Starting phenix.real_space_refine on Sun May 3 00:23:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uh8_64158/05_2026/9uh8_64158.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uh8_64158/05_2026/9uh8_64158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uh8_64158/05_2026/9uh8_64158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uh8_64158/05_2026/9uh8_64158.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uh8_64158/05_2026/9uh8_64158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uh8_64158/05_2026/9uh8_64158.map" } resolution = 2.98 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 6 5.49 5 Mg 1 5.21 5 S 53 5.16 5 C 5754 2.51 5 N 1605 2.21 5 O 1753 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 9172 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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {' MG': 1, 'ANP': 1, 'BCT': 1, 'BTN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 2.36, per 1000 atoms: 0.26 Number of scatterers: 9172 At special positions: 0 Unit cell: (96.9, 96.9, 136.85, 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 1753 8.00 N 1605 7.00 C 5754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 302.0 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 12 sheets defined 40.4% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 72 through 86 Processing helix chain 'A' and resid 100 through 106 removed outlier: 3.612A pdb=" N LYS A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) 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 160 removed outlier: 3.557A pdb=" N ALA A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 178 through 187 Processing helix chain 'A' and resid 201 through 213 removed outlier: 3.926A 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 358 through 364 removed outlier: 3.594A pdb=" N GLU A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 4.245A 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: 3.525A pdb=" N ASP A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 3.886A 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 305 removed outlier: 4.303A pdb=" N THR B 304 " --> pdb=" O GLU B 301 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 305 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 324 removed outlier: 3.993A 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: 3.645A pdb=" N PHE B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 407 removed outlier: 3.566A pdb=" N GLU B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 422 removed outlier: 3.595A pdb=" N HIS B 411 " --> pdb=" O GLY B 407 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 442 removed outlier: 3.762A pdb=" N ASP B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.751A 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 479 through 491 removed outlier: 3.755A pdb=" N ALA B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 499 removed outlier: 3.820A 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: 3.816A 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 36 through 48 Processing helix chain 'F' and resid 51 through 61 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 165 through 168 removed outlier: 3.703A pdb=" N GLU F 168 " --> pdb=" O ARG F 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 165 through 168' Processing helix chain 'F' and resid 169 through 186 removed outlier: 4.355A pdb=" N LEU F 173 " --> pdb=" O GLY F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 210 removed outlier: 3.729A pdb=" N ALA F 209 " --> pdb=" O VAL F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 235 removed outlier: 3.648A pdb=" N VAL F 231 " --> pdb=" O GLY F 227 " (cutoff:3.500A) 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: 8.742A pdb=" N VAL A 110 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA A 91 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 92 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 138 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 199 removed outlier: 8.801A pdb=" N PHE A 195 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N LYS A 262 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLY A 197 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ILE A 260 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU A 258 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 218 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG A 230 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 351 removed outlier: 3.850A pdb=" N GLU A 336 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET A 350 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR A 334 " --> pdb=" O MET A 350 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N HIS A 269 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU A 289 " --> pdb=" O HIS A 269 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLU A 271 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU A 287 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLN A 273 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER A 291 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL A 300 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN A 293 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS A 298 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 14.558A pdb=" N GLN A 297 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 11.024A pdb=" N TYR A 401 " --> pdb=" O GLN A 297 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 299 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP A 394 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR A 455 " --> pdb=" O TRP A 394 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL A 396 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE A 453 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS A 398 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS A 451 " --> pdb=" O CYS A 398 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 400 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 415 through 416 removed outlier: 4.152A pdb=" N GLY A 415 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 419 through 421 Processing sheet with id=AA6, first strand: chain 'A' and resid 558 through 565 removed outlier: 6.615A pdb=" N SER A 626 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG A 619 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ASN A 624 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 696 through 698 removed outlier: 7.046A pdb=" N VAL A 689 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 680 through 681 removed outlier: 3.644A pdb=" N GLY A 705 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLU A 726 " --> pdb=" O LYS A 708 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 330 through 332 removed outlier: 4.611A pdb=" N VAL B 342 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ILE B 389 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 353 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N PHE B 391 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 355 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ASP B 393 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASN B 357 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N VAL B 394 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LYS B 433 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU B 459 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ARG B 432 " --> pdb=" O GLU B 459 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ALA B 461 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ALA B 434 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 330 through 332 removed outlier: 4.611A pdb=" N VAL B 342 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ILE B 389 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 353 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N PHE B 391 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 355 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ASP B 393 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASN B 357 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N VAL B 394 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LYS B 433 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 451 " --> pdb=" O LYS B 426 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 504 " --> pdb=" O ASN B 452 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 80 through 82 removed outlier: 4.591A pdb=" N THR F 109 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N ILE F 156 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR F 120 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LEU F 158 " --> pdb=" O TYR F 120 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N PHE F 122 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL F 155 " --> pdb=" O ILE F 193 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N LEU F 195 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY F 157 " --> pdb=" O LEU F 195 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE F 213 " --> pdb=" O GLN F 192 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG F 259 " --> pdb=" O THR F 214 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 199 through 201 414 hydrogen bonds defined for protein. 