Starting phenix.real_space_refine on Thu Feb 5 16:19:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oxn_70990/02_2026/9oxn_70990_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oxn_70990/02_2026/9oxn_70990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oxn_70990/02_2026/9oxn_70990_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oxn_70990/02_2026/9oxn_70990_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oxn_70990/02_2026/9oxn_70990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oxn_70990/02_2026/9oxn_70990.map" } resolution = 3.2 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= 0.080 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 Fe 1 7.16 5 S 57 5.16 5 C 5817 2.51 5 N 1555 2.21 5 O 1677 1.98 5 H 9001 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18108 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 8854 Classifications: {'peptide': 571} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 546} Chain breaks: 6 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 9211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 9211 Classifications: {'peptide': 587} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.04, per 1000 atoms: 0.17 Number of scatterers: 18108 At special positions: 0 Unit cell: (81.012, 100.794, 148.836, 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) Fe 1 26.01 S 57 16.00 O 1677 8.00 N 1555 7.00 C 5817 6.00 H 9001 1.00 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=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 581.9 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 8 sheets defined 47.5% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 50 through 63 removed outlier: 3.704A pdb=" N LEU A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.971A pdb=" N ALA A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A 72 " --> pdb=" O CYS A 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 67 through 72' Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.619A pdb=" N ILE A 109 " --> pdb=" O TYR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 140 removed outlier: 3.643A pdb=" N LEU A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 153 through 169 removed outlier: 3.903A pdb=" N ASP A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASP A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N HIS A 169 " --> pdb=" O HIS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 222 removed outlier: 3.719A pdb=" N ALA A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.808A pdb=" N ALA A 269 " --> pdb=" O ALA A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.595A pdb=" N LEU A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 321 through 325 removed outlier: 4.290A pdb=" N TYR A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 321 through 325' Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.826A pdb=" N ARG A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 397 removed outlier: 3.582A pdb=" N ARG A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 421 removed outlier: 3.604A pdb=" N VAL A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY A 417 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 removed outlier: 3.522A pdb=" N MET A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 457 removed outlier: 3.540A pdb=" N VAL A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 448 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 457 " --> pdb=" O SER A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 469 removed outlier: 3.539A pdb=" N LYS A 465 " --> pdb=" O PRO A 461 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 498 removed outlier: 3.504A pdb=" N THR A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 512 Processing helix chain 'A' and resid 545 through 564 removed outlier: 4.015A pdb=" N ALA A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 570 removed outlier: 4.007A pdb=" N ASN A 570 " --> pdb=" O HIS A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 611 removed outlier: 3.608A pdb=" N THR A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 removed outlier: 3.798A pdb=" N TRP A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS A 629 " --> pdb=" O GLU A 625 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE A 630 " --> pdb=" O TRP A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 643 Processing helix chain 'A' and resid 676 through 681 removed outlier: 3.604A pdb=" N LYS A 681 " --> pdb=" O ARG A 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 17 removed outlier: 3.970A pdb=" N ALA B 8 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 9 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 removed outlier: 3.575A pdb=" N TRP B 22 " --> pdb=" O ASP B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 60 removed outlier: 3.937A pdb=" N THR B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 81 Processing helix chain 'B' and resid 83 through 89 Processing helix chain 'B' and resid 93 through 100 Processing helix chain 'B' and resid 100 through 112 removed outlier: 4.409A pdb=" N THR B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU B 111 " --> pdb=" O HIS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 157 removed outlier: 4.270A pdb=" N VAL B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 Processing helix chain 'B' and resid 231 through 238 Processing helix chain 'B' and resid 239 through 242 Processing helix chain 'B' and resid 247 through 250 Processing helix chain 'B' and resid 262 through 269 Processing helix chain 'B' and resid 320 through 327 removed outlier: 3.526A pdb=" N LEU B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 339 through 344 Processing helix chain 'B' and resid 351 through 366 removed outlier: 4.179A pdb=" N THR B 357 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 358 " --> pdb=" O TYR B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 379 removed outlier: 3.652A pdb=" N LEU B 376 " --> pdb=" O ARG B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 386 Processing helix chain 'B' and resid 390 through 399 removed outlier: 3.695A pdb=" N GLU B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 428 removed outlier: 3.783A pdb=" N ARG B 427 " --> pdb=" O ASN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 435 through 452 removed outlier: 3.943A pdb=" N ARG B 439 " --> pdb=" O MET B 435 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 535 through 541 removed outlier: 3.531A pdb=" N ASN B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 569 removed outlier: 3.700A pdb=" N HIS B 569 " --> pdb=" O