Starting phenix.real_space_refine on Wed Sep 25 08:42:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcz_21618/09_2024/6wcz_21618.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcz_21618/09_2024/6wcz_21618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcz_21618/09_2024/6wcz_21618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcz_21618/09_2024/6wcz_21618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcz_21618/09_2024/6wcz_21618.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcz_21618/09_2024/6wcz_21618.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 56 5.16 5 C 6251 2.51 5 N 1776 2.21 5 O 1809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9894 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2829 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 7063 Classifications: {'peptide': 881} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 32, 'TRANS': 848} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6330 SG CYS B 448 58.566 50.765 29.088 1.00170.38 S ATOM 6352 SG CYS B 451 56.478 53.324 30.558 1.00177.22 S ATOM 9587 SG CYS B 849 21.281 71.420 51.638 1.00143.74 S Time building chain proxies: 5.87, per 1000 atoms: 0.59 Number of scatterers: 9894 At special positions: 0 Unit cell: (82.39, 105.93, 157.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 56 16.00 O 1809 8.00 N 1776 7.00 C 6251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 443 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 451 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 448 " pdb=" ZN B1002 " pdb="ZN ZN B1002 " - pdb=" NE2 HIS B 714 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 849 " 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2278 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 47.4% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 140 through 182 removed outlier: 3.669A pdb=" N GLU A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASP A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 243 removed outlier: 3.802A pdb=" N ARG A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 256 through 277 Processing helix chain 'A' and resid 294 through 314 Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.819A pdb=" N GLY A 391 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 387 through 392' Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.771A pdb=" N GLU A 426 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 427 " --> pdb=" O VAL A 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 423 through 427' Processing helix chain 'A' and resid 460 through 474 removed outlier: 4.109A pdb=" N ILE A 464 " --> pdb=" O ASN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 508 Processing helix chain 'B' and resid 8 through 10 No H-bonds generated for 'chain 'B' and resid 8 through 10' Processing helix chain 'B' and resid 11 through 19 removed outlier: 4.316A pdb=" N ASN B 17 " --> pdb=" O LYS B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 29 removed outlier: 3.792A pdb=" N PHE B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 29 " --> pdb=" O TYR B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 47 removed outlier: 4.536A pdb=" N LYS B 45 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 69 Processing helix chain 'B' and resid 85 through 93 removed outlier: 3.931A pdb=" N THR B 93 " --> pdb=" O TYR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.826A pdb=" N HIS B 134 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET B 135 " --> pdb=" O VAL B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 131 through 135' Processing helix chain 'B' and resid 153 through 172 removed outlier: 4.123A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 201 removed outlier: 4.251A pdb=" N ARG B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU B 198 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 237 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 274 through 277 Processing helix chain 'B' and resid 278 through 287 removed outlier: 3.810A pdb=" N ILE B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 removed outlier: 3.663A pdb=" N