Starting phenix.real_space_refine on Sun Aug 4 08:33:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9a_37362/08_2024/8w9a_37362_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9a_37362/08_2024/8w9a_37362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9a_37362/08_2024/8w9a_37362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9a_37362/08_2024/8w9a_37362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9a_37362/08_2024/8w9a_37362_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9a_37362/08_2024/8w9a_37362_trim.cif" } resolution = 2.7 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= 0.009 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 S 72 5.16 5 Cl 1 4.86 5 C 6548 2.51 5 N 1778 2.21 5 O 1890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 951": "NH1" <-> "NH2" Residue "A ARG 1047": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10289 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 969, 7922 Classifications: {'peptide': 969} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 923} Chain breaks: 5 Chain: "B" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2330 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 271} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'UEX': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 6.19, per 1000 atoms: 0.60 Number of scatterers: 10289 At special positions: 0 Unit cell: (88.06, 125.06, 117.66, 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) Cl 1 17.00 S 72 16.00 O 1890 8.00 N 1778 7.00 C 6548 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 - 3.50 Amino acid : False - 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: 4.07 Conformation dependent library (CDL) restraints added in 1.8 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 9 sheets defined 48.5% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 41 through 53 removed outlier: 3.626A pdb=" N PHE A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS A 51 " --> pdb=" O HIS A 47 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 122 removed outlier: 3.672A pdb=" N LEU A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 4.017A pdb=" N ASP A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 130 " --> pdb=" O CYS A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 125 through 130' Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.711A pdb=" N ARG A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 152 removed outlier: 3.541A pdb=" N VAL A 151 " --> pdb=" O CYS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 216 through 229 removed outlier: 3.540A pdb=" N ALA A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A 223 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 278 removed outlier: 4.003A pdb=" N MET A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.994A pdb=" N ARG A 309 " --> pdb=" O PRO A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 488 through 497 removed outlier: 3.578A pdb=" N ASN A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 536 removed outlier: 3.943A pdb=" N LEU A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 557 through 563 Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 564 through 570 removed outlier: 3.835A pdb=" N LEU A 570 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 588 removed outlier: 3.541A pdb=" N GLN A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 600 through 603 removed outlier: 3.534A pdb=" N ASP A 603 " --> pdb=" O GLU A 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 600 through 603' Processing helix chain 'A' and resid 608 through 623 removed outlier: 3.583A pdb=" N PHE A 614 " --> pdb=" O MET A 610 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 639 through 641 No H-bonds generated for 'chain 'A' and resid 639 through 641' Processing helix chain 'A' and resid 647 through 658 Processing helix chain 'A' and resid 660 through 673 removed outlier: 3.775A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 693 Processing helix chain 'A' and resid 697 through 722 removed outlier: 4.340A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 718 " --> pdb=" O ASN