1164 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: 1.65 Time building geometry restraints manager: 1.26 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: 2262 1.42 - 1.56: 5411 1.56 - 1.70: 18 1.70 - 1.84: 88 Bond restraints: 9339 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 1.435 0.389 2.00e-02 2.50e+03 3.77e+02 bond pdb=" C1' ANP A 802 " pdb=" C2' ANP A 802 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1' ANP A 802 " pdb=" O4' ANP A 802 " ideal model delta sigma weight residual 1.394 1.617 -0.223 2.00e-02 2.50e+03 1.24e+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 ... (remaining 9334 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.17: 12633 11.17 - 22.35: 8 22.35 - 33.52: 3 33.52 - 44.70: 0 44.70 - 55.87: 1 Bond angle restraints: 12645 Sorted by residual: angle pdb=" O14 1VU F5601 " pdb=" P2 1VU F5601 " pdb=" O15 1VU F5601 " ideal model delta sigma weight residual 53.72 109.59 -55.87 3.00e+00 1.11e-01 3.47e+02 angle pdb=" O8 1VU F5601 " pdb=" P1 1VU F5601 " pdb=" O9 1VU F5601 " ideal model delta sigma weight residual 140.21 108.95 31.26 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 78.74 109.09 -30.35 3.00e+00 1.11e-01 1.02e+02 angle pdb=" O10 1VU F5601 " pdb=" P1 1VU F5601 " pdb=" O7 1VU F5601 " ideal model delta sigma weight residual 85.76 110.03 -24.27 3.00e+00 1.11e-01 6.54e+01 angle pdb=" P 1VU F5601 " pdb=" O7 1VU F5601 " pdb=" P1 1VU F5601 " ideal model delta sigma weight residual 143.93 123.74 20.19 3.00e+00 1.11e-01 4.53e+01 ... (remaining 12640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 5622 35.50 - 71.00: 80 71.00 - 106.51: 6 106.51 - 142.01: 2 142.01 - 177.51: 6 Dihedral angle restraints: 5716 sinusoidal: 2333 harmonic: 3383 Sorted by residual: dihedral pdb=" CA ASP A 160 " pdb=" C ASP A 160 " pdb=" N VAL A 161 " pdb=" CA VAL A 161 " ideal model delta harmonic sigma weight residual -180.00 -153.50 -26.50 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" O1A ANP A 802 " pdb=" O3A ANP A 802 " pdb=" PA ANP A 802 " pdb=" PB ANP A 802 " ideal model delta sinusoidal sigma weight residual 83.11 -99.38 -177.51 1 3.00e+01 1.11e-03 2.13e+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 52.76 -176.64 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1407 0.120 - 0.239: 19 0.239 - 0.359: 1 0.359 - 0.479: 0 0.479 - 0.598: 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 -2.39 -0.60 2.00e-01 2.50e+01 8.94e+00 chirality pdb=" C2' ANP A 802 " pdb=" C1' ANP A 802 " pdb=" C3' ANP A 802 " pdb=" O2' ANP A 802 " both_signs ideal model delta sigma weight residual False -2.72 -2.39 -0.34 2.00e-01 2.50e+01 2.84e+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 2.48 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1425 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 537 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO B 538 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 538 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 538 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 394 " -0.010 2.00e-02 2.50e+03 9.99e-03 2.49e+00 pdb=" CG TRP A 394 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A 394 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 394 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 394 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 394 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 394 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 394 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 394 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 394 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 494 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.16e+00 pdb=" N PRO B 495 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 495 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 495 " 0.021 5.00e-02 4.00e+02 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 54 2.57 - 3.16: 7382 3.16 - 3.74: 13410 3.74 - 4.32: 18497 4.32 - 4.90: 31870 Nonbonded interactions: 71213 Sorted by model distance: nonbonded pdb=" O1G ANP A 802 " pdb="MG MG A 803 " model vdw 1.993 2.170 nonbonded pdb=" OE1 GLU A 487 " pdb=" OH TYR A 508 " model vdw 2.059 3.040 nonbonded pdb=" O2A ANP A 802 " pdb="MG MG A 803 " model vdw 2.086 2.170 nonbonded pdb=" OH TYR A 214 " pdb=" OD1 ASP A 234 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASP F 178 " pdb=" NH1 ARG F 182 " model vdw 2.279 