ARG B 327 " --> pdb=" O ASN B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 360 Processing helix chain 'B' and resid 368 through 390 removed outlier: 3.957A pdb=" N ARG B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 407 removed outlier: 3.908A pdb=" N SER B 406 " --> pdb=" O ASN B 402 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN B 407 " --> pdb=" O LYS B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 430 through 446 Processing helix chain 'B' and resid 479 through 491 Processing helix chain 'B' and resid 491 through 496 Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 515 through 522 removed outlier: 3.564A pdb=" N ILE B 519 " --> pdb=" O ARG B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 543 removed outlier: 3.870A pdb=" N ILE B 543 " --> pdb=" O ASP B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 549 removed outlier: 3.793A pdb=" N LEU B 548 " --> pdb=" O SER B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 558 removed outlier: 3.660A pdb=" N LEU B 553 " --> pdb=" O ASN B 550 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 554 " --> pdb=" O GLU B 551 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET B 558 " --> pdb=" O THR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 574 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 607 through 628 removed outlier: 3.617A pdb=" N LEU B 611 " --> pdb=" O VAL B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 658 removed outlier: 4.152A pdb=" N VAL B 645 " --> pdb=" O LYS B 641 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N TRP B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP B 655 " --> pdb=" O SER B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 679 removed outlier: 3.748A pdb=" N ALA B 677 " --> pdb=" O ASP B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 733 through 738 Processing helix chain 'B' and resid 750 through 767 Processing helix chain 'B' and resid 772 through 785 removed outlier: 3.584A pdb=" N LEU B 776 " --> pdb=" O ARG B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 807 removed outlier: 3.901A pdb=" N MET B 806 " --> pdb=" O GLY B 803 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR B 807 " --> pdb=" O GLU B 804 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 803 through 807' Processing helix chain 'B' and resid 810 through 820 removed outlier: 3.706A pdb=" N VAL B 814 " --> pdb=" O ASP B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 849 Processing helix chain 'B' and resid 855 through 862 Processing helix chain 'B' and resid 865 through 876 removed outlier: 3.831A pdb=" N VAL B 872 " --> pdb=" O THR B 868 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 320 removed outlier: 5.874A pdb=" N VAL A 318 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ARG A 345 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 343 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 335 Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 386 removed outlier: 6.198A pdb=" N THR A 358 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS A 436 " --> pdb=" O THR A 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 378 Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 127 removed outlier: 8.596A pdb=" N ARG B 125 " --> pdb=" O GLN B 98 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL B 100 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LYS B 127 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLY B 102 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLY B 75 " --> pdb=" O GLN B 98 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N VAL B 100 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 77 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLY B 102 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP B 79 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B 143 " --> pdb=" O CYS B 180 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LYS B 182 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N CYS B 145 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 207 " --> pdb=" O TYR B 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 305 through 310 removed outlier: 3.514A pdb=" N HIS B 307 " --> pdb=" O ILE B 594 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE B 594 " --> pdb=" O HIS B 307 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER B 309 " --> pdb=" O MET B 592 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N MET B 592 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 453 through 457 Processing sheet with id=AA8, first strand: chain 'B' and resid 660 through 661 Processing sheet with id=AA9, first strand: chain 'B' and resid 714 through 718 404 hydrogen bonds defined for protein. 