GLU B 566 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 189 removed outlier: 4.066A pdb=" N ILE A 196 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 303 removed outlier: 6.521A pdb=" N ILE A 293 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU A 303 " --> pdb=" O HIS A 291 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N HIS A 291 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N MET A 350 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 3.519A pdb=" N ASP A 522 " --> pdb=" O CYS A 534 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N CYS A 534 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 533 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N SER A 477 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA A 585 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASP A 479 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 583 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 522 removed outlier: 3.519A pdb=" N ASP A 522 " --> pdb=" O CYS A 534 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N CYS A 534 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 533 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N SER A 477 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA A 585 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASP A 479 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 583 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS A 616 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ILE A 617 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 658 " --> pdb=" O ILE A 617 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 124 removed outlier: 3.539A pdb=" N LEU B 131 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN B 177 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 227 through 230 removed outlier: 3.588A pdb=" N VAL B 309 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 275 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 460 through 463 removed outlier: 4.442A pdb=" N MET B 471 " --> pdb=" O VAL B 463 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 412 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ARG B 407 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THR B 521 " --> pdb=" O ARG B 407 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ASP B 409 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL B 519 " --> pdb=" O ASP B 409 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 460 through 463 removed outlier: 4.442A pdb=" N MET B 471 " --> pdb=" O VAL B 463 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 412 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ARG B 407 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THR B 521 " --> pdb=" O ARG B 407 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ASP B 409 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL B 519 " --> pdb=" O ASP B 409 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N SER B 516 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE B 553 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N MET B 590 " --> pdb=" O HIS B 580 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N HIS B 580 " --> pdb=" O MET B 590 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR B 592 " --> pdb=" O ARG B 578 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1266 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: 3.48 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.22: 9001 1.22 - 1.61: 9203 1.61 - 1.99: 91 1.99 - 2.38: 4 2.38 - 2.76: 2 Bond restraints: 18301 Sorted by residual: bond pdb=" C ASN A 435 " pdb=" N SER A 436 " ideal model delta sigma weight residual 1.331 2.764 -1.434 1.43e-02 4.89e+03 1.01e+04 bond pdb=" C LYS B 366 " pdb=" N LEU B 367 " ideal model delta sigma weight residual 1.334 2.716 -1.382 1.49e-02 4.50e+03 8.60e+03 bond pdb=" CAB HEM B 701 " pdb=" CBB HEM B 701 " ideal model delta sigma weight residual 1.337 1.501 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" C2B HEM B 701 " pdb=" C3B HEM B 701 " ideal model delta sigma weight residual 1.334 1.465 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" C2A HEM B 701 " pdb=" C3A HEM B 701 " ideal model delta sigma weight residual 1.334 1.465 -0.131 2.00e-02 2.50e+03 4.27e+01 ... (remaining 18296 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.22: 33066 6.22 - 12.43: 16 12.43 - 18.65: 0 18.65 - 24.87: 2 24.87 - 31.09: 2 Bond angle restraints: 33086 Sorted by residual: angle pdb=" C ASN A 435 " pdb=" N SER A 436 " pdb=" CA SER A 436 " ideal model delta sigma weight residual 122.56 91.47 31.09 1.72e+00 3.38e-01 3.27e+02 angle pdb=" CA ASN A 435 " pdb=" C ASN A 435 " pdb=" N SER A 436 " ideal model delta sigma weight residual 117.82 94.86 22.96 1.42e+00 4.96e-01 2.62e+02 angle pdb=" CA LYS B 366 " pdb=" C LYS B 366 " pdb=" N LEU B 367 " ideal model delta sigma weight residual 117.72 98.33 19.39 1.31e+00 5.83e-01 2.19e+02 angle pdb=" C LYS B 366 " pdb=" N LEU B 367 " pdb=" CA LEU B 367 " ideal model delta sigma weight residual 121.14 96.16 24.98 1.75e+00 3.27e-01 2.04e+02 angle pdb=" O LYS B 366 " pdb=" C LYS B 366 " pdb=" N LEU B 367 " ideal model delta sigma weight residual 122.27 132.93 -10.66 1.23e+00 6.61e-01 7.52e+01 ... (remaining 33081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 7648 17.83 - 35.66: 655 35.66 - 53.49: 226 53.49 - 71.32: 65 71.32 - 89.14: 17 Dihedral angle restraints: 8611 sinusoidal: 4665 harmonic: 3946 Sorted by residual: dihedral pdb=" CA ASN B 561 " pdb=" C ASN B 561 " pdb=" N TYR B 562 " pdb=" CA TYR B 562 " ideal model delta harmonic sigma weight residual 180.00 152.76 27.24 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" C2C HEM B 701 " pdb=" C3C HEM B 701 " pdb=" CAC HEM B 701 " pdb=" CBC HEM B 701 " ideal model delta sinusoidal sigma weight residual 0.00 38.48 -38.48 2 1.00e+01 1.00e-02 1.86e+01 dihedral pdb=" C2B HEM B 701 " pdb=" C3B HEM B 701 " pdb=" CAB HEM B 701 " pdb=" CBB HEM B 701 " ideal model delta sinusoidal sigma weight residual 180.00 144.47 35.53 2 1.00e+01 1.00e-02 1.62e+01 ... (remaining 8608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 931 0.028 - 0.057: 357 0.057 - 0.085: 82 0.085 - 0.113: 68 0.113 - 0.141: 25 Chirality restraints: 1463 Sorted by residual: chirality pdb=" CA ILE A 279 " pdb=" N ILE A 279 " pdb=" C ILE A 279 " pdb=" CB ILE A 279 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA VAL A 248 " pdb=" N VAL A 248 " pdb=" C VAL A 248 " pdb=" CB VAL A 248 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE A 367 " pdb=" N ILE A 367 " pdb=" C