Starting phenix.real_space_refine on Sun Nov 17 08:41:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7j_37339/11_2024/8w7j_37339.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7j_37339/11_2024/8w7j_37339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7j_37339/11_2024/8w7j_37339.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7j_37339/11_2024/8w7j_37339.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7j_37339/11_2024/8w7j_37339.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7j_37339/11_2024/8w7j_37339.cif" } resolution = 3.98 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= 0.003 sd= 0.047 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 P 4 5.49 5 S 30 5.16 5 C 8689 2.51 5 N 2207 2.21 5 O 2507 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13437 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 857, 7020 Classifications: {'peptide': 857} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 828} Chain breaks: 2 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 6310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6310 Classifications: {'peptide': 770} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 748} Chain breaks: 9 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'GTP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.30, per 1000 atoms: 0.69 Number of scatterers: 13437 At special positions: 0 Unit cell: (106.392, 112.398, 135.564, 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) S 30 16.00 P 4 15.00 O 2507 8.00 N 2207 7.00 C 8689 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: 3.33 Conformation dependent library (CDL) restraints added in 1.9 seconds 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3072 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 40.3% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.616A pdb=" N PHE A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.799A pdb=" N ARG A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 206 removed outlier: 3.736A pdb=" N ASP A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 274 removed outlier: 3.759A pdb=" N ALA A 266 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 325 through 340 removed outlier: 3.603A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 346 removed outlier: 3.545A pdb=" N SER A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 417 Processing helix chain 'A' and resid 429 through 443 removed outlier: 3.874A pdb=" N THR A 433 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS A 439 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 462 removed outlier: 4.119A pdb=" N ILE A 451 " --> pdb=" O THR A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 512 removed outlier: 3.993A pdb=" N ILE A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 548 removed outlier: 3.624A pdb=" N LEU A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 548 " --> pdb=" O GLN A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 568 Processing helix chain 'A' and resid 586 through 595 Processing helix chain 'A' and resid 601 through 614 removed outlier: 5.958A pdb=" N ILE A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLU A 611 " --> pdb=" O THR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 639 removed outlier: 4.097A pdb=" N ILE A 628 " --> pdb=" O GLY A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 663 removed outlier: 3.538A pdb=" N LEU A 650 " --> pdb=" O GLY A 646 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLU A 655 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 660 " --> pdb=" O TYR A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 705 removed outlier: 4.098A pdb=" N LEU A 697 " --> pdb=" O GLY A 693 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 722 removed outlier: 3.904A pdb=" N LYS A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 722 " --> pdb=" O VAL A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 759 removed outlier: 3.804A pdb=" N LEU A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 754 " --> pdb=" O ALA A 750 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 755 " --> pdb=" O GLY A 751 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 770 through 778 removed outlier: 3.977A pdb=" N ARG A 776 " --> pdb=" O THR A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 823 removed outlier: 4.440A pdb=" N GLY A 811 " --> pdb=" O ASP