A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 removed outlier: 3.633A pdb=" N VAL A 736 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 748 Processing helix chain 'A' and resid 807 through 826 removed outlier: 3.578A pdb=" N ARG A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN A 822 " --> pdb=" O ARG A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 864 Processing helix chain 'A' and resid 875 through 884 Processing helix chain 'A' and resid 886 through 888 No H-bonds generated for 'chain 'A' and resid 886 through 888' Processing helix chain 'A' and resid 889 through 911 removed outlier: 3.600A pdb=" N ALA A 893 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY A 903 " --> pdb=" O ARG A 899 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 909 " --> pdb=" O CYS A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 965 removed outlier: 3.591A pdb=" N ILE A 962 " --> pdb=" O GLN A 958 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 973 removed outlier: 3.849A pdb=" N LYS A 973 " --> pdb=" O GLU A 970 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 970 through 973' Processing helix chain 'A' and resid 974 through 992 removed outlier: 3.531A pdb=" N ILE A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.776A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A1002 " --> pdb=" O PHE A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1026 removed outlier: 3.961A pdb=" N ARG A1023 " --> pdb=" O ILE A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1045 removed outlier: 3.640A pdb=" N LEU A1036 " --> pdb=" O GLU A1032 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A1037 " --> pdb=" O GLN A1033 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A1045 " --> pdb=" O LYS A1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 344 Processing helix chain 'B' and resid 400 through 409 removed outlier: 3.549A pdb=" N TYR B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'B' and resid 417 through 421 removed outlier: 3.852A pdb=" N ASP B 421 " --> pdb=" O PRO B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 437 removed outlier: 3.682A pdb=" N VAL B 437 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 504 removed outlier: 3.805A pdb=" N VAL B 445 " --> pdb=" O ASN B 441 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR B 452 " --> pdb=" O LYS B 448 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 457 " --> pdb=" O ASN B 453 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG B 465 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 471 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 496 " --> pdb=" O LYS B 492 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 500 " --> pdb=" O GLU B 496 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 502 " --> pdb=" O CYS B 498 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG B 503 " --> pdb=" O GLN B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 524 removed outlier: 4.248A pdb=" N GLN B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 553 removed outlier: 3.525A pdb=" N GLU B 537 " --> pdb=" O SER B 533 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 541 " --> pdb=" O GLU B 537 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 544 " --> pdb=" O ASP B 540 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP B 548 " --> pdb=" O ARG B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 582 removed outlier: 3.642A pdb=" N ASP B 560 " --> pdb=" O TYR B 556 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Proline residue: B 568 - end of helix removed outlier: 3.543A pdb=" N ILE B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN B 572 " --> pdb=" O PRO B 568 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 573 " --> pdb=" O ASP B 569 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 574 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR B 580 " --> pdb=" O THR B 576 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 581 " --> pdb=" O ARG B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 598 removed outlier: 3.711A pdb=" N LEU B 598 " --> pdb=" O LEU B 