1155 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: 2.89 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2401 1.33 - 1.45: 2089 1.45 - 1.57: 5527 1.57 - 1.69: 1 1.69 - 1.81: 91 Bond restraints: 10109 Sorted by residual: bond pdb=" N ARG B 42 " pdb=" CA ARG B 42 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.31e-02 5.83e+03 6.36e+00 bond pdb=" N GLY B 107 " pdb=" CA GLY B 107 " ideal model delta sigma weight residual 1.443 1.477 -0.034 1.37e-02 5.33e+03 6.21e+00 bond pdb=" N GLN A 141 " pdb=" CA GLN A 141 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.55e+00 bond pdb=" CB TRP B 498 " pdb=" CG TRP B 498 " ideal model delta sigma weight residual 1.498 1.426 0.072 3.10e-02 1.04e+03 5.47e+00 bond pdb=" CB THR B 263 " pdb=" CG2 THR B 263 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.31e+00 ... (remaining 10104 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 12370 1.90 - 3.79: 1071 3.79 - 5.69: 160 5.69 - 7.59: 37 7.59 - 9.48: 24 Bond angle restraints: 13662 Sorted by residual: angle pdb=" N VAL B 132 " pdb=" CA VAL B 132 " pdb=" CB VAL B 132 " ideal model delta sigma weight residual 112.39 105.29 7.10 1.17e+00 7.31e-01 3.68e+01 angle pdb=" C LEU A 307 " pdb=" N LEU A 308 " pdb=" CA LEU A 308 " ideal model delta sigma weight residual 121.14 113.38 7.76 1.75e+00 3.27e-01 1.97e+01 angle pdb=" CG ARG A 300 " pdb=" CD ARG A 300 " pdb=" NE ARG A 300 " ideal model delta sigma weight residual 112.00 121.48 -9.48 2.20e+00 2.07e-01 1.86e+01 angle pdb=" C ARG B 681 " pdb=" N PHE B 682 " pdb=" CA PHE B 682 " ideal model delta sigma weight residual 121.54 129.66 -8.12 1.91e+00 2.74e-01 1.81e+01 angle pdb=" N LEU A 232 " pdb=" CA LEU A 232 " pdb=" C LEU A 232 " ideal model delta sigma weight residual 109.81 118.81 -9.00 2.21e+00 2.05e-01 1.66e+01 ... (remaining 13657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 5545 16.81 - 33.63: 432 33.63 - 50.44: 87 50.44 - 67.26: 8 67.26 - 84.07: 4 Dihedral angle restraints: 6076 sinusoidal: 2539 harmonic: 3537 Sorted by residual: dihedral pdb=" CA ASN B 407 " pdb=" C ASN B 407 " pdb=" N ALA B 408 " pdb=" CA ALA B 408 " ideal model delta harmonic sigma weight residual -180.00 -135.58 -44.42 0 5.00e+00 4.00e-02 7.89e+01 dihedral pdb=" CA LYS A 375 " pdb=" C LYS A 375 " pdb=" N PHE A 376 " pdb=" CA PHE A 376 " ideal model delta harmonic sigma weight residual 180.00 144.33 35.67 0 5.00e+00 4.00e-02 5.09e+01 dihedral pdb=" CA ILE B 278 " pdb=" C ILE B 278 " pdb=" N GLY B 279 " pdb=" CA GLY B 279 " ideal model delta harmonic sigma weight residual -180.00 -145.72 -34.28 0 5.00e+00 4.00e-02 4.70e+01 ... (remaining 6073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 875 0.050 - 0.100: 427 0.100 - 0.150: 135 0.150 - 0.199: 30 0.199 - 0.249: 7 Chirality restraints: 1474 Sorted by residual: chirality pdb=" CG LEU B 435 " pdb=" CB LEU B 435 " pdb=" CD1 LEU B 435 " pdb=" CD2 LEU B 435 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB ILE A 431 " pdb=" CA ILE A 431 " pdb=" CG1 ILE A 431 " pdb=" CG2 ILE A 431 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB ILE A 363 " pdb=" CA ILE A 363 " pdb=" CG1 ILE A 363 " pdb=" CG2 ILE A 363 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1471 not shown) Planarity restraints: 1749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 107 " 0.065 5.00e-02 4.00e+02 9.85e-02 1.55e+01 pdb=" N PRO B 108 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 42 " -0.239 9.50e-02 1.11e+02 1.07e-01 7.01e+00 pdb=" NE ARG B 42 