A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 861 removed outlier: 3.548A pdb=" N VAL A 851 " --> pdb=" O GLY A 847 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N MET A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 81 removed outlier: 3.729A pdb=" N LEU B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 267 through 274 Processing helix chain 'B' and resid 305 through 314 Processing helix chain 'B' and resid 325 through 345 removed outlier: 3.555A pdb=" N ARG B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 414 removed outlier: 4.127A pdb=" N ASP B 404 " --> pdb=" O PRO B 400 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TRP B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 445 removed outlier: 3.799A pdb=" N ARG B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 435 " --> pdb=" O SER B 431 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU B 440 " --> pdb=" O GLU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 463 Processing helix chain 'B' and resid 473 through 477 removed outlier: 3.729A pdb=" N VAL B 476 " --> pdb=" O ARG B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 509 removed outlier: 3.784A pdb=" N ILE B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 501 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 502 " --> pdb=" O LYS B 498 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 514 removed outlier: 4.346A pdb=" N GLU B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 550 removed outlier: 4.090A pdb=" N TRP B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER B 542 " --> pdb=" O ALA B 538 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B 550 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 572 removed outlier: 4.724A pdb=" N GLU B 568 " --> pdb=" O GLN B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 575 No H-bonds generated for 'chain 'B' and resid 573 through 575' Processing helix chain 'B' and resid 586 through 595 Processing helix chain 'B' and resid 598 through 614 removed outlier: 6.129A pdb=" N ILE B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N GLU B 611 " --> pdb=" O THR B 607 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 614 " --> pdb=" O ILE B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 626 No H-bonds generated for 'chain 'B' and resid 625 through 626' Processing helix chain 'B' and resid 628 through 628 No H-bonds generated for 'chain 'B' and resid 628 through 628' Processing helix chain 'B' and resid 629 through 639 removed outlier: 3.955A pdb=" N LYS B 638 " --> pdb=" O TYR B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 663 Processing helix chain 'B' and resid 690 through 692 No H-bonds generated for 'chain 'B' and resid 690 through 692' Processing helix chain 'B' and resid 693 through 705 removed outlier: 4.305A pdb=" N LEU B 697 " --> pdb=" O GLY B 693 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 705 " --> pdb=" O ALA B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 722 Processing helix chain 'B' and resid 748 through 757 removed outlier: 3.580A pdb=" N LEU B 752 " --> pdb=" O GLY B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 778 Processing helix chain 'B' and resid 791 through 800 removed outlier: 3.675A pdb=" N LEU B 795 " --> pdb=" O GLY B 791 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN B 800 " --> pdb=" O GLU B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 820 Processing helix chain 'B' and resid 847 through 860 removed outlier: 3.765A pdb=" N VAL B 851 " --> pdb=" O GLY B 847 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 46 removed outlier: 3.734A pdb=" N HIS A 89 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS A 115 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE A 60 " --> pdb=" O CYS A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 217 through 221 removed outlier: 3.526A pdb=" N ASP A 220 " --> pdb=" O ASN A 233 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ASN A 233 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 230 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 243 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLY A 297 " --> pdb=" O TYR A 285 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 351 removed outlier: 3.543A pdb=" N VAL A 376 " --> pdb=" O TYR A 350 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 725 through 727 removed outlier: 3.708A pdb=" N TYR A 