3.120 ... (remaining 71208 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: 5.590 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.230 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:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 9340 Z= 0.590 Angle : 1.060 55.870 12645 Z= 0.435 Chirality : 0.049 0.598 1428 Planarity : 0.004 0.057 1640 Dihedral : 15.009 177.509 3540 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 0.27 (0.25), residues: 1175 helix: 0.88 (0.26), residues: 412 sheet: 1.57 (0.36), residues: 207 loop : -0.91 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 210 TYR 0.024 0.001 TYR A 473 PHE 0.009 0.001 PHE F 122 TRP 0.027 0.002 TRP A 394 HIS 0.005 0.001 HIS F 88 Details of bonding type rmsd covalent geometry : bond 0.01148 ( 9339) covalent geometry : angle 1.05990 (12645) hydrogen bonds : bond 0.17629 ( 398) hydrogen bonds : angle 5.59994 ( 1164) Misc. bond : bond 0.13148 ( 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 169 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.242 Fit side-chains REVERT: A 100 SER cc_start: 0.8382 (m) cc_final: 0.8136 (m) REVERT: A 259 LEU cc_start: 0.8175 (mm) cc_final: 0.7954 (mm) REVERT: A 448 MET cc_start: 0.8539 (ttp) cc_final: 0.8318 (ttm) REVERT: B 443 SER cc_start: 0.8948 (t) cc_final: 0.8449 (p) REVERT: B 503 ASP cc_start: 0.7777 (t70) cc_final: 0.7198 (t0) REVERT: B 504 ASP cc_start: 0.8089 (m-30) cc_final: 0.7518 (m-30) REVERT: F 243 GLU cc_start: 0.8508 (pm20) cc_final: 0.8230 (pm20) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.5979 time to fit residues: 107.6190 Evaluate side-chains 121 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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: 0.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.120466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.081975 restraints weight = 15238.653| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.93 r_work: 0.2865 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9340 Z= 0.221 Angle : 0.639 7.591 12645 Z= 0.329 Chirality : 0.048 0.173 1428 Planarity : 0.004 0.055 1640 Dihedral : 14.162 172.084 1391 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.63 % Allowed : 9.50 % Favored : 88.87 % 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: 0.39 (0.25), residues: 1175 helix: 1.08 (0.26), residues: 418 sheet: 1.28 (0.35), residues: 214 loop : -0.82 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 207 TYR 0.025 0.001 TYR A 473 PHE 0.017 0.002 PHE A 163 TRP 0.015 0.002 TRP A 394 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 9339) covalent geometry : angle 0.63887 (12645) hydrogen bonds : bond 0.05319 ( 398) hydrogen bonds : angle 4.35595 ( 1164) Misc. bond : bond 0.00032 ( 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 142 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.392 Fit side-chains REVERT: A 100 SER cc_start: 0.8450 (m) cc_final: 0.8178 (m) REVERT: A 259 LEU cc_start: 0.8428 (mm) cc_final: 0.8022 (mm) REVERT: A 650 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.7051 (mpp) REVERT: B 443 SER cc_start: 0.9132 (t) cc_final: 0.8851 (t) REVERT: B 459 GLU cc_start: 0.8302 (pp20) cc_final: 0.7932 (pp20) REVERT: B 503 ASP cc_start: 0.8287 (t70) cc_final: 0.7685 (t70) REVERT: B 504 ASP cc_start: 0.8342 (m-30) cc_final: 0.7687 (m-30) REVERT: F 259 ARG cc_start: 0.4861 (mpt180) cc_final: 0.4306 (mpt180) REVERT: F 290 GLU cc_start: 0.4726 (pp20) cc_final: 0.4476 (pp20) outliers start: 16 outliers final: 4 residues processed: 134 average time/residue: 0.6129 time to fit residues: 87.7545 Evaluate side-chains 125 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 278 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 87 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.0270 chunk 64 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 91 optimal weight: 0.0270 chunk 114 optimal weight: 0.8980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 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 = 0.3642 r_free = 0.3642 target = 0.122963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.084626 restraints weight = 15146.250| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.96 r_work: 0.2916 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9340 Z= 0.111 Angle : 0.556 9.130 12645 Z= 0.285 Chirality : 0.045 0.150 1428 Planarity : 0.004 0.050 1640 Dihedral : 12.972 176.194 1391 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.53 % Allowed : 12.56 % 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: 0.63 (0.25), residues: 1175 helix: 1.36 (0.27), residues: 418 sheet: 1.38 (0.35), residues: 212 loop : -0.72 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 207 TYR 0.012 0.001 TYR A 473 PHE 0.019 0.001 PHE A 195 TRP 0.013 0.001 TRP A 233 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9339) covalent geometry : angle 0.55623 (12645) hydrogen bonds : bond 0.03933 ( 398) hydrogen bonds : angle 4.08578 ( 1164) Misc. bond : bond 0.00006 ( 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 138 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 100 SER cc_start: 0.8422 (m) cc_final: 0.8127 (m) REVERT: A 179 GLU cc_start: 0.8286 (tp30) cc_final: 0.7864 (tp30) REVERT: A 259 LEU cc_start: 0.8475 (mm) cc_final: 0.8022 (mm) REVERT: A 693 MET cc_start: 0.9168 (mtm) cc_final: 0.8892 (mtm) REVERT: B 443 SER cc_start: 0.9103 (t) cc_final: 0.8600 (p) REVERT: B 459 GLU cc_start: 0.8285 (pp20) cc_final: 0.7733 (pp20) REVERT: B 503 ASP cc_start: 0.8317 (t70) cc_final: 0.7705 (t70) REVERT: B 504 ASP cc_start: 0.8321 (m-30) cc_final: 0.7601 (m-30) REVERT: F 242 GLU cc_start: 0.8559 (tp30) cc_final: 0.8303 (tp30) REVERT: F 259 ARG cc_start: 0.4709 (mpt180) cc_final: 0.3697 (mpt180) REVERT: F 290 GLU cc_start: 0.4597 (pp20) cc_final: 0.4282 (pp20) outliers start: 15 outliers final: 9 residues processed: 132 average time/residue: 0.5673 time to fit residues: 80.4144 Evaluate side-chains 129 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 278 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 27 optimal weight: 0.9980 chunk 109 optimal weight: 0.0030 chunk 85 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 8 optimal weight: 0.0670 chunk 89 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.6130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 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 = 0.3639 r_free = 0.3639 target = 0.122707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.084139 restraints weight = 15344.622| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.98 r_work: 0.2894 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9340 Z= 0.123 Angle : 0.546 10.126 12645 Z= 0.280 Chirality : 0.045 0.221 1428 Planarity : 0.004 0.050 1640 Dihedral : 11.926 176.133 1391 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.49 % Rotamer: Outliers : 2.04 % Allowed : 13.48 % Favored : 84.47 % 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: 0.68 (0.25), residues: 1175 helix: 1.38 (0.27), residues: 417 sheet: 1.35 (0.36), residues: 216 loop : -0.65 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 207 TYR 0.014 0.001 TYR B 417 PHE 0.022 0.001 PHE F 129 TRP 0.012 0.001 TRP A 233 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9339) covalent geometry : angle 0.54574 (12645) hydrogen bonds : bond 0.04023 ( 398) hydrogen bonds : angle 4.00591 ( 1164) Misc. bond : bond 0.00027 ( 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 139 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.356 Fit side-chains REVERT: A 100 SER cc_start: 0.8447 (m) cc_final: 0.8141 (m) REVERT: A 179 GLU cc_start: 0.8294 (tp30) cc_final: 0.7885 (tp30) REVERT: A 259 LEU cc_start: 0.8464 (mm) cc_final: 0.8006 (mm) REVERT: A 691 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7348 (OUTLIER) REVERT: B 338 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9051 (mtmt) REVERT: B 459 GLU cc_start: 0.8240 (pp20) cc_final: 0.7617 (pp20) REVERT: B 503 ASP cc_start: 0.8305 (t70) cc_final: 0.8044 (t70) REVERT: F 197 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8172 (mtp) REVERT: F 242 GLU cc_start: 0.8572 (tp30) cc_final: 0.8330 (tp30) REVERT: F 290 GLU cc_start: 0.4593 (pp20) cc_final: 0.4246 (pp20) outliers start: 20 outliers final: 12 residues processed: 131 average time/residue: 0.5824 time to fit residues: 81.6515 Evaluate side-chains 128 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 278 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 106 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 49 optimal weight: 0.0870 chunk 85 optimal weight: 10.0000 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 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 = 0.3620 r_free = 0.3620 target = 0.121581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.082450 restraints weight = 15322.517| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.00 r_work: 0.2851 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9340 Z= 0.175 Angle : 0.583 10.663 12645 Z= 0.301 Chirality : 0.046 0.201 1428 Planarity : 0.004 0.051 1640 Dihedral : 10.913 169.821 1391 