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 36 removed outlier: 7.815A pdb=" N LEU A 99 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU A 23 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL A 101 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 25 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N PHE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL A 73 " --> pdb=" O PHE A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 204 through 212 removed outlier: 5.832A pdb=" N ILE A 197 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ALA A 289 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU A 252 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.558A pdb=" N LYS A 325 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 392 removed outlier: 7.000A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE A 338 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLU A 476 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS A 340 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.910A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 372 removed outlier: 6.601A pdb=" N LEU A 402 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN A 426 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU A 404 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TRP A 424 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 406 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 770 through 771 removed outlier: 6.819A pdb=" N VAL A 845 " --> pdb=" O ILE A 841 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 854 through 856 Processing sheet with id=AA9, first strand: chain 'B' and resid 377 through 381 removed outlier: 4.132A pdb=" N THR B 354 " --> pdb=" O ARG B 373 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1182 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: 3.15 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1725 1.30 - 1.43: 2679 1.43 - 1.56: 5984 1.56 - 1.69: 1 1.69 - 1.82: 113 Bond restraints: 10502 Sorted by residual: bond pdb=" C25 UEX A1101 " pdb=" N35 UEX A1101 " ideal model delta sigma weight residual 1.291 1.455 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" C15 UEX A1101 " pdb=" N35 UEX A1101 " ideal model delta sigma weight residual 1.364 1.479 -0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" C04 UEX A1101 " pdb=" N03 UEX A1101 " ideal model delta sigma weight residual 1.359 1.456 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C25 UEX A1101 " pdb=" N26 UEX A1101 " ideal model delta sigma weight residual 1.367 1.449 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C25 UEX A1101 " pdb=" N23 UEX A1101 " ideal model delta sigma weight residual 1.379 1.452 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 10497 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.74: 199 105.74 - 113.00: 5532 113.00 - 120.26: 4242 120.26 - 127.52: 4090 127.52 - 134.78: 104 Bond angle restraints: 14167 Sorted by residual: angle pdb=" N ILE B 509 " pdb=" CA ILE B 509 " pdb=" C ILE B 509 " ideal model delta sigma weight residual 113.71 108.94 4.77 9.50e-01 1.11e+00 2.52e+01 angle pdb=" C25 UEX A1101 " pdb=" N26 UEX A1101 " pdb=" C27 UEX A1101 " ideal model delta sigma weight residual 121.93 132.20 -10.27 3.00e+00 1.11e-01 1.17e+01 angle pdb=" C ARG B 386 " pdb=" N ASP B 387 " pdb=" CA ASP B 387 " ideal model delta sigma weight residual 121.54 127.95 -6.41 1.91e+00 2.74e-01 1.13e+01 angle pdb=" N23 UEX A1101 " pdb=" C25 UEX A1101 " pdb=" N26 UEX A1101 " ideal model delta sigma weight residual 118.03 127.92 -9.89 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CA TYR A 392 " pdb=" CB TYR A 392 " pdb=" CG TYR A 392 " ideal model delta sigma weight residual 113.90 119.11 -5.21 1.80e+00 3.09e-01 8.37e+00 ... (remaining 14162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.59: 6090 15.59 - 31.18: 271 31.18 - 46.77: 55 46.77 - 62.35: 3 62.35 - 77.94: 10 Dihedral angle restraints: 6429 sinusoidal: 2754 harmonic: 3675 Sorted by residual: dihedral pdb=" CA ARG A1047 " pdb=" C ARG A1047 " pdb=" N HIS A1048 " pdb=" CA HIS A1048 " ideal model delta harmonic sigma weight residual -180.00 -153.04 -26.96 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA LYS B 506 " pdb=" C LYS B 506 " pdb=" N GLU B 507 " pdb=" CA GLU B 507 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA TRP B 597 " pdb=" C TRP B 597 " pdb=" N LEU B 598 " pdb=" CA LEU B 598 " ideal model delta harmonic sigma weight residual -180.00 -159.04 -20.96 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 6426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1174 0.062 - 0.123: 327 0.123 - 0.185: 28 0.185 - 0.246: 1 0.246 - 0.308: 1 Chirality restraints: 1531 Sorted by residual: chirality pdb=" CG LEU A 456 " pdb=" CB LEU A 456 " pdb=" CD1 LEU A 456 " pdb=" CD2 LEU A 456 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA ASP A 258 " pdb=" N ASP A 258 " pdb=" C ASP A 258 " pdb=" CB ASP A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CB ILE A 391 " pdb=" CA ILE A 391 " pdb=" CG1 ILE A 391 " pdb=" CG2 ILE A 391 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 1528 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 759 " -0.014 2.00e-02 2.50e+03 1.86e-02 5.20e+00 pdb=" CG HIS A 759 " 0.039 2.00e-02 2.50e+03 pdb=" ND1 HIS A 759 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS A 759 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 HIS A 759 " 0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS A 759 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 780 " -0.007 2.00e-02 2.50e+03 1.35e-02 4.58e+00 pdb=" CG TRP A 780 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 780 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 780 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 780 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 780 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 780 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 780 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 780 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 780 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 174 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO A 175 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " 0.028 5.00e-02 4.00e+02 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 302 2.70 - 3.25: 9967 3.25 - 3.80: 14712 3.80 - 4.35: 21567 4.35 - 4.90: 34523 Nonbonded interactions: 81071 Sorted by model distance: nonbonded pdb=" OG1 THR A 358 " pdb=" OH TYR A 389 " model vdw 2.156 3.040 nonbonded pdb=" N ARG A 19 " pdb=" O CYS A 36 " model vdw 2.170 3.120 nonbonded pdb=" OE1 GLU A 768 " pdb=" ND2 ASN A 782 " model vdw 2.212 3.120 nonbonded pdb=" O SER A 66 " pdb=" OG SER A 67 " model vdw 2.228 3.040 nonbonded pdb=" NZ LYS A 733 " pdb=" OE2 GLU A 737 " model vdw 2.229 3.120 ... (remaining 81066 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.100 Find NCS groups from input model: 0.090 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:10.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 43.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.008 0.164 10502 Z= 0.506 Angle : 0.803 10.272 14167 Z= 0.429 Chirality : 0.053 0.308 1531 Planarity : 0.006 0.051 1818 Dihedral : 10.206 77.942 4043 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.18 % Allowed : 1.31 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -4.40 (0.20), residues: 1231 helix: -3.79 (0.14), residues: 563 sheet: -1.75 (0.35), residues: 166 loop : -1.98 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP A 780 HIS 0.023 0.003 HIS A 759 PHE 0.023 0.004 PHE A 937 TYR 0.032 0.004 TYR B 426 ARG 0.012 0.001 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 240 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 ASP cc_start: 0.7485 (m-30) cc_final: 0.7239 (m-30) REVERT: B 364 MET cc_start: 0.5882 (tmm) cc_final: 0.3614 (mtp) REVERT: B 367 ASP cc_start: 0.5420 (m-30) cc_final: 0.4975 (m-30) REVERT: B 420 LEU cc_start: 0.8383 (tp) cc_final: 0.8122 (tp) REVERT: B 465 ARG cc_start: 0.6916 (ttp80) cc_final: 0.6703 (ttm-80) REVERT: B 478 GLN cc_start: 0.7819 (tp-100) cc_final: 0.7435 (tp-100) REVERT: B 528 TYR cc_start: 0.8020 (t80) cc_final: 0.7747 (t80) outliers start: 2 outliers final: 0 residues processed: 242 average