735 " --> pdb=" O LEU A 742 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 824 through 826 removed outlier: 3.563A pdb=" N CYS A 824 " --> pdb=" O VAL A 831 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 826 " --> pdb=" O GLY A 829 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 38 removed outlier: 3.601A pdb=" N TYR B 47 " --> pdb=" O HIS B 35 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 44 " --> pdb=" O HIS B 89 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 114 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS B 115 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE B 60 " --> pdb=" O CYS B 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 725 through 727 Processing sheet with id=AA9, first strand: chain 'B' and resid 823 through 826 removed outlier: 3.807A pdb=" N CYS B 824 " --> pdb=" O VAL B 831 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 831 " --> pdb=" O CYS B 824 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 829 " --> pdb=" O ILE B 826 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1239 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: 4.40 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2394 1.32 - 1.45: 3710 1.45 - 1.57: 7602 1.57 - 1.69: 9 1.69 - 1.81: 44 Bond restraints: 13759 Sorted by residual: bond pdb=" C5 GTP A 901 " pdb=" C6 GTP A 901 " ideal model delta sigma weight residual 1.390 1.476 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C4 GTP A 901 " pdb=" C5 GTP A 901 " ideal model delta sigma weight residual 1.390 1.463 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" CA LYS B 464 " pdb=" C LYS B 464 " ideal model delta sigma weight residual 1.526 1.487 0.039 1.22e-02 6.72e+03 1.00e+01 bond pdb=" O4 PO4 A 902 " pdb=" P PO4 A 902 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.75e+00 bond pdb=" O3 PO4 A 902 " pdb=" P PO4 A 902 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.63e+00 ... (remaining 13754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 18094 2.99 - 5.99: 434 5.99 - 8.98: 73 8.98 - 11.97: 12 11.97 - 14.96: 5 Bond angle restraints: 18618 Sorted by residual: angle pdb=" N LYS B 464 " pdb=" CA LYS B 464 " pdb=" C LYS B 464 " ideal model delta sigma weight residual 107.57 92.61 14.96 1.94e+00 2.66e-01 5.95e+01 angle pdb=" C LYS A 324 " pdb=" N ASP A 325 " pdb=" CA ASP A 325 " ideal model delta sigma weight residual 122.08 132.35 -10.27 1.47e+00 4.63e-01 4.88e+01 angle pdb=" C GLU A 827 " pdb=" CA GLU A 827 " pdb=" CB GLU A 827 " ideal model delta sigma weight residual 117.23 109.81 7.42 1.36e+00 5.41e-01 2.97e+01 angle pdb=" N GLU B 715 " pdb=" CA GLU B 715 " pdb=" CB GLU B 715 " ideal model delta sigma weight residual 110.16 118.05 -7.89 1.48e+00 4.57e-01 2.84e+01 angle pdb=" C ARG A 654 " pdb=" N GLU A 655 " pdb=" CA GLU A 655 " ideal model delta sigma weight residual 121.54 131.63 -10.09 1.91e+00 2.74e-01 2.79e+01 ... (remaining 18613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.87: 7477 23.87 - 47.74: 563 47.74 - 71.62: 40 71.62 - 95.49: 15 95.49 - 119.36: 3 Dihedral angle restraints: 8098 sinusoidal: 3303 harmonic: 4795 Sorted by residual: dihedral pdb=" O2G GTP A 901 " pdb=" O3B GTP A 901 " pdb=" PG GTP A 901 " pdb=" PB GTP A 901 " ideal model delta sinusoidal sigma weight residual 177.30 -63.34 -119.36 1 2.00e+01 2.50e-03 3.58e+01 dihedral pdb=" C8 GTP A 901 " pdb=" C1' GTP A 901 " pdb=" N9 GTP A 901 " pdb=" O4' GTP A 901 " ideal model delta sinusoidal sigma weight residual 104.59 -137.48 -117.93 1 2.00e+01 2.50e-03 3.52e+01 dihedral pdb=" CA GLU A 796 " pdb=" C GLU A 796 " pdb=" N VAL A 797 " pdb=" CA VAL A 797 " ideal model delta harmonic sigma weight residual 180.00 152.43 27.57 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 8095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1775 0.092 - 0.184: 209 0.184 - 0.276: 14 0.276 - 0.368: 6 0.368 - 0.460: 2 Chirality restraints: 2006 Sorted by residual: chirality pdb=" CB ILE B 532 " pdb=" CA ILE B 532 " pdb=" CG1 ILE B 532 " pdb=" CG2 ILE B 532 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CB ILE A 641 " pdb=" CA ILE A 641 " pdb=" CG1 ILE A 641 " pdb=" CG2 ILE A 641 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CB ILE A 175 " pdb=" CA ILE A 175 " pdb=" CG1 ILE A 175 " pdb=" CG2 ILE A 175 " both_signs ideal model delta sigma weight residual False 2.64 2.99 -0.35 2.00e-01 2.50e+01 3.04e+00 ... (remaining 2003 not shown) Planarity restraints: 2359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 465 " -0.057 5.00e-02 4.00e+02 8.72e-02 1.22e+01 pdb=" N PRO B 466 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 466 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 466 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 473 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.64e+00 pdb=" C ARG A 473 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG A 473 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS A 474 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 655 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.50e+00 pdb=" C GLU A 655 " -0.050 2.00e-02 2.50e+03 pdb=" O GLU A 655 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR A 656 " 0.017 2.00e-02 2.50e+03 ... (remaining 2356 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3776 2.81 - 3.33: 12137 3.33 - 3.86: 21477 3.86 - 4.38: 23419 4.38 - 4.90: 39654 Nonbonded interactions: 100463 Sorted by model distance: nonbonded pdb=" OH TYR B 524 " pdb=" OD1 ASP B 679 " model vdw 2.290 3.040 nonbonded pdb=" N UNK C 0 " pdb=" O UNK C 0 " model vdw 2.303 2.496 nonbonded pdb=" O CYS B 783 " pdb=" OH TYR B 822 " model vdw 2.315 3.040 nonbonded pdb=" O LEU B 337 " pdb=" OG1 THR B 341 " model vdw 2.318 3.040 nonbonded pdb=" O PRO B 139 " pdb=" OH TYR B 153 " model vdw 2.332 3.040 ... (remaining 100458 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB )) or resid 85 through 141 or resid 145 through 157 or res \ id 231 or resid 242 through 248 or resid 251 through 264 or resid 266 through 28 \ 9 or resid 293 through 595 or resid 597 through 626 or resid 628 through 670 or \ resid 673 through 869)) selection = chain 'B' } 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 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: 2.320 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.240 Process input model: 32.650 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 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 : 0.005 0.086 13759 Z= 0.307 Angle : 1.102 14.964 18618 Z= 0.567 Chirality : 0.062 0.460 2006 Planarity : 0.007 0.087 2359 Dihedral : 15.739 119.359 5026 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.37 % Favored : 88.07 % Rotamer: Outliers : 0.21 % Allowed : 0.41 % Favored : 99.38 % 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: -3.79 (0.17), residues: 1601 helix: -1.93 (0.17), residues: 597 sheet: -1.12 (0.63), residues: 74 loop : -3.19 (0.17), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 395 HIS 0.015 0.002 HIS A 9 PHE 0.048 0.002 PHE A 573 TYR 0.035 0.002 TYR B 656 ARG 0.013 0.001 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 215 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 CYS cc_start: 0.8375 (p) cc_final: 0.8157 (p) REVERT: A 469 GLU cc_start: 0.6118 (mp0) cc_final: 0.5862 (mp0) REVERT: A 507 TYR cc_start: 0.8051 (t80) cc_final: 0.7709 (t80) REVERT: A 747 THR cc_start: 0.8580 (p) cc_final: 0.8280 (p) REVERT: B 26 TYR cc_start: 0.6761 (m-10) cc_final: 0.6472 (m-80) REVERT: B 80 CYS cc_start: 0.8725 (m) cc_final: 0.8386 (m) REVERT: B 83 MET cc_start: 0.8300 (pmm) cc_final: 0.8002 (pmm) REVERT: B 744 TYR cc_start: 0.7014 (m-80) cc_final: 0.6702 (m-10) outliers start: 3 outliers final: 2 residues processed: 218 average time/residue: 0.2260 time to fit residues: 75.7767 Evaluate side-chains 158 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 465 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN A 432 GLN A 737 GLN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 HIS ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13759 Z= 0.283 Angle : 0.729 9.445 18618 Z= 0.385 Chirality : 0.046 0.202 2006 Planarity : 0.005 0.059 2359 Dihedral : 7.740 116.042 1803 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.93 % Favored : 88.57 % Rotamer: Outliers : 1.86 % Allowed : 11.84 % Favored : 86.30 % 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: -2.88 (0.19), residues: 1601 helix: -0.56 (0.21), residues: 608 sheet: -1.55 (0.62), residues: 74 loop : -3.07 (0.18), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 395 HIS 0.008 0.001 HIS B 9 PHE 0.017 0.002 PHE A 503 TYR 0.037 0.002 TYR B 656 ARG 0.005 0.001 ARG B 652 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 TYR cc_start: 0.8418 (m-10) cc_final: 0.8173 (m-80) REVERT: A 568 