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 42 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 42 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 42 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 497 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.42e+00 pdb=" N PRO A 498 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 498 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 498 " 0.035 5.00e-02 4.00e+02 ... (remaining 1746 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 255 2.65 - 3.21: 9063 3.21 - 3.77: 16102 3.77 - 4.34: 20515 4.34 - 4.90: 31925 Nonbonded interactions: 77860 Sorted by model distance: nonbonded pdb=" OE2 GLU B 439 " pdb="ZN ZN B1001 " model vdw 2.085 2.230 nonbonded pdb=" O ARG B 41 " pdb=" NE ARG B 42 " model vdw 2.115 3.120 nonbonded pdb=" O LEU B 611 " pdb=" OG1 THR B 615 " model vdw 2.201 3.040 nonbonded pdb=" O MET B 375 " pdb=" OG SER B 379 " model vdw 2.228 3.040 nonbonded pdb=" O GLU A 259 " pdb=" OG1 THR A 263 " model vdw 2.236 3.040 ... (remaining 77855 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=0.87 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.980 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 10109 Z= 0.594 Angle : 1.216 9.485 13662 Z= 0.659 Chirality : 0.064 0.249 1474 Planarity : 0.009 0.107 1749 Dihedral : 12.526 84.069 3798 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.94 % Favored : 87.06 % Rotamer: Outliers : 2.55 % Allowed : 8.40 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.18), residues: 1221 helix: -3.20 (0.15), residues: 510 sheet: -2.21 (0.47), residues: 93 loop : -3.34 (0.21), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.005 TRP A 238 HIS 0.011 0.003 HIS A 271 PHE 0.025 0.005 PHE B 432 TYR 0.031 0.004 TYR B 882 ARG 0.015 0.002 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 1.069 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: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 389 GLU cc_start: 0.8598 (pt0) cc_final: 0.8300 (pm20) REVERT: A 459 MET cc_start: 0.8583 (mmm) cc_final: 0.8344 (mmp) REVERT: A 502 TRP cc_start: 0.6829 (m-10) cc_final: 0.6444 (m-10) REVERT: B 17 ASN cc_start: 0.8891 (t160) cc_final: 0.8652 (m-40) REVERT: B 45 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6685 (tptt) REVERT: B 101 ARG cc_start: 0.8076 (mtt180) cc_final: 0.7603 (mtm180) REVERT: B 127 LYS cc_start: 0.8884 (tttt) cc_final: 0.8608 (ttmm) REVERT: B 167 MET cc_start: 0.8698 (tpp) cc_final: 0.8265 (tpp) REVERT: B 219 MET cc_start: 0.7572 (mtp) cc_final: 0.7096 (ttm) REVERT: B 403 LYS cc_start: 0.9098 (tttt) cc_final: 0.8763 (tptp) REVERT: B 531 MET cc_start: 0.8435 (mmp) cc_final: 0.7851 (mmm) REVERT: B 581 VAL cc_start: 0.9169 (m) cc_final: 0.8967 (m) REVERT: B 643 GLU cc_start: 0.9301 (tt0) cc_final: 0.9033 (tp30) REVERT: B 647 ARG cc_start: 0.9145 (ttm110) cc_final: 0.8658 (tpt90) REVERT: B 735 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8422 (mp0) outliers start: 27 outliers final: 12 residues processed: 194 average time/residue: 0.3016 time to fit residues: 75.3332 Evaluate side-chains 116 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 739 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 62 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 0.0020 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS A 313 HIS A 461 GLN A 473 ASN A 480 GLN B 17 ASN B 228 ASN B 402 ASN B 449 HIS B 550 ASN B 576 ASN B 762 GLN B 855 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10109 Z= 0.188 Angle : 0.719 7.527 13662 Z= 0.374 Chirality : 0.043 0.171 1474 Planarity : 0.006 0.065 1749 Dihedral : 7.672 57.106 1379 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.40 % Allowed : 11.80 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.22), residues: 1221 helix: -1.24 (0.21), residues: 506 sheet: -1.74 (0.49), residues: 92 loop : -2.86 (0.22), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 476 HIS 0.013 0.001 HIS A 313 PHE 0.027 0.002 PHE A 504 TYR 0.025 0.002 TYR A 402 ARG 0.006 0.001 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 140 time to evaluate : 1.300 