 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.63 % Allowed : 11.64 % 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: 0.75 (0.25), residues: 1175 helix: 1.66 (0.26), residues: 435 sheet: 0.84 (0.34), residues: 236 loop : -0.68 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 53 TYR 0.009 0.001 TYR F 206 PHE 0.008 0.001 PHE B 384 TRP 0.005 0.001 TRP A 284 HIS 0.004 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 9338) covalent geometry : angle 0.54186 (12646) hydrogen bonds : bond 0.03227 ( 429) hydrogen bonds : angle 4.31519 ( 1245) Misc. bond : bond 0.00065 ( 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 107 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: B 308 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8532 (mm) REVERT: B 470 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: B 485 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8254 (tm-30) REVERT: B 489 LYS cc_start: 0.8923 (ttmt) cc_final: 0.8641 (ttmt) REVERT: B 490 PHE cc_start: 0.8665 (m-80) cc_final: 0.8397 (m-80) outliers start: 16 outliers final: 7 residues processed: 101 average time/residue: 0.6904 time to fit residues: 73.6642 Evaluate side-chains 82 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain F residue 239 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.0870 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.126535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.078427 restraints weight = 15322.382| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.72 r_work: 0.2741 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9339 Z= 0.118 Angle : 0.563 12.081 12646 Z= 0.282 Chirality : 0.043 0.135 1430 Planarity : 0.004 0.066 1639 Dihedral : 8.669 106.685 1393 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.53 % Allowed : 12.05 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.70 (0.25), residues: 1175 helix: 1.57 (0.26), residues: 435 sheet: 0.80 (0.34), residues: 236 loop : -0.67 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 54 TYR 0.022 0.001 TYR B 417 PHE 0.013 0.001 PHE A 337 TRP 0.004 0.001 TRP A 559 HIS 0.005 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9338) covalent geometry : angle 0.56302 (12646) hydrogen bonds : bond 0.03419 ( 429) hydrogen bonds : angle 4.33061 ( 1245) Misc. bond : bond 0.00051 ( 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 94 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: B 308 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8483 (mm) REVERT: B 470 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: B 489 LYS cc_start: 0.8894 (ttmt) cc_final: 0.8606 (ttmt) REVERT: B 490 PHE cc_start: 0.8666 (m-80) cc_final: 0.8408 (m-80) outliers start: 15 outliers final: 9 residues processed: 89 average time/residue: 0.6595 time to fit residues: 62.4274 Evaluate side-chains 91 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain F residue 239 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.125549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.077301 restraints weight = 15223.015| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.73 r_work: 0.2719 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9339 Z= 0.149 Angle : 0.578 12.365 12646 Z= 0.289 Chirality : 0.044 0.137 1430 Planarity : 0.004 0.059 1639 Dihedral : 8.660 109.226 1393 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.74 % Allowed : 12.16 % Favored : 86.11 % 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: 0.70 (0.25), residues: 1175 helix: 1.57 (0.26), residues: 434 sheet: 0.83 (0.34), residues: 236 loop : -0.67 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 53 TYR 0.024 0.001 TYR B 417 PHE 0.013 0.001 PHE F 122 TRP 0.006 0.001 TRP B 531 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9338) covalent geometry : angle 0.57800 (12646) hydrogen bonds : bond 0.03770 ( 429) hydrogen bonds : angle 4.35187 ( 1245) Misc. bond : bond 0.00052 ( 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 102 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: B 308 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8505 (mm) REVERT: B 470 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: B 485 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8211 (tm-30) REVERT: B 489 LYS cc_start: 0.8862 (ttmt) cc_final: 0.8512 (ttmt) REVERT: B 490 PHE cc_start: 0.8698 (m-80) cc_final: 0.8438 (m-80) outliers start: 17 outliers final: 9 residues processed: 98 average time/residue: 0.6795 time to fit residues: 70.3532 Evaluate side-chains 86 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 239 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 15 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 55 optimal weight: 0.0970 chunk 110 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.126370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.078171 restraints weight = 15291.113| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.75 r_work: 0.2722 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9339 Z= 0.125 Angle : 0.586 17.786 12646 Z= 0.288 Chirality : 0.043 0.136 1430 Planarity : 0.003 0.045 1639 Dihedral : 8.572 112.151 1393 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.53 % Allowed : 12.77 % Favored : 85.70 % 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: 0.69 (0.25), residues: 1175 helix: 1.54 (0.26), residues: 435 sheet: 0.83 (0.34), residues: 236 loop : -0.66 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 54 TYR 0.026 0.001 TYR B 417 PHE 0.011 0.001 PHE F 122 TRP 0.005 0.001 TRP B 531 HIS 0.005 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9338) covalent geometry : angle 0.58598 (12646) hydrogen bonds : bond 0.03570 ( 429) hydrogen bonds : angle 4.34793 ( 1245) Misc. bond : bond 0.00045 ( 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 95 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.9595 (pt) cc_final: 0.9300 (mm) REVERT: B 308 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8490 (mm) REVERT: B 470 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: B 489 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8476 (ttmm) REVERT: B 490 PHE cc_start: 0.8619 (m-80) cc_final: 0.8357 (m-80) outliers start: 15 outliers final: 10 residues processed: 92 average time/residue: 0.6507 time to fit residues: 63.5130 Evaluate side-chains 98 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 239 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 49 optimal weight: 0.0770 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.126147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.078119 restraints weight = 15275.528| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.75 r_work: 0.2728 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9339 Z= 0.127 Angle : 0.594 16.189 12646 Z= 0.292 Chirality : 0.043 0.136 1430 Planarity : 0.003 0.039 1639 Dihedral : 8.514 114.260 1393 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.43 % Allowed : 12.97 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.25), residues: 1175 helix: 1.57 (0.26), residues: 434 sheet: 0.88 (0.34), residues: 227 loop : -0.67 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 54 TYR 0.028 0.001 TYR B 417 PHE 0.011 0.001 PHE F 122 TRP 0.005 0.001 TRP B 531 HIS 0.005 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9338) covalent geometry : angle 0.59430 (12646) hydrogen bonds : bond 0.03550 ( 429) hydrogen bonds : angle 4.31376 ( 1245) Misc. bond : bond 0.00050 ( 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 101 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 182 LEU cc_start: 0.9589 (pt) cc_final: 0.9280 (mm) REVERT: B 308 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8452 (mm) REVERT: B 470 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: B 485 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8256 (tm-30) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.6784 time to fit residues: 70.4382 Evaluate side-chains 89 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 239 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 56 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 91 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.126241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.077837 restraints weight = 15175.898| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.72 r_work: 0.2732 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9339 Z= 0.138 Angle : 0.602 15.814 12646 Z= 0.298 Chirality : 0.044 0.136 1430 Planarity : 0.003 0.036 1639 Dihedral : 8.501 115.619 1393 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.53 % Allowed : 12.77 % Favored : 85.70 % 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: 0.67 (0.25), residues: 1175 helix: 1.54 (0.26), residues: 434 sheet: 0.84 (0.34), residues: 236 loop : -0.69 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 243 TYR 0.029 0.001 TYR B 417 PHE 0.017 0.001 PHE A 242 TRP 0.005 0.001 TRP B 531 HIS 0.005 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9338) covalent geometry : angle 0.60173 (12646) hydrogen bonds : bond 0.03668 ( 429) hydrogen bonds : angle 4.34192 ( 1245) Misc. bond : bond 0.00056 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4091.08 seconds wall clock time: 70 minutes 12.26 seconds (4212.26 seconds total)