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.35 % Allowed : 14.30 % Favored : 83.35 % 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: 0.64 (0.25), residues: 1175 helix: 1.38 (0.27), residues: 412 sheet: 1.29 (0.36), residues: 218 loop : -0.68 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 207 TYR 0.015 0.001 TYR B 417 PHE 0.021 0.002 PHE F 129 TRP 0.010 0.001 TRP A 233 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 9339) covalent geometry : angle 0.58284 (12645) hydrogen bonds : bond 0.04558 ( 398) hydrogen bonds : angle 4.05948 ( 1164) Misc. bond : bond 0.00052 ( 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 135 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 SER cc_start: 0.8419 (m) cc_final: 0.8112 (m) REVERT: A 179 GLU cc_start: 0.8417 (tp30) cc_final: 0.7922 (tp30) REVERT: A 259 LEU cc_start: 0.8585 (mm) cc_final: 0.8087 (mm) REVERT: B 338 LYS cc_start: 0.9378 (OUTLIER) cc_final: 0.9099 (mtmt) REVERT: B 459 GLU cc_start: 0.8315 (pp20) cc_final: 0.7621 (pp20) REVERT: B 460 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7741 (mt) REVERT: B 503 ASP cc_start: 0.8252 (t70) cc_final: 0.8019 (t70) REVERT: F 242 GLU cc_start: 0.8615 (tp30) cc_final: 0.8374 (tp30) REVERT: F 259 ARG cc_start: 0.5278 (tpt170) cc_final: 0.4707 (mpt180) REVERT: F 290 GLU cc_start: 0.4693 (pp20) cc_final: 0.4318 (pp20) outliers start: 23 outliers final: 16 residues processed: 130 average time/residue: 0.6066 time to fit residues: 84.3133 Evaluate side-chains 131 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 278 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.121529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.082997 restraints weight = 15333.302| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.98 r_work: 0.2883 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9340 Z= 0.137 Angle : 0.562 9.716 12645 Z= 0.290 Chirality : 0.045 0.179 1428 Planarity : 0.004 0.051 1640 Dihedral : 10.438 164.705 1391 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.55 % Allowed : 14.81 % Favored : 82.64 % 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: 1.45 (0.27), residues: 411 sheet: 1.33 (0.36), residues: 218 loop : -0.64 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 207 TYR 0.017 0.001 TYR B 417 PHE 0.011 0.001 PHE A 629 TRP 0.009 0.001 TRP A 233 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9339) covalent geometry : angle 0.56211 (12645) hydrogen bonds : bond 0.04048 ( 398) hydrogen bonds : angle 3.97827 ( 1164) Misc. bond : bond 0.00033 ( 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 142 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 100 SER cc_start: 0.8414 (m) cc_final: 0.8112 (m) REVERT: A 179 GLU cc_start: 0.8408 (tp30) cc_final: 0.7948 (tp30) REVERT: A 259 LEU cc_start: 0.8590 (mm) cc_final: 0.8081 (mm) REVERT: B 338 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9077 (mtmt) REVERT: B 459 GLU cc_start: 0.8339 (pp20) cc_final: 0.7556 (pp20) REVERT: B 503 ASP cc_start: 0.8269 (t70) cc_final: 0.8034 (t70) REVERT: F 87 GLU cc_start: 0.7417 (mm-30) cc_final: 0.4043 (pm20) REVERT: F 242 GLU cc_start: 0.8611 (tp30) cc_final: 0.8374 (tp30) REVERT: F 259 ARG cc_start: 0.5033 (tpt170) cc_final: 0.4221 (mpt180) REVERT: F 290 GLU cc_start: 0.4682 (pp20) cc_final: 0.4288 (pp20) outliers start: 25 outliers final: 16 residues processed: 135 average time/residue: 0.5867 time to fit residues: 84.7245 Evaluate side-chains 124 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 278 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 115 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.0570 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 71 optimal weight: 0.0010 chunk 25 optimal weight: 0.9980 overall best weight: 0.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.123341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.085109 restraints weight = 15338.236| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.96 r_work: 0.2923 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9340 Z= 0.104 Angle : 0.561 13.376 12645 Z= 0.285 Chirality : 0.044 0.197 1428 Planarity : 0.003 0.051 1640 Dihedral : 10.120 159.279 1391 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.35 % Allowed : 15.63 % Favored : 82.02 % 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: 0.81 (0.25), residues: 1175 helix: 1.55 (0.27), residues: 411 sheet: 1.52 (0.37), residues: 210 loop : -0.64 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 210 TYR 0.019 0.001 TYR B 417 PHE 0.028 0.001 PHE F 129 TRP 