ILE A 367 " pdb=" CB ILE A 367 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 1460 not shown) Planarity restraints: 2698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 435 " 0.037 2.00e-02 2.50e+03 1.73e-01 2.98e+02 pdb=" N SER A 436 " -0.284 2.00e-02 2.50e+03 pdb=" CA SER A 436 " 0.063 2.00e-02 2.50e+03 pdb=" H SER A 436 " 0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 435 " -0.076 2.00e-02 2.50e+03 1.51e-01 2.29e+02 pdb=" C ASN A 435 " 0.256 2.00e-02 2.50e+03 pdb=" O ASN A 435 " -0.135 2.00e-02 2.50e+03 pdb=" N SER A 436 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM B 701 " 0.017 2.00e-02 2.50e+03 9.71e-02 2.12e+02 pdb=" C2A HEM B 701 " 0.121 2.00e-02 2.50e+03 pdb=" C3A HEM B 701 " 0.105 2.00e-02 2.50e+03 pdb=" C4A HEM B 701 " 0.104 2.00e-02 2.50e+03 pdb=" CAA HEM B 701 " -0.128 2.00e-02 2.50e+03 pdb=" CHA HEM B 701 " -0.061 2.00e-02 2.50e+03 pdb=" CHB HEM B 701 " -0.162 2.00e-02 2.50e+03 pdb=" CMA HEM B 701 " -0.027 2.00e-02 2.50e+03 pdb=" NA HEM B 701 " 0.030 2.00e-02 2.50e+03 ... (remaining 2695 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 530 2.15 - 2.76: 33639 2.76 - 3.38: 48502 3.38 - 3.99: 62213 3.99 - 4.60: 96672 Nonbonded interactions: 241556 Sorted by model distance: nonbonded pdb=" OE1 GLU B 518 " pdb=" H GLU B 518 " model vdw 1.538 2.450 nonbonded pdb=" OE1 GLU B 34 " pdb=" H GLU B 34 " model vdw 1.545 2.450 nonbonded pdb="HH12 ARG B 139 " pdb=" O2A HEM B 701 " model vdw 1.599 2.450 nonbonded pdb=" O LEU A 433 " pdb=" H SER A 436 " model vdw 1.609 2.450 nonbonded pdb=" OE1 GLN B 99 " pdb="HD21 ASN B 271 " model vdw 1.635 2.450 ... (remaining 241551 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: 1.950 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: 0.110 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.590 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 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 : 0.021 1.434 9300 Z= 1.438 Angle : 0.754 31.086 12626 Z= 0.407 Chirality : 0.039 0.141 1463 Planarity : 0.008 0.151 1601 Dihedral : 16.184 88.812 3391 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.30 % Allowed : 24.47 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.00 (0.26), residues: 1136 helix: 0.24 (0.25), residues: 451 sheet: 0.75 (0.35), residues: 221 loop : -0.47 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 466 TYR 0.005 0.001 TYR A 656 PHE 0.010 0.001 PHE A 137 TRP 0.014 0.001 TRP B 593 HIS 0.012 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.02128 ( 9300) covalent geometry : angle 0.75382 (12626) hydrogen bonds : bond 0.27507 ( 416) hydrogen bonds : angle 8.17645 ( 1266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 115 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue TYR 524 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 673 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue ILE 197 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 465 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue MET 528 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 263 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8058 (tttt) cc_final: 0.7656 (mmmm) REVERT: A 54 MET cc_start: 0.8254 (tpp) cc_final: 0.7756 (mmm) REVERT: A 109 ILE cc_start: 0.8164 (mt) cc_final: 0.7954 (mp) REVERT: A 127 LYS cc_start: 0.7558 (mmtp) cc_final: 0.7275 (mmtp) REVERT: A 205 GLU cc_start: 0.7022 (tt0) cc_final: 0.6637 (tp30) REVERT: A 230 ARG cc_start: 0.6699 (tpp80) cc_final: 0.6480 (tpp80) REVERT: A 273 LYS cc_start: 0.7185 (mtpp) cc_final: 0.6753 (mmmm) REVERT: A 286 LYS cc_start: 0.8544 (ttmm) cc_final: 0.8146 (tttm) REVERT: A 297 ARG cc_start: 0.7420 (ttm110) cc_final: 0.7128 (mtm110) REVERT: A 317 THR cc_start: 0.7926 (m) cc_final: 0.7623 (p) REVERT: A 327 ARG cc_start: 0.7784 (ttp-170) cc_final: 0.7510 (ttp-170) REVERT: A 330 ARG cc_start: 0.8109 (mtt180) cc_final: 0.7672 (mtm-85) REVERT: A 397 ARG cc_start: 0.8562 (mmt180) cc_final: 0.8082 (mmt180) REVERT: A 476 LYS cc_start: 0.8178 (mttt) cc_final: 0.7429 (mtpp) REVERT: A 540 HIS cc_start: 0.7771 (p-80) cc_final: 0.7550 (p-80) REVERT: A 573 LYS cc_start: 0.8041 (mttt) cc_final: 0.7369 (mtmm) REVERT: A 594 LYS cc_start: 0.7654 (tptp) cc_final: 0.6850 (ttpp) REVERT: A 607 LYS cc_start: 0.7584 (mmtm) cc_final: 0.6937 (mmtm) REVERT: B 7 TYR cc_start: 0.8391 (t80) cc_final: 0.7994 (t80) REVERT: B 14 MET cc_start: 0.7249 (mmt) cc_final: 0.7005 (mmm) REVERT: B 15 LYS cc_start: 0.6779 (mtpp) cc_final: 0.6572 (mtpt) REVERT: B 41 GLN cc_start: 0.7835 (tt0) cc_final: 0.6449 (mm110) REVERT: B 76 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7674 (mt-10) REVERT: B 151 LYS cc_start: 0.8394 (mttt) cc_final: 0.8099 (mtpt) REVERT: B 165 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6517 (mm-30) REVERT: B 168 LYS cc_start: 0.8384 (mttp) cc_final: 0.8030 (mttt) REVERT: B 240 ARG cc_start: 0.7955 (mtp180) cc_final: 0.7570 (ttt180) REVERT: B 260 GLU cc_start: 0.7637 (pm20) cc_final: 0.7335 (tp30) REVERT: B 261 MET cc_start: 0.8418 (mmm) cc_final: 0.7991 (tpt) REVERT: B 326 ARG cc_start: 0.7492 (mtm180) cc_final: 0.7201 (mtm110) REVERT: B 342 ASP cc_start: 0.7116 (m-30) cc_final: 0.6802 (m-30) REVERT: B 359 ASN cc_start: 0.7851 (m-40) cc_final: 0.7594 (t0) REVERT: B 373 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7836 (mt-10) REVERT: B 443 ASP cc_start: 0.7754 (t70) cc_final: 0.7441 (t0) REVERT: B 583 MET cc_start: 0.7889 (mtt) cc_final: 0.7668 (mtt) REVERT: B 588 GLU cc_start: 0.7271 (tm-30) cc_final: 0.6634 (tm-30) outliers start: 3 outliers final: 2 residues processed: 264 average time/residue: 0.3010 time to fit residues: 99.9421 Evaluate side-chains 217 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 215 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 675 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.0980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS A 462 HIS B 258 HIS B 554 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.156595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.129652 restraints weight = 31236.994| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.90 r_work: 0.3125 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9300 Z= 0.140 Angle : 0.570 6.949 12626 Z= 0.298 Chirality : 0.040 0.156 1463 Planarity : 0.004 0.043 1601 Dihedral : 5.257 64.736 1260 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.94 % Allowed : 20.51 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.10 (0.25), residues: 1140 helix: 0.46 (0.23), residues: 477 sheet: 0.79 (0.35), residues: 229 loop : -0.66 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 