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7198 (pm20) REVERT: A 593 TYR cc_start: 0.8541 (t80) cc_final: 0.8300 (t80) REVERT: A 747 THR cc_start: 0.8619 (p) cc_final: 0.8374 (p) REVERT: B 80 CYS cc_start: 0.8998 (m) cc_final: 0.8709 (m) REVERT: B 324 LYS cc_start: 0.5322 (mmtt) cc_final: 0.4866 (mmtp) REVERT: B 678 ASN cc_start: 0.7284 (t0) cc_final: 0.7016 (t0) REVERT: B 744 TYR cc_start: 0.7348 (m-80) cc_final: 0.6825 (m-10) outliers start: 27 outliers final: 17 residues processed: 178 average time/residue: 0.2202 time to fit residues: 61.2388 Evaluate side-chains 158 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 414 TYR Chi-restraints excluded: chain B residue 465 CYS Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 840 ILE Chi-restraints excluded: chain B residue 855 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 123 optimal weight: 0.2980 chunk 100 optimal weight: 40.0000 chunk 40 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN B 9 HIS ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 509 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 13759 Z= 0.243 Angle : 0.673 7.722 18618 Z= 0.354 Chirality : 0.045 0.202 2006 Planarity : 0.004 0.055 2359 Dihedral : 7.449 116.989 1799 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.93 % Favored : 88.69 % Rotamer: Outliers : 2.55 % Allowed : 15.69 % Favored : 81.76 % 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: -2.64 (0.20), residues: 1601 helix: -0.18 (0.21), residues: 607 sheet: -1.65 (0.61), residues: 74 loop : -3.04 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 395 HIS 0.006 0.001 HIS A 9 PHE 0.024 0.002 PHE A 573 TYR 0.020 0.002 TYR A 45 ARG 0.003 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 TYR cc_start: 0.8313 (m-10) cc_final: 0.8077 (m-80) REVERT: A 568 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7423 (pm20) REVERT: A 593 TYR cc_start: 0.8631 (t80) cc_final: 0.8292 (t80) REVERT: A 747 THR cc_start: 0.8593 (p) cc_final: 0.8385 (p) REVERT: B 80 CYS cc_start: 0.8974 (m) cc_final: 0.8638 (m) REVERT: B 744 TYR cc_start: 0.7390 (m-80) cc_final: 0.6867 (m-80) outliers start: 37 outliers final: 25 residues processed: 175 average time/residue: 0.2193 time to fit residues: 60.4039 Evaluate side-chains 154 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 414 TYR Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 840 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 9.9990 chunk 111 optimal weight: 0.0870 chunk 76 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 99 optimal weight: 30.0000 chunk 148 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 overall best weight: 2.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 530 GLN B 33 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13759 Z= 0.228 Angle : 0.663 10.950 18618 Z= 0.345 Chirality : 0.044 0.209 2006 Planarity : 0.004 0.054 2359 Dihedral : 7.277 116.275 1798 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.12 % Favored : 88.57 % Rotamer: Outliers : 2.75 % Allowed : 17.76 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.51 (0.20), residues: 1601 helix: 0.00 (0.22), residues: 606 sheet: -1.79 (0.62), residues: 74 loop : -3.01 (0.18), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 395 HIS 0.010 0.001 HIS B 9 PHE 0.020 0.001 PHE A 189 TYR 0.043 0.002 TYR B 656 ARG 0.006 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 1.602 Fit side-chains revert: symmetry clash REVERT: A 232 TYR cc_start: 0.7297 (OUTLIER) cc_final: 0.6882 (m-80) REVERT: A 260 TYR cc_start: 0.8350 (m-10) cc_final: 0.8134 (m-80) REVERT: A 363 ASP cc_start: 0.7668 (t0) cc_final: 0.7338 (t0) REVERT: A 593 TYR cc_start: 0.8659 (t80) cc_final: 0.8312 (t80) REVERT: A 747 THR cc_start: 0.8563 (p) cc_final: 0.8339 (p) REVERT: B 80 CYS cc_start: 0.8976 (m) cc_final: 0.8652 (m) REVERT: B 154 LEU cc_start: 0.7751 (pt) cc_final: 0.7236 (tp) REVERT: B 744 TYR cc_start: 0.7247 (m-10) cc_final: 0.6743 (m-80) outliers start: 40 outliers final: 25 residues processed: 169 average time/residue: 0.2031 time to fit residues: 55.2551 Evaluate side-chains 157 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 414 TYR Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 840 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 2 optimal weight: 0.2980 chunk 117 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 564 GLN B 683 ASN ** B 