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ILE cc_start: 0.8613 (pt) cc_final: 0.8171 (tp) REVERT: A 232 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.6588 (tp) REVERT: A 389 GLU cc_start: 0.8402 (pt0) cc_final: 0.8128 (pm20) REVERT: A 459 MET cc_start: 0.8510 (mmm) cc_final: 0.8274 (mmp) REVERT: A 507 TYR cc_start: 0.7269 (m-10) cc_final: 0.7050 (m-10) REVERT: B 70 TYR cc_start: 0.7688 (m-10) cc_final: 0.7406 (m-10) REVERT: B 80 LEU cc_start: 0.8708 (tp) cc_final: 0.8438 (tt) REVERT: B 127 LYS cc_start: 0.8680 (tttt) cc_final: 0.8462 (ttmm) REVERT: B 161 THR cc_start: 0.9031 (m) cc_final: 0.8807 (p) REVERT: B 455 MET cc_start: 0.8573 (pmm) cc_final: 0.8115 (pmm) REVERT: B 531 MET cc_start: 0.8425 (mmp) cc_final: 0.7885 (mmt) REVERT: B 643 GLU cc_start: 0.9357 (tt0) cc_final: 0.8947 (tp30) REVERT: B 735 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8451 (mp0) outliers start: 36 outliers final: 19 residues processed: 169 average time/residue: 0.2477 time to fit residues: 57.1057 Evaluate side-chains 130 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 550 ASN Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 852 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS B 562 HIS B 598 GLN B 870 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10109 Z= 0.198 Angle : 0.679 8.277 13662 Z= 0.350 Chirality : 0.043 0.158 1474 Planarity : 0.005 0.060 1749 Dihedral : 6.691 58.063 1361 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.87 % Allowed : 13.88 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.23), residues: 1221 helix: -0.63 (0.22), residues: 511 sheet: -1.49 (0.52), residues: 92 loop : -2.73 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 848 HIS 0.003 0.001 HIS B 800 PHE 0.027 0.002 PHE A 504 TYR 0.022 0.002 TYR A 288 ARG 0.004 0.000 ARG B 563 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 121 time to evaluate : 1.213 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.8981 (mt) cc_final: 0.8741 (pp) REVERT: A 389 GLU cc_start: 0.8331 (pt0) cc_final: 0.8092 (pm20) REVERT: A 459 MET cc_start: 0.8514 (mmm) cc_final: 0.8279 (mmp) REVERT: A 502 TRP cc_start: 0.6838 (m-10) cc_final: 0.6604 (m-10) REVERT: A 507 TYR cc_start: 0.7192 (m-10) cc_final: 0.6978 (m-10) REVERT: B 19 MET cc_start: 0.6115 (mmt) cc_final: 0.5735 (ptp) REVERT: B 127 LYS cc_start: 0.8751 (tttt) cc_final: 0.8515 (ttmm) REVERT: B 344 MET cc_start: 0.5725 (mtt) cc_final: 0.5215 (ppp) REVERT: B 531 MET cc_start: 0.8436 (mmp) cc_final: 0.7877 (mmm) REVERT: B 623 ARG cc_start: 0.8941 (ttt180) cc_final: 0.8441 (ttt180) REVERT: B 643 GLU cc_start: 0.9341 (tt0) cc_final: 0.8971 (tp30) REVERT: B 735 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8452 (mp0) outliers start: 41 outliers final: 26 residues processed: 154 average time/residue: 0.2082 time to fit residues: 45.7192 Evaluate side-chains 132 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 852 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS B 732 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10109 Z= 0.169 Angle : 0.655 8.425 13662 Z= 0.331 Chirality : 0.042 0.202 1474 Planarity : 0.004 0.061 1749 Dihedral : 6.250 59.417 1361 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.68 % Allowed : 15.01 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.23), residues: 1221 helix: -0.26 (0.22), residues: 514 sheet: -1.35 (0.53), residues: 98 loop : -2.59 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 539 HIS 0.003 0.001 HIS A 313 PHE 0.027 0.002 PHE A 504 TYR 0.015 0.001 TYR A 288 ARG 0.004 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 125 time to evaluate : 1.225 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: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 389 GLU cc_start: 0.8239 (pt0) cc_final: 0.8004 (pm20) REVERT: A 459 MET cc_start: 0.8444 (mmm) cc_final: 0.8190 (mmp) REVERT: B 127 LYS cc_start: 0.8642 (tttt) cc_final: 0.8437 (ttmm) REVERT: B 218 GLU cc_start: 0.8984 (pt0) cc_final: 0.8275 (pm20) REVERT: B 344 MET cc_start: 0.5810 (mtt) cc_final: 0.5408 (ppp) REVERT: B 531 MET cc_start: 0.8472 (mmp) cc_final: 0.7926 (mmm) REVERT: B 614 PHE cc_start: 0.8453 (t80) cc_final: 0.8229 (t80) REVERT: B 643 GLU cc_start: 0.9315 (tt0) cc_final: 0.9029 (tp30) REVERT: B 735 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8467 (mp0) outliers start: 39 outliers final: 29 residues processed: 156 average time/residue: 0.2367 time to fit residues: 51.1006 Evaluate side-chains 142 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 113 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 580 LYS Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 852 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 88 optimal weight: 0.0770 chunk 49 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 106 optimal weight: 0.0670 chunk 30 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS B 562 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10109 Z= 0.160 Angle : 0.652 9.659 13662 Z= 0.325 Chirality : 0.042 0.160 1474 Planarity : 0.004 0.062 1749 Dihedral : 6.008 59.561 1361 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.68 % Allowed : 16.53 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.23), residues: 1221 helix: -0.03 (0.23), residues: 519 sheet: -1.46 (0.51), residues: 103 loop : -2.50 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 539 HIS 0.005 0.001 HIS A 313 PHE 0.027 0.002 PHE A 504 TYR 0.016 0.001 TYR A 402 ARG 0.003 0.000 ARG B 501 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 118 time to evaluate : 1.156 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: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.9064 (mt) cc_final: 0.8667 (pp) REVERT: A 365 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7505 (pmt-80) REVERT: A 389 GLU cc_start: 0.8151 (pt0) cc_final: 0.7911 (pm20) REVERT: A 459 MET cc_start: 0.8395 (mmm) cc_final: 0.8138 (mmp) REVERT: B 127 LYS cc_start: 0.8638 (tttt) cc_final: 0.8425 (ttmm) REVERT: B 344 MET cc_start: 0.5923 (mtt) cc_final: 0.5560 (ppp) REVERT: B 465 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6276 (tt0) REVERT: B 531 MET cc_start: 0.8440 (mmp) cc_final: 0.8095 (mmt) outliers start: 39 outliers final: 30 residues processed: 149 average time/residue: 0.2194 time to fit residues: 46.4480 Evaluate side-chains 134 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 471 TRP Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 852 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN A 313 HIS B 442 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10109 Z= 0.245 Angle : 0.696 9.183 13662 Z= 0.352 Chirality : 0.044 0.155 1474 Planarity : 0.005 0.070 1749 Dihedral : 6.098 57.424 1361 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 4.63 % Allowed : 17.66 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.23), residues: 1221 helix: -0.14 (0.22), residues: 530 sheet: -1.40 (0.53), residues: 97 loop : -2.45 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 539 HIS 0.007 0.001 HIS B 562 PHE 0.025 0.002 PHE A 504 TYR 0.022 0.002 TYR A 507 ARG 0.008 0.000 ARG B 675 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 100 time to evaluate : 1.194 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: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 459 MET cc_start: 0.8459 (mmm) cc_final: 0.8195 (mmp) REVERT: B 127 LYS cc_start: 0.8760 (tttt) cc_final: 0.8543 (ttmm) REVERT: B 218 GLU cc_start: 0.8872 (pt0) cc_final: 0.8384 (pm20) REVERT: B 219 MET cc_start: 0.7727 (mmm) cc_final: 0.7219 (mmm) REVERT: B 531 MET cc_start: 0.8527 (mmp) cc_final: 0.8165 (mmt) REVERT: B 592 MET cc_start: 0.8375 (mmm) cc_final: 0.8029 (tpp) REVERT: B 777 MET cc_start: 0.8230 (tpt) cc_final: 0.7986 (tpt) outliers start: 49 outliers final: 34 residues processed: 137 average time/residue: 0.2173 time to fit residues: 43.0912 Evaluate side-chains 129 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 95 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 763 MET Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 852 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10109 Z= 0.178 Angle : 0.675 10.923 13662 Z= 0.331 Chirality : 0.043 0.194 1474 Planarity : 0.004 0.061 1749 Dihedral : 5.753 53.355 1359 