0.010 0.001 TRP A 233 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 9339) covalent geometry : angle 0.56097 (12645) hydrogen bonds : bond 0.03357 ( 398) hydrogen bonds : angle 3.90430 ( 1164) Misc. bond : bond 0.00013 ( 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 139 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 100 SER cc_start: 0.8427 (m) cc_final: 0.8111 (m) REVERT: A 179 GLU cc_start: 0.8391 (tp30) cc_final: 0.7905 (tp30) REVERT: A 259 LEU cc_start: 0.8510 (mm) cc_final: 0.8005 (mm) REVERT: B 338 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9037 (mtmt) REVERT: B 459 GLU cc_start: 0.8290 (pp20) cc_final: 0.7559 (pp20) REVERT: F 83 ASP cc_start: 0.8252 (t0) cc_final: 0.7653 (t0) REVERT: F 87 GLU cc_start: 0.7452 (mm-30) cc_final: 0.4370 (pm20) REVERT: F 242 GLU cc_start: 0.8613 (tp30) cc_final: 0.8371 (tp30) REVERT: F 259 ARG cc_start: 0.5247 (tpt170) cc_final: 0.4522 (mpt180) REVERT: F 290 GLU cc_start: 0.4612 (pp20) cc_final: 0.4328 (pp20) outliers start: 23 outliers final: 13 residues processed: 132 average time/residue: 0.6107 time to fit residues: 86.1170 Evaluate side-chains 126 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 278 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 83 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 0.0470 chunk 114 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.122366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.084118 restraints weight = 15306.735| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.97 r_work: 0.2904 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9340 Z= 0.126 Angle : 0.588 11.673 12645 Z= 0.302 Chirality : 0.045 0.223 1428 Planarity : 0.004 0.052 1640 Dihedral : 10.271 159.242 1391 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.04 % Allowed : 17.26 % Favored : 80.69 % 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: 0.81 (0.25), residues: 1175 helix: 1.55 (0.27), residues: 410 sheet: 1.48 (0.36), residues: 212 loop : -0.62 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 207 TYR 0.007 0.001 TYR F 206 PHE 0.023 0.001 PHE A 263 TRP 0.008 0.001 TRP A 233 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9339) covalent geometry : angle 0.58797 (12645) hydrogen bonds : bond 0.03730 ( 398) hydrogen bonds : angle 3.91619 ( 1164) Misc. bond : bond 0.00026 ( 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 133 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 100 SER cc_start: 0.8415 (m) cc_final: 0.8105 (m) REVERT: A 179 GLU cc_start: 0.8416 (tp30) cc_final: 0.7950 (tp30) REVERT: A 259 LEU cc_start: 0.8498 (mm) cc_final: 0.7984 (mm) REVERT: A 555 ASP cc_start: 0.8774 (m-30) cc_final: 0.8502 (t0) REVERT: B 338 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.9036 (mtmt) REVERT: B 459 GLU cc_start: 0.8307 (pp20) cc_final: 0.7510 (pp20) REVERT: F 83 ASP cc_start: 0.8255 (t0) cc_final: 0.7707 (t0) REVERT: F 242 GLU cc_start: 0.8629 (tp30) cc_final: 0.8385 (tp30) REVERT: F 259 ARG cc_start: 0.4973 (tpt170) cc_final: 0.4629 (mpt180) REVERT: F 290 GLU cc_start: 0.4552 (pp20) cc_final: 0.4254 (pp20) outliers start: 20 outliers final: 15 residues processed: 128 average time/residue: 0.5709 time to fit residues: 78.4653 Evaluate side-chains 123 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 278 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 71 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 33 optimal weight: 0.3980 chunk 50 optimal weight: 0.0010 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 73 optimal weight: 0.0050 chunk 76 optimal weight: 0.8980 overall best weight: 0.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.123620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.085645 restraints weight = 15301.771| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.94 r_work: 0.2917 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9340 Z= 0.109 Angle : 0.588 11.611 12645 Z= 0.300 Chirality : 0.044 0.231 1428 Planarity : 0.004 0.051 1640 Dihedral : 10.161 157.446 1391 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.84 % Allowed : 17.26 % Favored : 80.90 % 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: 0.85 (0.25), residues: 1175 helix: 1.60 (0.27), residues: 410 sheet: 1.46 (0.36), residues: 214 loop : -0.60 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG A 207 TYR 0.024 0.001 TYR B 417 PHE 0.026 0.001 PHE F 129 TRP 0.011 0.001 TRP A 233 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9339) covalent geometry : angle 0.58822 (12645) hydrogen bonds : bond 0.03315 ( 