95 TYR 0.012 0.001 TYR B 83 PHE 0.011 0.001 PHE B 70 TRP 0.004 0.001 TRP B 22 HIS 0.007 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9300) covalent geometry : angle 0.56965 (12626) hydrogen bonds : bond 0.05831 ( 416) hydrogen bonds : angle 5.45054 ( 1266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 115 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue TYR 524 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 673 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue ILE 197 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 465 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue MET 528 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 THR cc_start: 0.7792 (OUTLIER) cc_final: 0.7567 (p) REVERT: A 52 LYS cc_start: 0.7942 (tttt) cc_final: 0.7568 (mmmm) REVERT: A 54 MET cc_start: 0.8228 (tpp) cc_final: 0.7975 (mmm) REVERT: A 109 ILE cc_start: 0.8058 (mt) cc_final: 0.7815 (mm) REVERT: A 127 LYS cc_start: 0.7661 (mmtp) cc_final: 0.7391 (mmtp) REVERT: A 128 LEU cc_start: 0.7925 (tt) cc_final: 0.7705 (tp) REVERT: A 130 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.6212 (mt-10) REVERT: A 205 GLU cc_start: 0.6939 (tt0) cc_final: 0.6510 (tp30) REVERT: A 210 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7222 (tp) REVERT: A 286 LYS cc_start: 0.8547 (ttmm) cc_final: 0.8243 (tttm) REVERT: A 317 THR cc_start: 0.7970 (m) cc_final: 0.7588 (p) REVERT: A 327 ARG cc_start: 0.7974 (ttp-170) cc_final: 0.7696 (ttp80) REVERT: A 330 ARG cc_start: 0.8202 (mtt180) cc_final: 0.7756 (mtp180) REVERT: A 378 ASP cc_start: 0.7761 (t0) cc_final: 0.7520 (t70) REVERT: A 397 ARG cc_start: 0.8550 (mmt180) cc_final: 0.8222 (mmt180) REVERT: A 476 LYS cc_start: 0.8683 (mttt) cc_final: 0.8303 (mtpp) REVERT: A 515 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7459 (m-30) REVERT: A 557 MET cc_start: 0.4814 (tpt) cc_final: 0.3270 (tpp) REVERT: A 560 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8709 (t) REVERT: A 573 LYS cc_start: 0.8559 (mttt) cc_final: 0.8034 (mtmm) REVERT: A 594 LYS cc_start: 0.8454 (tptp) cc_final: 0.7827 (ttpp) REVERT: A 625 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: B 14 MET cc_start: 0.8036 (mmt) cc_final: 0.7661 (mmm) REVERT: B 26 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8609 (mtmm) REVERT: B 27 LYS cc_start: 0.8035 (tttp) cc_final: 0.7821 (tttm) REVERT: B 41 GLN cc_start: 0.8085 (tt0) cc_final: 0.6902 (mm110) REVERT: B 76 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7972 (mt-10) REVERT: B 151 LYS cc_start: 0.8678 (mttt) cc_final: 0.8471 (mtpt) REVERT: B 165 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6915 (mm-30) REVERT: B 240 ARG cc_start: 0.8246 (mtp180) cc_final: 0.8030 (ttt180) REVERT: B 260 GLU cc_start: 0.7862 (pm20) cc_final: 0.7639 (tp30) REVERT: B 261 MET cc_start: 0.8318 (mmm) cc_final: 0.7950 (tpt) REVERT: B 282 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8311 (mm-30) REVERT: B 326 ARG cc_start: 0.7732 (mtm180) cc_final: 0.7423 (mtm110) REVERT: B 358 GLN cc_start: 0.7266 (mt0) cc_final: 0.6876 (mm110) REVERT: B 359 ASN cc_start: 0.8257 (m-40) cc_final: 0.8037 (t0) REVERT: B 480 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: B 588 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6712 (tm-30) outliers start: 29 outliers final: 10 residues processed: 229 average time/residue: 0.2445 time to fit residues: 72.6512 Evaluate side-chains 221 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 675 HIS Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 588 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 75 optimal weight: 0.0020 chunk 78 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.153714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.126162 restraints weight = 31091.859| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.93 r_work: 0.3072 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9300 Z= 0.139 Angle : 0.533 6.919 12626 Z= 0.274 Chirality : 0.040 0.150 1463 Planarity : 0.004 0.043 1601 Dihedral : 5.121 64.920 1259 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.64 % Allowed : 20.20 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.25), residues: 1140 helix: 0.68 (0.24), residues: 475 sheet: 0.64 (0.34), residues: 231 loop : -0.70 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 242 TYR 0.011 0.001 TYR B 83 PHE 0.009 0.001 PHE A 485 TRP 0.006 0.001 TRP A 468 HIS 0.006 0.001 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9300) covalent geometry : angle 0.53307 (12626) hydrogen bonds : bond 0.04823 ( 416) hydrogen bonds : angle 4.83386 ( 1266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 115 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue TYR 524 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 673 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue ILE 197 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 465 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue MET 528 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.7998 (tttt) cc_final: 0.7605 (mmmm) REVERT: A 109 ILE cc_start: 0.8129 (mt) cc_final: 0.7890 (mm) REVERT: A 128 LEU cc_start: 0.8008 (tt) cc_final: 0.7780 (tp) REVERT: A 205 GLU cc_start: 0.7249 (tt0) cc_final: 0.6803 (tp30) REVERT: A 232 ARG cc_start: 0.6830 (mtm110) cc_final: 0.6627 (ttp-110) REVERT: A 286 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8242 (tttm) REVERT: A 317 THR cc_start: 0.8081 (m) cc_final: 0.7712 (p) REVERT: A 330 ARG cc_start: 0.8249 (mtt180) cc_final: 0.7760 (mtp180) REVERT: A 378 ASP cc_start: 0.7762 (t0) cc_final: 0.7501 (t70) REVERT: A 397 ARG cc_start: 0.8633 (mmt180) cc_final: 0.8254 (mmt180) REVERT: A 476 LYS cc_start: 0.8765 (mttt) cc_final: 0.8383 (mtpp) REVERT: A 515 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7207 (m-30) REVERT: A 557 MET cc_start: 0.4735 (tpt) cc_final: 0.3000 (mtp) REVERT: A 560 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8616 (t) REVERT: A 567 HIS cc_start: 0.7175 (OUTLIER) cc_final: 0.6692 (p-80) REVERT: A 573 LYS cc_start: 0.8598 (mtmt) cc_final: 0.8068 (mtmm) REVERT: A 594 LYS cc_start: 0.8433 (tptp) cc_final: 0.7741 (ttpp) REVERT: A 625 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: B 14 MET cc_start: 0.8087 (mmt) cc_final: 0.7811 (mmm) REVERT: B 72 LYS cc_start: 0.8343 (tttt) cc_final: 0.8048 (tttp) REVERT: B 76 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7977 (mt-10) REVERT: B 165 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7036 (mm-30) REVERT: B 240 ARG cc_start: 0.8312 (mtp180) cc_final: 0.8107 (ttt90) REVERT: B 253 