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.87 % Allowed : 18.04 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.24), residues: 1221 helix: 0.09 (0.23), residues: 528 sheet: -1.67 (0.49), residues: 109 loop : -2.28 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 238 HIS 0.011 0.001 HIS A 313 PHE 0.026 0.002 PHE A 504 TYR 0.016 0.001 TYR A 507 ARG 0.009 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 108 time to evaluate : 1.158 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: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 150 LEU cc_start: 0.8997 (mt) cc_final: 0.8603 (pp) REVERT: A 459 MET cc_start: 0.8387 (mmm) cc_final: 0.8116 (mmp) REVERT: B 135 MET cc_start: 0.8554 (mmm) cc_final: 0.8301 (mmm) REVERT: B 219 MET cc_start: 0.7755 (mmm) cc_final: 0.7307 (mmm) REVERT: B 344 MET cc_start: 0.5986 (mtt) cc_final: 0.5594 (ppp) REVERT: B 531 MET cc_start: 0.8483 (mmp) cc_final: 0.8162 (mmt) REVERT: B 592 MET cc_start: 0.8308 (mmm) cc_final: 0.7985 (tpp) REVERT: B 777 MET cc_start: 0.7997 (tpt) cc_final: 0.7662 (tpt) REVERT: B 826 MET cc_start: 0.8291 (tpt) cc_final: 0.7987 (tpp) outliers start: 41 outliers final: 33 residues processed: 140 average time/residue: 0.2087 time to fit residues: 42.0580 Evaluate side-chains 134 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 101 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 852 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 30.0000 chunk 22 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 93 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS B 652 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10109 Z= 0.186 Angle : 0.664 9.265 13662 Z= 0.328 Chirality : 0.043 0.151 1474 Planarity : 0.004 0.060 1749 Dihedral : 5.659 50.431 1359 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.87 % Allowed : 19.07 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.24), residues: 1221 helix: 0.11 (0.23), residues: 534 sheet: -1.68 (0.49), residues: 109 loop : -2.28 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 539 HIS 0.015 0.001 HIS A 313 PHE 0.026 0.002 PHE A 504 TYR 0.013 0.001 TYR B 90 ARG 0.009 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 102 time to evaluate : 1.252 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 150 LEU cc_start: 0.8997 (mt) cc_final: 0.8654 (pp) REVERT: A 365 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7741 (pmt-80) REVERT: A 459 MET cc_start: 0.8380 (mmm) cc_final: 0.8093 (mmp) REVERT: B 135 MET cc_start: 0.8590 (mmm) cc_final: 0.8372 (mmm) REVERT: B 219 MET cc_start: 0.7795 (mmm) cc_final: 0.7404 (mmm) REVERT: B 344 MET cc_start: 0.5964 (mtt) cc_final: 0.5591 (ppp) REVERT: B 531 MET cc_start: 0.8500 (mmp) cc_final: 0.7972 (mmm) REVERT: B 592 MET cc_start: 0.8304 (mmm) cc_final: 0.8010 (tpp) REVERT: B 777 MET cc_start: 0.7970 (tpt) cc_final: 0.7629 (tpt) outliers start: 41 outliers final: 32 residues processed: 133 average time/residue: 0.2174 time to fit residues: 41.3062 Evaluate side-chains 133 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 100 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 471 TRP Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 852 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 113 optimal weight: 0.1980 chunk 66 optimal weight: 20.0000 chunk 48 optimal weight: 0.0030 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 overall best weight: 0.8532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10109 Z= 0.165 Angle : 0.653 8.807 13662 Z= 0.320 Chirality : 0.042 0.154 1474 Planarity : 0.004 0.060 1749 Dihedral : 5.182 37.545 1355 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.68 % Allowed : 18.98 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.24), residues: 1221 helix: 0.16 (0.23), residues: 535 sheet: -1.67 (0.49), residues: 111 loop : -2.20 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 539 HIS 0.018 0.001 HIS A 313 PHE 0.027 0.002 PHE A 504 TYR 0.013 0.001 TYR B 187 ARG 0.007 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 107 time to evaluate : 1.121 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 