time/residue: 1.4083 time to fit residues: 362.2697 Evaluate side-chains 169 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 157 ASN A 213 HIS A 370 ASN A 380 ASN A 384 ASN A 419 HIS A 630 GLN A 738 GLN A 795 GLN A 917 HIS ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS B 499 GLN ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 0.040 10502 Z= 0.209 Angle : 0.650 9.743 14167 Z= 0.337 Chirality : 0.045 0.182 1531 Planarity : 0.005 0.050 1818 Dihedral : 5.287 21.992 1381 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.23 % Allowed : 8.41 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.30 (0.22), residues: 1231 helix: -1.60 (0.20), residues: 555 sheet: -1.00 (0.38), residues: 160 loop : -1.41 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 780 HIS 0.008 0.001 HIS A 759 PHE 0.020 0.002 PHE A 744 TYR 0.026 0.002 TYR A 392 ARG 0.005 0.001 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 176 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7626 (m-30) REVERT: A 227 LYS cc_start: 0.7680 (ttmt) cc_final: 0.7238 (tttt) REVERT: A 454 ASP cc_start: 0.7434 (m-30) cc_final: 0.7193 (m-30) REVERT: A 528 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7022 (mtmt) REVERT: A 883 ASP cc_start: 0.6502 (m-30) cc_final: 0.6155 (m-30) REVERT: A 1044 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.7488 (t0) REVERT: B 326 MET cc_start: 0.6599 (mpp) cc_final: 0.6364 (ptp) REVERT: B 342 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6538 (tm-30) REVERT: B 364 MET cc_start: 0.5833 (tmm) cc_final: 0.3677 (mtp) REVERT: B 367 ASP cc_start: 0.5244 (m-30) cc_final: 0.4776 (m-30) REVERT: B 420 LEU cc_start: 0.8332 (tp) cc_final: 0.8030 (tp) REVERT: B 492 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8327 (ttmm) REVERT: B 537 GLU cc_start: 0.6464 (tt0) cc_final: 0.6243 (tt0) outliers start: 14 outliers final: 2 residues processed: 185 average time/residue: 1.3397 time to fit residues: 265.2816 Evaluate side-chains 152 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 213 HIS A1048 HIS B 417 ASN B 527 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10502 Z= 0.286 Angle : 0.654 9.731 14167 Z= 0.337 Chirality : 0.047 0.176 1531 Planarity : 0.005 0.046 1818 Dihedral : 5.123 20.754 1381 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.98 % Allowed : 8.93 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 (0.23), residues: 1231 helix: -0.70 (0.21), residues: 566 sheet: -0.69 (0.38), residues: 160 loop : -1.26 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 597 HIS 0.009 0.002 HIS A 759 PHE 0.022 0.002 PHE A 667 TYR 0.023 0.002 TYR A 392 ARG 0.006 0.001 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 155 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7659 (m-30) REVERT: A 162 ARG cc_start: 0.7654 (mtm-85) cc_final: 0.7368 (mtm-85) REVERT: A 186 ASP cc_start: 0.7884 (p0) cc_final: 0.7613 (p0) REVERT: A 227 LYS cc_start: 0.7786 (ttmt) cc_final: 0.7425 (tttt) REVERT: A 454 ASP cc_start: 0.7498 (m-30) cc_final: 0.7252 (m-30) REVERT: A 883 ASP cc_start: 0.6549 (m-30) cc_final: 0.6253 (m-30) REVERT: B 342 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6518 (tm-30) REVERT: B 364 MET cc_start: 0.5753 (tmm) cc_final: 0.3560 (mtp) REVERT: B 367 ASP cc_start: 0.5531 (m-30) cc_final: 0.5015 (m-30) REVERT: B 469 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6671 (tt0) REVERT: B 478 GLN cc_start: 0.7708 (tp-100) cc_final: 0.7456 (tm-30) REVERT: B 492 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8248 (ttmm) REVERT: B 537 GLU cc_start: 0.6433 (tt0) cc_final: 0.6217 (tt0) outliers start: 34 outliers final: 11 residues processed: 176 average time/residue: 1.2821 time to fit residues: 241.9871 Evaluate side-chains 164 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 525 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 chunk 99 optimal weight: 5.