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7545 (m-30) REVERT: B 261 MET cc_start: 0.8309 (mmm) cc_final: 0.7944 (tpt) REVERT: B 301 MET cc_start: 0.8918 (mmt) cc_final: 0.7869 (mmt) REVERT: B 326 ARG cc_start: 0.7753 (mtm180) cc_final: 0.7436 (mtm110) REVERT: B 358 GLN cc_start: 0.7350 (mt0) cc_final: 0.6900 (mm110) REVERT: B 375 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7733 (mm-30) REVERT: B 480 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: B 588 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6706 (tm-30) outliers start: 26 outliers final: 11 residues processed: 220 average time/residue: 0.2888 time to fit residues: 82.6416 Evaluate side-chains 214 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 567 HIS Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 675 HIS Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 588 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 93 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 99 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.151750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.124559 restraints weight = 31427.461| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.93 r_work: 0.3049 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9300 Z= 0.139 Angle : 0.523 6.461 12626 Z= 0.270 Chirality : 0.040 0.145 1463 Planarity : 0.004 0.051 1601 Dihedral : 5.089 63.969 1259 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.84 % Allowed : 19.80 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 1140 helix: 0.87 (0.24), residues: 476 sheet: 0.60 (0.34), residues: 236 loop : -0.77 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 95 TYR 0.007 0.001 TYR B 577 PHE 0.009 0.001 PHE A 292 TRP 0.004 0.001 TRP A 468 HIS 0.006 0.001 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9300) covalent geometry : angle 0.52288 (12626) hydrogen bonds : bond 0.04298 ( 416) hydrogen bonds : angle 4.54574 ( 1266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 115 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue TYR 524 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 673 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue ILE 197 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 465 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue MET 528 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8061 (tttt) cc_final: 0.7598 (mmmm) REVERT: A 110 TYR cc_start: 0.6693 (t80) cc_final: 0.5837 (t80) REVERT: A 128 LEU cc_start: 0.8087 (tt) cc_final: 0.7855 (tp) REVERT: A 205 GLU cc_start: 0.7182 (tt0) cc_final: 0.6918 (tt0) REVERT: A 279 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8587 (mp) REVERT: A 286 LYS cc_start: 0.8549 (ttmm) cc_final: 0.8197 (tttm) REVERT: A 330 ARG cc_start: 0.8251 (mtt180) cc_final: 0.7769 (mtp180) REVERT: A 378 ASP cc_start: 0.7681 (t0) cc_final: 0.7471 (t70) REVERT: A 476 LYS cc_start: 0.8740 (mttt) cc_final: 0.8348 (mtpp) REVERT: A 515 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7348 (m-30) REVERT: A 557 MET cc_start: 0.4729 (tpt) cc_final: 0.2881 (mtp) REVERT: A 560 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8649 (t) REVERT: A 567 HIS cc_start: 0.7204 (OUTLIER) cc_final: 0.6740 (p-80) REVERT: A 573 LYS cc_start: 0.8582 (mtmt) cc_final: 0.8037 (mtmm) REVERT: A 625 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: B 72 LYS cc_start: 0.8355 (tttt) cc_final: 0.8068 (tttp) REVERT: B 96 ASP cc_start: 0.8262 (m-30) cc_final: 0.8060 (m-30) REVERT: B 165 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7139 (mm-30) REVERT: B 261 MET cc_start: 0.8382 (mmm) cc_final: 0.8045 (tpt) REVERT: B 282 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8356 (mm-30) REVERT: B 301 MET cc_start: 0.8938 (mmt) cc_final: 0.7814 (mmt) REVERT: B 326 ARG cc_start: 0.7804 (mtm180) cc_final: 0.7509 (mtm110) REVERT: B 358 GLN cc_start: 0.7455 (mt0) cc_final: 0.6901 (mm-40) REVERT: B 480 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: B 588 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6683 (tm-30) outliers start: 28 outliers final: 16 residues processed: 211 average time/residue: 0.2685 time to fit residues: 74.1767 Evaluate side-chains 210 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 567 HIS Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 675 HIS Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 588 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 108 optimal weight: 0.9980 chunk 94 optimal weight: 0.2980 chunk 96 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.151021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.123623 restraints weight = 31268.666| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.97 r_work: 0.3041 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9300 Z= 0.134 Angle : 0.510 6.325 12626 Z= 0.262 Chirality : 0.039 0.143 1463 Planarity : 0.004 0.050 1601 Dihedral : 5.046 62.347 1259 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.64 % Allowed : 20.71 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.25), residues: 1140 helix: 1.00 (0.24), residues: 479 sheet: 0.59 (0.34), residues: 236 loop : -0.75 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.007 0.001 TYR B 577 PHE 0.009 0.001 PHE B 75 TRP 0.004 0.001 TRP A 290 HIS 0.006 0.001 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9300) covalent geometry : angle 0.50951 (12626) hydrogen bonds : bond 0.04145 ( 416) hydrogen bonds : angle 4.43134 ( 1266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 115 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue TYR 524 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 673 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue ILE 197 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 465 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue MET 528 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8046 (tttt) cc_final: 0.7605 (mmmm) REVERT: A 110 TYR cc_start: 0.6840 (t80) cc_final: 0.5913 (t80) REVERT: A 156 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7056 (mt-10) REVERT: A 205 GLU cc_start: 0.7227 (tt0) cc_final: 0.6931 (mp0) REVERT: A 220 LYS cc_start: 0.7809 (tttm) cc_final: 0.7602 (tttt) REVERT: A 232 ARG cc_start: 0.6900 (mtm110) cc_final: 0.6492 (ttp-110) REVERT: A 286 LYS cc_start: 0.8539 (ttmm) cc_final: 0.8207 (tttm) REVERT: A 330 ARG cc_start: 0.8255 (mtt180) cc_final: 0.7776 (mtp180) REVERT: A 378 ASP cc_start: 0.7709 (t0) cc_final: 0.7494 (t70) REVERT: A 476 LYS cc_start: 0.8761 (mttt) cc_final: 0.8320 (mtpp) REVERT: A 557 MET cc_start: 0.4817 (tpt) cc_final: 0.2875 (mtp) REVERT: A 560 