150 LEU cc_start: 0.8979 (mt) cc_final: 0.8674 (pp) REVERT: A 298 ASP cc_start: 0.6380 (m-30) cc_final: 0.6152 (m-30) REVERT: A 365 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7753 (pmt-80) REVERT: A 459 MET cc_start: 0.8346 (mmm) cc_final: 0.8058 (mmp) REVERT: B 135 MET cc_start: 0.8573 (mmm) cc_final: 0.8350 (mmm) REVERT: B 219 MET cc_start: 0.7764 (mmm) cc_final: 0.7372 (mmm) REVERT: B 344 MET cc_start: 0.5885 (mtt) cc_final: 0.5588 (ppp) REVERT: B 531 MET cc_start: 0.8451 (mmp) cc_final: 0.7939 (mmm) REVERT: B 592 MET cc_start: 0.8380 (mmm) cc_final: 0.8114 (tpp) outliers start: 39 outliers final: 30 residues processed: 138 average time/residue: 0.2122 time to fit residues: 42.0060 Evaluate side-chains 132 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 101 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 471 TRP Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 852 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 0.0000 chunk 81 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 103 optimal weight: 0.5980 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10109 Z= 0.191 Angle : 0.681 12.431 13662 Z= 0.332 Chirality : 0.043 0.147 1474 Planarity : 0.004 0.059 1749 Dihedral : 5.181 37.532 1355 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.93 % Allowed : 20.40 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.24), residues: 1221 helix: 0.22 (0.23), residues: 533 sheet: -1.65 (0.49), residues: 111 loop : -2.19 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 238 HIS 0.003 0.001 HIS B 134 PHE 0.027 0.002 PHE A 504 TYR 0.014 0.001 TYR B 187 ARG 0.006 0.000 ARG A 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 100 time to evaluate : 1.200 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: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 150 LEU cc_start: 0.9029 (mt) cc_final: 0.8696 (pp) REVERT: A 238 TRP cc_start: 0.7964 (t-100) cc_final: 0.7711 (t-100) REVERT: A 298 ASP cc_start: 0.6369 (m-30) cc_final: 0.6136 (m-30) REVERT: A 365 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7712 (pmt-80) REVERT: A 459 MET cc_start: 0.8374 (mmm) cc_final: 0.8082 (mmp) REVERT: B 104 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8267 (m) REVERT: B 135 MET cc_start: 0.8454 (mmm) cc_final: 0.8244 (mmm) REVERT: B 219 MET cc_start: 0.7759 (mmm) cc_final: 0.7396 (mmm) REVERT: B 344 MET cc_start: 0.5985 (mtt) cc_final: 0.5619 (ppp) REVERT: B 523 MET cc_start: 0.8382 (mmm) cc_final: 0.8140 (mmt) REVERT: B 531 MET cc_start: 0.8500 (mmp) cc_final: 0.7964 (mmm) REVERT: B 558 MET cc_start: 0.6583 (tpt) cc_final: 0.6279 (tpt) REVERT: B 592 MET cc_start: 0.8265 (mmm) cc_final: 0.7936 (tpp) REVERT: B 623 ARG cc_start: 0.8895 (ttt180) cc_final: 0.8453 (ttt180) outliers start: 31 outliers final: 28 residues processed: 125 average time/residue: 0.2125 time to fit residues: 38.1946 Evaluate side-chains 127 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 97 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 471 TRP Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 852 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.082599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.067448 restraints weight = 41883.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.069740 restraints weight = 23909.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.071331 restraints weight = 15831.233| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10109 Z= 0.176 Angle : 0.675 12.350 13662 Z= 0.328 Chirality : 0.043 0.146 1474 Planarity : 0.004 0.060 1749 Dihedral : 5.100 37.699 1355 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.12 % Allowed : 20.11 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.24), residues: 1221 helix: 0.29 (0.23), residues: 533 sheet: -1.65 (0.49), residues: 112 loop : -2.13 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 238 HIS 0.003 0.001 HIS B 443 PHE 0.027 0.002 PHE A 504 TYR 0.014 0.001 TYR A 402 ARG 0.006 0.000 ARG A 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2096.13 seconds wall clock time: 38 minutes 13.41 seconds (2293.41 seconds total)