398) hydrogen bonds : angle 3.88741 ( 1164) Misc. bond : bond 0.00011 ( 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 130 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 SER cc_start: 0.8395 (m) cc_final: 0.8080 (m) REVERT: A 179 GLU cc_start: 0.8412 (tp30) cc_final: 0.7935 (tp30) REVERT: A 259 LEU cc_start: 0.8468 (mm) cc_final: 0.7954 (mm) REVERT: A 555 ASP cc_start: 0.8782 (m-30) cc_final: 0.8514 (t0) REVERT: B 338 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8993 (mtmt) REVERT: B 459 GLU cc_start: 0.8288 (pp20) cc_final: 0.7496 (pp20) REVERT: F 83 ASP cc_start: 0.8244 (t0) cc_final: 0.7710 (t0) REVERT: F 87 GLU cc_start: 0.7576 (mm-30) cc_final: 0.4287 (pm20) REVERT: F 232 LYS cc_start: 0.8462 (tppt) cc_final: 0.8031 (mmpt) REVERT: F 242 GLU cc_start: 0.8661 (tp30) cc_final: 0.8414 (tp30) REVERT: F 259 ARG cc_start: 0.4955 (tpt170) cc_final: 0.4428 (mpt180) REVERT: F 290 GLU cc_start: 0.4488 (pp20) cc_final: 0.4262 (pp20) outliers start: 18 outliers final: 14 residues processed: 124 average time/residue: 0.5832 time to fit residues: 77.3563 Evaluate side-chains 125 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 92 optimal weight: 0.0770 chunk 88 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 0.0170 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.121895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.083628 restraints weight = 15342.237| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.95 r_work: 0.2896 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9340 Z= 0.142 Angle : 0.605 11.268 12645 Z= 0.311 Chirality : 0.045 0.237 1428 Planarity : 0.004 0.052 1640 Dihedral : 10.151 156.269 1391 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.74 % Allowed : 17.67 % Favored : 80.59 % 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: 0.82 (0.25), residues: 1175 helix: 1.56 (0.27), residues: 411 sheet: 1.50 (0.36), residues: 212 loop : -0.63 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 207 TYR 0.015 0.001 TYR B 417 PHE 0.013 0.001 PHE A 263 TRP 0.014 0.001 TRP A 233 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9339) covalent geometry : angle 0.60516 (12645) hydrogen bonds : bond 0.03958 ( 398) hydrogen bonds : angle 3.93713 ( 1164) Misc. bond : bond 0.00029 ( 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 128 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 SER cc_start: 0.8420 (m) cc_final: 0.8110 (m) REVERT: A 179 GLU cc_start: 0.8417 (tp30) cc_final: 0.7951 (tp30) REVERT: A 259 LEU cc_start: 0.8550 (mm) cc_final: 0.8020 (mm) REVERT: A 555 ASP cc_start: 0.8787 (m-30) cc_final: 0.8502 (t0) REVERT: B 338 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.9046 (mtmt) REVERT: B 459 GLU cc_start: 0.8279 (pp20) cc_final: 0.7427 (pp20) REVERT: F 83 ASP cc_start: 0.8287 (t0) cc_final: 0.7812 (t0) REVERT: F 242 GLU cc_start: 0.8658 (tp30) cc_final: 0.8425 (tp30) REVERT: F 259 ARG cc_start: 0.4904 (tpt170) cc_final: 0.4409 (mpt180) REVERT: F 290 GLU cc_start: 0.4540 (pp20) cc_final: 0.4228 (pp20) outliers start: 17 outliers final: 14 residues processed: 124 average time/residue: 0.5966 time to fit residues: 79.1840 Evaluate side-chains 124 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 62 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.0060 chunk 110 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 54 optimal weight: 0.0270 overall best weight: 0.5454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.122510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.084629 restraints weight = 15163.159| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.92 r_work: 0.2913 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9340 Z= 0.121 Angle : 0.586 11.218 12645 Z= 0.302 Chirality : 0.045 0.276 1428 Planarity : 0.004 0.052 1640 Dihedral : 10.042 154.137 1391 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.84 % Allowed : 17.67 % Favored : 80.49 % 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: 0.87 (0.25), residues: 1175 helix: 1.61 (0.27), residues: 410 sheet: 1.66 (0.37), residues: 208 loop : -0.66 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 207 TYR 0.017 0.001 TYR B 417 PHE 0.024 0.001 PHE F 129 TRP 0.015 0.001 TRP A 233 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9339) covalent geometry : angle 0.58622 (12645) hydrogen bonds : bond 0.03627 ( 398) hydrogen bonds : angle 3.90497 ( 1164) Misc. bond : bond 0.00021 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3022.15 seconds wall clock time: 52 minutes 16.69 seconds (3136.69 seconds total)