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8641 (t) REVERT: A 573 LYS cc_start: 0.8593 (mtmt) cc_final: 0.8057 (mtmm) REVERT: A 625 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: B 72 LYS cc_start: 0.8369 (tttt) cc_final: 0.8098 (tttp) REVERT: B 96 ASP cc_start: 0.8258 (m-30) cc_final: 0.8033 (m-30) REVERT: B 165 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7140 (mm-30) REVERT: B 261 MET cc_start: 0.8395 (mmm) cc_final: 0.8055 (tpt) REVERT: B 301 MET cc_start: 0.8923 (mmt) cc_final: 0.7651 (mmt) REVERT: B 326 ARG cc_start: 0.7684 (mtm180) cc_final: 0.7376 (mtm110) REVERT: B 358 GLN cc_start: 0.7433 (mt0) cc_final: 0.6888 (mm110) REVERT: B 480 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: B 564 MET cc_start: 0.8585 (mmm) cc_final: 0.8350 (mmm) REVERT: B 588 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6747 (tm-30) outliers start: 26 outliers final: 17 residues processed: 209 average time/residue: 0.2893 time to fit residues: 77.8949 Evaluate side-chains 212 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 675 HIS Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 588 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.149300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.122340 restraints weight = 31241.070| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.97 r_work: 0.3022 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9300 Z= 0.146 Angle : 0.519 6.412 12626 Z= 0.268 Chirality : 0.040 0.141 1463 Planarity : 0.004 0.051 1601 Dihedral : 5.072 62.428 1259 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.05 % Allowed : 20.30 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.44 (0.25), residues: 1140 helix: 1.12 (0.24), residues: 473 sheet: 0.65 (0.35), residues: 216 loop : -0.72 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 95 TYR 0.007 0.001 TYR B 577 PHE 0.010 0.001 PHE A 485 TRP 0.004 0.001 TRP A 626 HIS 0.006 0.001 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9300) covalent geometry : angle 0.51864 (12626) hydrogen bonds : bond 0.04164 ( 416) hydrogen bonds : angle 4.39959 ( 1266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 115 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue TYR 524 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 673 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue ILE 197 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 465 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue MET 528 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8075 (tttt) cc_final: 0.7645 (mmmm) REVERT: A 110 TYR cc_start: 0.6991 (t80) cc_final: 0.5948 (t80) REVERT: A 156 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7206 (mt-10) REVERT: A 205 GLU cc_start: 0.7232 (tt0) cc_final: 0.6953 (mp0) REVERT: A 220 LYS cc_start: 0.7847 (tttm) cc_final: 0.7630 (tttt) REVERT: A 230 ARG cc_start: 0.6263 (tpp80) cc_final: 0.5489 (mmm160) REVERT: A 232 ARG cc_start: 0.6940 (mtm110) cc_final: 0.6576 (mtm110) REVERT: A 286 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8193 (tttm) REVERT: A 330 ARG cc_start: 0.8279 (mtt180) cc_final: 0.7784 (mtp180) REVERT: A 343 LYS cc_start: 0.8179 (mttt) cc_final: 0.7764 (mtpp) REVERT: A 378 ASP cc_start: 0.7676 (t0) cc_final: 0.7435 (t70) REVERT: A 476 LYS cc_start: 0.8770 (mttt) cc_final: 0.8336 (mtpp) REVERT: A 515 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7022 (m-30) REVERT: A 557 MET cc_start: 0.4898 (tpt) cc_final: 0.2942 (mtp) REVERT: A 560 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8685 (t) REVERT: A 573 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8289 (mtmt) REVERT: A 625 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7792 (mt-10) REVERT: B 72 LYS cc_start: 0.8376 (tttt) cc_final: 0.8112 (tttp) REVERT: B 96 ASP cc_start: 0.8343 (m-30) cc_final: 0.8106 (m-30) REVERT: B 165 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7129 (mm-30) REVERT: B 261 MET cc_start: 0.8411 (mmm) cc_final: 0.8083 (tpt) REVERT: B 301 MET cc_start: 0.8959 (mmt) cc_final: 0.7692 (mmt) REVERT: B 326 ARG cc_start: 0.7730 (mtm180) cc_final: 0.7418 (mtm110) REVERT: B 358 GLN cc_start: 0.7483 (mt0) cc_final: 0.6851 (mm-40) REVERT: B 480 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: B 564 MET cc_start: 0.8714 (mmm) cc_final: 0.8501 (mmm) REVERT: B 588 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.6794 (tm-30) outliers start: 30 outliers final: 20 residues processed: 212 average time/residue: 0.2851 time to fit residues: 77.5448 Evaluate side-chains 216 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 675 HIS Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 588 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.148667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.121654 restraints weight = 31543.408| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.97 r_work: 0.3013 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9300 Z= 0.148 Angle : 0.519 6.083 12626 Z= 0.267 Chirality : 0.040 0.141 1463 Planarity : 0.004 0.058 1601 Dihedral : 5.083 61.888 1259 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.15 % Allowed : 20.41 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.25), residues: 1140 helix: 1.12 (0.24), residues: 477 sheet: 0.67 (0.35), residues: 216 loop : -0.80 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 95 TYR 0.007 0.001 TYR B 112 PHE 0.013 0.001 PHE A 485 TRP 0.004 0.001 TRP A 290 HIS 0.006 0.001 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9300) covalent geometry : angle 0.51905 (12626) hydrogen bonds : bond 0.04157 ( 416) hydrogen bonds : angle 4.38127 ( 1266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 115 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue TYR 524 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 673 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue ILE 197 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 465 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue MET 528 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8085 (tttt) cc_final: 0.7663 (mmmm) REVERT: A 156 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7207 (mt-10) REVERT: A 205 GLU cc_start: 0.7275 (tt0) cc_final: 0.7000 (mp0) REVERT: A 220 LYS cc_start: 0.7847 (tttm) cc_final: 0.7626 (tttt) REVERT: A 230 ARG cc_start: 0.6320 (tpp80) cc_final: 0.5531 (mmm160) REVERT: A 232 ARG cc_start: 0.6859 (mtm110) cc_final: 0.6597 (mtm110) REVERT: A 286 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8177 (tttm) REVERT: A 330 ARG cc_start: 0.8231 (mtt180) cc_final: 0.7734 (mtp180) REVERT: A 343 LYS