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 384 ASN A 796 ASN A 936 HIS A1048 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10502 Z= 0.182 Angle : 0.568 9.936 14167 Z= 0.292 Chirality : 0.044 0.167 1531 Planarity : 0.004 0.046 1818 Dihedral : 4.791 20.137 1381 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.45 % Allowed : 10.68 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -0.83 (0.24), residues: 1231 helix: 0.02 (0.22), residues: 558 sheet: -0.42 (0.39), residues: 161 loop : -1.13 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 597 HIS 0.007 0.001 HIS A 213 PHE 0.017 0.002 PHE A 667 TYR 0.020 0.001 TYR A 392 ARG 0.002 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 1.219 Fit side-chains revert: symmetry clash REVERT: A 162 ARG cc_start: 0.7614 (mtm-85) cc_final: 0.7397 (mtm-85) REVERT: A 186 ASP cc_start: 0.7826 (p0) cc_final: 0.7547 (p0) REVERT: A 227 LYS cc_start: 0.7785 (ttmt) cc_final: 0.7505 (tttt) REVERT: A 529 GLU cc_start: 0.6701 (mp0) cc_final: 0.6488 (mp0) REVERT: A 768 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7047 (mt-10) REVERT: B 326 MET cc_start: 0.6446 (mmt) cc_final: 0.6170 (ptp) REVERT: B 342 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6548 (tm-30) REVERT: B 364 MET cc_start: 0.5635 (tmm) cc_final: 0.3509 (mtp) REVERT: B 367 ASP cc_start: 0.5437 (m-30) cc_final: 0.4955 (m-30) REVERT: B 492 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8185 (ttmm) REVERT: B 525 MET cc_start: 0.6474 (OUTLIER) cc_final: 0.6134 (mpp) REVERT: B 537 GLU cc_start: 0.6396 (tt0) cc_final: 0.6150 (tt0) outliers start: 28 outliers final: 10 residues processed: 179 average time/residue: 1.2722 time to fit residues: 244.0258 Evaluate side-chains 160 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 525 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 9.9990 chunk 1 optimal weight: 0.0040 chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 overall best weight: 3.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 738 GLN ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS B 415 GLN ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10502 Z= 0.306 Angle : 0.648 9.765 14167 Z= 0.332 Chirality : 0.048 0.170 1531 Planarity : 0.005 0.042 1818 Dihedral : 4.974 21.970 1381 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.15 % Allowed : 11.91 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -0.90 (0.24), residues: 1231 helix: -0.08 (0.22), residues: 569 sheet: -0.37 (0.39), residues: 164 loop : -1.14 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 479 HIS 0.008 0.002 HIS A 759 PHE 0.020 0.002 PHE A 667 TYR 0.020 0.002 TYR A 392 ARG 0.004 0.001 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 158 time to evaluate : 1.243 Fit side-chains REVERT: A 162 ARG cc_start: 0.7628 (mtm-85) cc_final: 0.7390 (mtm-85) REVERT: A 186 ASP cc_start: 0.7856 (p0) cc_final: 0.7551 (p0) REVERT: A 227 LYS cc_start: 0.7791 (ttmt) cc_final: 0.7478 (tttm) REVERT: A 454 ASP cc_start: 0.7512 (m-30) cc_final: 0.7273 (m-30) REVERT: A 768 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7082 (mt-10) REVERT: A 883 ASP cc_start: 0.6586 (m-30) cc_final: 0.6285 (m-30) REVERT: B 326 MET cc_start: 0.6472 (mmt) cc_final: 0.6126 (ptp) REVERT: B 342 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6686 (tm-30) REVERT: B 364 MET cc_start: 0.5661 (tmm) cc_final: 0.3494 (mtp) REVERT: B 367 ASP cc_start: 0.5454 (m-30) cc_final: 0.4909 (m-30) REVERT: B 469 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6615 (tt0) REVERT: B 492 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8199 (ttmm) REVERT: B 525 MET cc_start: 0.6536 (OUTLIER) cc_final: 0.6204 (mpp) REVERT: B 537 GLU cc_start: 0.6480 (tt0) cc_final: 0.6247 (tt0) outliers start: 36 outliers final: 15 residues processed: 181 average time/residue: 1.2545 time to fit residues: 243.7397 Evaluate side-chains 168 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 561 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 219 GLN A 936 HIS A1048 HIS B 415 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10502 Z= 0.168 Angle : 0.554 10.036 14167 Z= 0.284 Chirality : 0.043 0.162 1531 Planarity : 0.004 0.042 1818 Dihedral : 4.644 20.535 1381 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.01 % Allowed : 13.40 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -0.41 (0.24), residues: 1231 helix: 0.38 (0.22), residues: 563 sheet: -0.13 (0.39), residues: 160 loop : -0.97 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 597 HIS 0.007 0.001 HIS A 213 PHE 0.015 0.002 PHE A 667 TYR 0.017 0.001 TYR A 392 ARG 0.003 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 1.330 Fit side-chains revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7029 (mtm180) cc_final: 0.6690 (mtm180) REVERT: A 162 ARG cc_start: 0.7556 (mtm-85) cc_final: 0.7345 (mtm-85) REVERT: A 186 ASP cc_start: 0.7834 (p0) cc_final: 0.7563 (p0) REVERT: A 227 LYS cc_start: 0.7795 (ttmt) cc_final: 0.7497 (tttm) REVERT: A 529 GLU cc_start: 0.6658 (mp0) cc_final: 0.6442 (mp0) REVERT: A 766 LEU cc_start: 0.8870 (mm) cc_final: 0.8556 (mm) REVERT: A 768 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6991 (mt-10) REVERT: B 326 MET cc_start: 0.6387 (mmt) cc_final: 0.6043 (ptp) REVERT: B 342 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6699 (tm-30) REVERT: B 364 MET cc_start: 0.5595 (tmm) cc_final: 0.3507 (mtp) REVERT: B 367 ASP cc_start: 0.5361 (m-30) cc_final: 0.4865 (m-30) REVERT: B 492 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8066 (ttmm) REVERT: B 525 MET cc_start: 0.6480 (OUTLIER) cc_final: 0.6142 (mpp) outliers start: 23 outliers final: 8 residues processed: 169 average time/residue: 1.3747 time to fit residues: 248.7244 Evaluate side-chains 156 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 525 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 219 GLN A 826 ASN ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 10502 Z= 0.460 Angle : 0.751 9.516 14167 Z= 0.386 Chirality : 0.053 0.182 1531 Planarity : 0.006 0.042 1818 Dihedral : 5.193 23.239 1381 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.15 % Allowed : 12.61 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -0.92 (0.24), residues: 1231 helix: -0.14 (0.22), residues: 567 sheet: -0.17 (0.39), residues: 164 loop : -1.19 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 479 HIS 0.009 0.002 HIS A 759 PHE 0.022 0.003 PHE A 734 TYR 0.022 0.003 TYR A 56 ARG 0.007 0.001 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 151 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.6928 (mt-10) REVERT: A 162 ARG cc_start: 0.7643 (mtm-85) cc_final: 0.7363 (mtm-85) REVERT: A 186 ASP cc_start: 0.7946 (p0) cc_final: 0.7634 (p0) REVERT: A 227 LYS cc_start: 0.7799 (ttmt) cc_final: 0.7491 (tttt) REVERT: A 454 ASP cc_start: 0.7580 (m-30) cc_final: 0.7354 (m-30) REVERT: A 459 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8460 (mp) REVERT: A 768 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7107 (mt-10) REVERT: A 883 ASP cc_start: 0.6609 (m-30) cc_final: 0.6405 (m-30) REVERT: B 326 MET cc_start: 0.6633 (mmt) cc_final: 0.6286 (ptp) REVERT: B 342 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6895 (tm-30) REVERT: B 364 MET cc_start: 0.5746 (tmm) cc_final: 0.3553 (mtp) REVERT: B 367 ASP cc_start: 0.5744 (m-30) cc_final: 0.5122 (m-30) REVERT: B 469 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6686 (tt0) REVERT: B 478 GLN cc_start: 0.7754 (tp-100) cc_final: 0.7510 (tm-30) REVERT: B 492 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8278 (ttmt) REVERT: B 525 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.6252 (mpp) REVERT: B 537 GLU cc_start: 0.6470 (tt0) cc_final: 0.6241 (tt0) outliers start: 36 outliers final: 15 residues processed: 174 average time/residue: 1.2376 time to fit residues: 231.7387 Evaluate side-chains 167 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 107 optimal weight: 0.1980 chunk 113 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 219 GLN A 936 HIS A1048 HIS ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10502 Z= 0.166 Angle : 0.561 10.086 14167 Z= 0.287 Chirality : 0.043 0.162 1531 Planarity : 0.004 0.039 1818 Dihedral : 4.709 21.208 1381 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.10 % Allowed : 13.92 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -0.40 (0.24), residues: 1231 helix: 0.44 (0.22), residues: 562 sheet: 0.07 (0.40), residues: 156 loop : -1.09 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 