cc_start: 0.8175 (mttt) cc_final: 0.7829 (mttm) REVERT: A 378 ASP cc_start: 0.7732 (t0) cc_final: 0.7490 (t70) REVERT: A 476 LYS cc_start: 0.8791 (mttt) cc_final: 0.8404 (mtpp) REVERT: A 515 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.6903 (m-30) REVERT: A 557 MET cc_start: 0.4887 (tpt) cc_final: 0.2903 (mtp) REVERT: A 560 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8681 (t) REVERT: A 573 LYS cc_start: 0.8568 (mtmt) cc_final: 0.8269 (mtmt) REVERT: A 625 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7777 (mt-10) REVERT: B 72 LYS cc_start: 0.8396 (tttt) cc_final: 0.8136 (tttp) REVERT: B 96 ASP cc_start: 0.8388 (m-30) cc_final: 0.8149 (m-30) REVERT: B 165 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7155 (mm-30) REVERT: B 261 MET cc_start: 0.8438 (mmm) cc_final: 0.8102 (tpt) REVERT: B 301 MET cc_start: 0.8952 (mmt) cc_final: 0.7583 (mmt) REVERT: B 326 ARG cc_start: 0.7756 (mtm180) cc_final: 0.7465 (mtm110) REVERT: B 358 GLN cc_start: 0.7481 (mt0) cc_final: 0.6864 (mm110) REVERT: B 480 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: B 564 MET cc_start: 0.8717 (mmm) cc_final: 0.8510 (mmm) REVERT: B 588 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6777 (tm-30) outliers start: 31 outliers final: 22 residues processed: 212 average time/residue: 0.2888 time to fit residues: 78.5402 Evaluate side-chains 217 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 675 HIS Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 588 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 47 optimal weight: 0.9990 chunk 43 optimal weight: 0.0270 chunk 23 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.148509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.121733 restraints weight = 31382.946| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.96 r_work: 0.3019 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9300 Z= 0.139 Angle : 0.517 7.707 12626 Z= 0.266 Chirality : 0.039 0.140 1463 Planarity : 0.004 0.057 1601 Dihedral : 5.084 61.569 1259 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.05 % Allowed : 20.30 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.44 (0.25), residues: 1140 helix: 1.15 (0.24), residues: 477 sheet: 0.75 (0.36), residues: 214 loop : -0.82 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 95 TYR 0.007 0.001 TYR B 577 PHE 0.009 0.001 PHE B 75 TRP 0.004 0.001 TRP A 290 HIS 0.006 0.001 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9300) covalent geometry : angle 0.51698 (12626) hydrogen bonds : bond 0.04025 ( 416) hydrogen bonds : angle 4.34525 ( 1266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 115 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue TYR 524 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 673 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue ILE 197 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 465 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue MET 528 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8073 (tttt) cc_final: 0.7664 (mmmm) REVERT: A 156 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7184 (mt-10) REVERT: A 220 LYS cc_start: 0.7849 (tttm) cc_final: 0.7626 (tttt) REVERT: A 230 ARG cc_start: 0.6304 (tpp80) cc_final: 0.5518 (mmm160) REVERT: A 232 ARG cc_start: 0.6843 (mtm110) cc_final: 0.6550 (mtm110) REVERT: A 286 LYS cc_start: 0.8497 (ttmm) cc_final: 0.8172 (tttm) REVERT: A 330 ARG cc_start: 0.8226 (mtt180) cc_final: 0.7719 (mtp180) REVERT: A 341 ILE cc_start: 0.8031 (mt) cc_final: 0.7816 (mt) REVERT: A 343 LYS cc_start: 0.8196 (mttt) cc_final: 0.7834 (mttm) REVERT: A 378 ASP cc_start: 0.7697 (t0) cc_final: 0.7456 (t70) REVERT: A 476 LYS cc_start: 0.8796 (mttt) cc_final: 0.8400 (mtpp) REVERT: A 515 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7036 (m-30) REVERT: A 557 MET cc_start: 0.4864 (tpt) cc_final: 0.2892 (mtp) REVERT: A 560 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8669 (t) REVERT: A 573 LYS cc_start: 0.8576 (mtmt) cc_final: 0.8268 (mtmt) REVERT: A 625 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7710 (mt-10) REVERT: B 72 LYS cc_start: 0.8392 (tttt) cc_final: 0.8132 (tttp) REVERT: B 96 ASP cc_start: 0.8391 (m-30) cc_final: 0.8145 (m-30) REVERT: B 124 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7132 (mp0) REVERT: B 165 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7147 (mm-30) REVERT: B 261 MET cc_start: 0.8445 (mmm) cc_final: 0.8106 (tpt) REVERT: B 301 MET cc_start: 0.8955 (mmt) cc_final: 0.7584 (mmt) REVERT: B 326 ARG cc_start: 0.7752 (mtm180) cc_final: 0.7423 (mtm110) REVERT: B 480 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: B 588 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6769 (tm-30) outliers start: 30 outliers final: 23 residues processed: 207 average time/residue: 0.2871 time to fit residues: 76.2499 Evaluate side-chains 214 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 675 HIS Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 588 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.148887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.121938 restraints weight = 31104.318| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.89 r_work: 0.3019 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9300 Z= 0.135 Angle : 0.508 6.551 12626 Z= 0.260 Chirality : 0.039 0.140 1463 Planarity : 0.004 0.063 1601 Dihedral : 5.066 61.093 1259 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.15 % Allowed : 20.00 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.48 (0.25), residues: 1140 helix: 1.20 (0.24), residues: 478 sheet: 0.78 (0.36), residues: 214 loop : -0.84 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 95 TYR 0.007 0.001 TYR B 136 PHE 0.009 0.001 PHE B 75 TRP 0.004 0.001 TRP A 290 HIS 0.005 0.001 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9300) covalent geometry : angle 0.50752 (12626) hydrogen bonds : bond 0.03988 ( 416) hydrogen bonds : angle 4.31987 ( 1266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 115 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue TYR 524 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 673 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue ILE 197 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 465 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue MET 528 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8065 (tttt) cc_final: 0.7665 (mmmm) REVERT: A 156 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7176 (mt-10) REVERT: A 220 LYS cc_start: 0.7852 (tttm) cc_final: 0.7628 (tttt) REVERT: A 230 ARG cc_start: 0.6339 (tpp80) cc_final: 0.5518 (mmm160) REVERT: A 232 ARG cc_start: 0.6850 (mtm110) cc_final: 0.6533 (mtm110) REVERT: A 286 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8190 (tttm) REVERT: A 330 ARG cc_start: 0.8116 (mtt180) cc_final: 0.7620 (mtp180) REVERT: A 341 ILE cc_start: 0.7987 (mt) cc_final: 0.7773 (mt) REVERT: A 343 LYS cc_start: 0.8177 (mttt) cc_final: 0.7831 (mttm) REVERT: A 378 ASP cc_start: 0.7680 (t0) cc_final: 0.7442 (t70) REVERT: A 476 LYS cc_start: 0.8811 (mttt) cc_final: 0.8406 (mtpp) REVERT: A 515 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.6860 (m-30) REVERT: A 557 MET cc_start: 0.4947 (tpt) cc_final: 0.2964 (mtp) REVERT: A 560 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8682 (t) REVERT: A 573 LYS cc_start: 0.8588 (mtmt) cc_final: 0.8286 (mtmt) REVERT: A 625 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: B 72 LYS cc_start: 0.8392 (tttt) cc_final: 0.8137 (tttp) REVERT: B 96 ASP cc_start: 0.8370 (m-30) cc_final: 0.8125 (m-30) REVERT: B 165 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7139 (mm-30) REVERT: B 261 MET cc_start: 0.8476 (mmm) cc_final: 0.8131 (tpt) REVERT: B 301 MET cc_start: 0.8954 (mmt) cc_final: 0.7563 (mmt) REVERT: B 326 ARG cc_start: 0.7703 (mtm180) cc_final: 0.7378 (mtm110) REVERT: B 375 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7746 (mm-30) REVERT: B 480 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: B 588 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.6769 (tm-30) outliers start: 31 outliers final: 23 residues processed: 207 average time/residue: 0.3064 time to fit residues: 81.2935 Evaluate side-chains 213 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 675 HIS Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 588 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 106 optimal weight: 0.0970 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.149199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.122247 restraints weight = 31133.551| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.90 r_work: 0.3027 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9300 Z= 0.120 Angle : 0.505 7.909 12626 Z= 0.259 Chirality : 0.039 0.140 1463 Planarity : 0.004 0.065 1601 Dihedral : 5.035 60.746 1259 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.94 % Allowed : 20.10 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.56 (0.25), residues: 1140 helix: 1.28 (0.24), residues: 478 sheet: 0.80 (0.36), residues: 214 loop : -0.81 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 95 TYR 0.006 0.001 TYR B 136 PHE 0.009 0.001 PHE A 485 TRP 0.005 0.001 TRP A 290 HIS 0.005 0.001 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9300) covalent geometry : angle 0.50532 (12626) hydrogen bonds : bond 0.03800 ( 416) hydrogen bonds : angle 4.28137 ( 1266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 115 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue SER 191 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue TYR 524 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 673 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue ILE 197 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 465 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue MET 528 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8058 (tttt) cc_final: 0.7642 (mmmm) REVERT: A 156 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7167 (mt-10) REVERT: A 220 LYS cc_start: 0.7854 (tttm) cc_final: 0.7631 (tttt) REVERT: A 230 ARG cc_start: 0.6304 (tpp80) cc_final: 0.5495 (mmm160) REVERT: A 232 ARG cc_start: 0.6847 (mtm110) cc_final: 0.6550 (mtm110) REVERT: A 286 LYS cc_start: 0.8510 (ttmm) cc_final: 0.8181 (tttm) REVERT: A 330 ARG cc_start: 0.8111 (mtt180) cc_final: 0.7618 (mtp180) REVERT: A 341 ILE cc_start: 0.7983 (mt) cc_final: 0.7765 (mt) REVERT: A 343 LYS cc_start: 0.8170 (mttt) cc_final: 0.7817 (mttm) REVERT: A 378 ASP cc_start: 0.7655 (t0) cc_final: 0.7410 (t70) REVERT: A 476 LYS cc_start: 0.8792 (mttt) cc_final: 0.8389 (mtpp) REVERT: A 515 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.6948 (m-30) REVERT: A 557 MET cc_start: 0.4895 (tpt) cc_final: 0.2927 (mtp) REVERT: A 560 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8661 (t) REVERT: A 573 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8275 (mtmt) REVERT: A 625 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7669 (mt-10) REVERT: B 72 LYS cc_start: 0.8377 (tttt) cc_final: 0.8122 (tttp) REVERT: B 165 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7116 (mm-30) REVERT: B 301 MET cc_start: 0.8957 (mmt) cc_final: 0.7566 (mmt) REVERT: B 326 ARG cc_start: 0.7687 (mtm180) cc_final: 0.7361 (mtm110) REVERT: B 375 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7731 (mm-30) REVERT: B 480 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: B 588 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6754 (tm-30) outliers start: 29 outliers final: 23 residues processed: 205 average time/residue: 0.3128 time to fit residues: 81.7117 Evaluate side-chains 215 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 675 HIS Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 588 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 96 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 106 optimal weight: 0.0980 chunk 2 optimal weight: 0.0770 chunk 91 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 0.0060 chunk 35 optimal weight: 0.0870 chunk 11 optimal weight: 0.0470 chunk 50 optimal weight: 0.5980 overall best weight: 0.0630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.153055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.126400 restraints weight = 31177.378| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.89 r_work: 0.3089 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9300 Z= 0.086 Angle : 0.467 7.082 12626 Z= 0.235 Chirality : 0.038 0.144 1463 Planarity : 0.004 0.066 1601 Dihedral : 4.741 58.928 1259 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.42 % Allowed : 21.62 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 1140 helix: 1.52 (0.24), residues: 483 sheet: 0.90 (0.37), residues: 202 loop : -0.67 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 95 TYR 0.007 0.001 TYR B 470 PHE 0.006 0.001 PHE A 292 TRP 0.004 0.001 TRP A 290 HIS 0.005 0.001 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 9300) covalent geometry : angle 0.46728 (12626) hydrogen bonds : bond 0.02960 ( 416) hydrogen bonds : angle 4.07376 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5147.01 seconds wall clock time: 87 minutes 49.82 seconds (5269.82 seconds total)