597 HIS 0.007 0.001 HIS A 213 PHE 0.015 0.002 PHE A 667 TYR 0.017 0.001 TYR A 392 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7541 (tt0) REVERT: A 93 ARG cc_start: 0.7024 (mtm180) cc_final: 0.6709 (mtm180) REVERT: A 162 ARG cc_start: 0.7572 (mtm-85) cc_final: 0.7274 (mtm-85) REVERT: A 186 ASP cc_start: 0.7837 (p0) cc_final: 0.7551 (p0) REVERT: A 227 LYS cc_start: 0.7818 (ttmt) cc_final: 0.7529 (tttt) REVERT: A 529 GLU cc_start: 0.6613 (mp0) cc_final: 0.6353 (mp0) REVERT: A 766 LEU cc_start: 0.8803 (mm) cc_final: 0.8562 (mm) REVERT: B 326 MET cc_start: 0.6523 (mmt) cc_final: 0.6157 (ptp) REVERT: B 342 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6816 (tm-30) REVERT: B 364 MET cc_start: 0.5634 (tmm) cc_final: 0.3572 (mtp) REVERT: B 367 ASP cc_start: 0.5455 (m-30) cc_final: 0.4900 (m-30) REVERT: B 492 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8037 (ttmm) REVERT: B 525 MET cc_start: 0.6494 (OUTLIER) cc_final: 0.6160 (mpp) outliers start: 24 outliers final: 9 residues processed: 169 average time/residue: 1.3565 time to fit residues: 245.5623 Evaluate side-chains 155 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 525 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.7746 > 50: distance: 40 - 68: 19.507 distance: 47 - 77: 15.368 distance: 54 - 59: 7.717 distance: 55 - 85: 21.050 distance: 59 - 60: 11.756 distance: 60 - 61: 8.840 distance: 60 - 63: 18.374 distance: 61 - 62: 30.936 distance: 61 - 68: 20.644 distance: 62 - 96: 23.096 distance: 63 - 64: 24.596 distance: 64 - 65: 6.507 distance: 65 - 66: 11.195 distance: 65 - 67: 9.798 distance: 68 - 69: 10.415 distance: 69 - 70: 23.704 distance: 69 - 72: 11.399 distance: 70 - 71: 8.685 distance: 70 - 77: 18.575 distance: 71 - 104: 27.589 distance: 72 - 73: 16.309 distance: 73 - 74: 7.291 distance: 74 - 75: 27.194 distance: 75 - 76: 6.965 distance: 77 - 78: 19.863 distance: 78 - 79: 18.368 distance: 78 - 81: 14.530 distance: 79 - 80: 12.424 distance: 79 - 85: 16.959 distance: 80 - 118: 10.424 distance: 81 - 82: 28.898 distance: 82 - 83: 6.518 distance: 82 - 84: 11.305 distance: 85 - 86: 36.352 distance: 86 - 87: 18.036 distance: 86 - 89: 29.389 distance: 87 - 88: 21.022 distance: 87 - 96: 19.633 distance: 88 - 124: 27.301 distance: 89 - 90: 20.021 distance: 90 - 91: 5.061 distance: 90 - 92: 13.631 distance: 91 - 93: 21.444 distance: 92 - 94: 14.127 distance: 93 - 95: 12.518 distance: 94 - 95: 13.804 distance: 96 - 97: 16.330 distance: 97 - 98: 33.434 distance: 97 - 100: 36.398 distance: 98 - 99: 16.705 distance: 98 - 104: 19.475 distance: 100 - 101: 27.065 distance: 101 - 102: 13.312 distance: 101 - 103: 13.440 distance: 104 - 105: 11.451 distance: 105 - 106: 9.020 distance: 105 - 108: 23.969 distance: 106 - 107: 14.964 distance: 106 - 118: 14.512 distance: 108 - 109: 10.219 distance: 109 - 110: 10.113 distance: 109 - 111: 3.905 distance: 110 - 112: 3.808 distance: 111 - 113: 5.267 distance: 112 - 113: 6.461 distance: 113 - 115: 5.328 distance: 114 - 116: 6.841 distance: 115 - 117: 5.418 distance: 116 - 117: 3.706 distance: 118 - 119: 3.335 distance: 119 - 120: 14.569 distance: 119 - 122: 12.322 distance: 120 - 121: 26.496 distance: 120 - 124: 12.625 distance: 122 - 123: 10.570 distance: 124 - 125: 6.323 distance: 125 - 126: 14.400 distance: 125 - 128: 10.061 distance: 126 - 127: 11.203 distance: 128 - 129: 28.578 distance: 129 - 130: 43.403 distance: 129 - 131: 37.653 distance: 130 - 132: 39.012 distance: 131 - 133: 32.281 distance: 132 - 133: 32.446 distance: 134 - 135: 12.777 distance: 135 - 136: 7.945 distance: 135 - 138: 18.668 distance: 136 - 137: 23.382 distance: 136 - 145: 24.457 distance: 138 - 139: 21.960 distance: 139 - 140: 19.338 distance: 140 - 141: 5.823 distance: 141 - 142: 7.015 distance: 142 - 143: 13.614 distance: 142 - 144: 12.796 distance: 145 - 146: 12.249 distance: 146 - 147: 25.590 distance: 146 - 149: 30.566 distance: 147 - 148: 20.914 distance: 147 - 155: 30.032 distance: 149 - 150: 19.478 distance: 150 - 151: 28.247 distance: 150 - 152: 28.740 distance: 151 - 153: 29.855 distance: 152 - 154: 31.909 distance: 153 - 154: 21.285