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 13759 Z= 0.282 Angle : 0.690 7.735 18618 Z= 0.361 Chirality : 0.046 0.229 2006 Planarity : 0.004 0.054 2359 Dihedral : 7.347 114.535 1798 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.56 % Favored : 88.13 % Rotamer: Outliers : 3.30 % Allowed : 18.72 % Favored : 77.98 % 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: -2.56 (0.20), residues: 1601 helix: -0.05 (0.21), residues: 609 sheet: -1.85 (0.61), residues: 74 loop : -3.03 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 395 HIS 0.008 0.001 HIS A 9 PHE 0.028 0.002 PHE A 573 TYR 0.037 0.002 TYR B 656 ARG 0.004 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7722 (tmm) cc_final: 0.7409 (ttm) REVERT: A 115 CYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8051 (p) REVERT: A 232 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.6955 (m-80) REVERT: A 363 ASP cc_start: 0.7775 (t0) cc_final: 0.7427 (t0) REVERT: A 747 THR cc_start: 0.8643 (p) cc_final: 0.8426 (p) REVERT: A 796 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: B 12 PHE cc_start: 0.5751 (OUTLIER) cc_final: 0.5531 (t80) REVERT: B 80 CYS cc_start: 0.9025 (m) cc_final: 0.8699 (m) REVERT: B 154 LEU cc_start: 0.7753 (pt) cc_final: 0.7212 (tp) REVERT: B 744 TYR cc_start: 0.7387 (m-10) cc_final: 0.6890 (m-80) REVERT: B 848 PHE cc_start: 0.7815 (t80) cc_final: 0.7593 (t80) outliers start: 48 outliers final: 34 residues processed: 170 average time/residue: 0.2168 time to fit residues: 58.6571 Evaluate side-chains 166 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 414 TYR Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 691 HIS Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 855 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.0070 chunk 141 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 157 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 overall best weight: 1.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 355 HIS ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13759 Z= 0.163 Angle : 0.626 8.265 18618 Z= 0.324 Chirality : 0.044 0.190 2006 Planarity : 0.004 0.055 2359 Dihedral : 6.986 109.339 1798 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.99 % Favored : 89.63 % Rotamer: Outliers : 2.62 % Allowed : 19.89 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.35 (0.20), residues: 1601 helix: 0.12 (0.22), residues: 608 sheet: -1.77 (0.64), residues: 68 loop : -2.89 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 590 HIS 0.015 0.001 HIS B 9 PHE 0.034 0.001 PHE A 573 TYR 0.031 0.001 TYR B 656 ARG 0.007 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 CYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7791 (p) REVERT: A 232 TYR cc_start: 0.7227 (OUTLIER) cc_final: 0.6882 (m-80) REVERT: A 363 ASP cc_start: 0.7751 (t0) cc_final: 0.7409 (t0) REVERT: A 747 THR cc_start: 0.8399 (p) cc_final: 0.8134 (p) REVERT: B 12 PHE cc_start: 0.5307 (OUTLIER) cc_final: 0.4777 (t80) REVERT: B 80 CYS cc_start: 0.9018 (m) cc_final: 0.8706 (m) REVERT: B 154 LEU cc_start: 0.7742 (pt) cc_final: 0.7203 (tp) REVERT: B 405 TRP cc_start: 0.7474 (t60) cc_final: 0.7264 (t60) REVERT: B 509 GLN cc_start: 0.7801 (mp-120) cc_final: 0.7547 (mp10) REVERT: B 568 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8845 (pm20) REVERT: B 744 TYR cc_start: 0.7156 (m-10) cc_final: 0.6630 (m-80) outliers start: 38 outliers final: 26 residues processed: 177 average time/residue: 0.2226 time to fit residues: 61.4221 Evaluate side-chains 161 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 414 TYR Chi-restraints excluded: chain B residue 465 CYS Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 691 HIS Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain B residue 866 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 0.6980 chunk 17 optimal weight: 30.0000 chunk 89 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN B 9 HIS B 351 HIS B 410 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.138 13759 Z= 0.421 Angle : 0.807 9.910 18618 Z= 0.421 Chirality : 0.048 0.215 2006 Planarity : 0.005 0.055 2359 Dihedral : 7.586 111.574 1798 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.44 % Allowed : 12.99 % Favored : 86.57 % Rotamer: Outliers : 4.13 % Allowed : 20.23 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.80 (0.20), residues: 1601 helix: -0.29 (0.21), residues: 607 sheet: -2.29 (0.58), residues: 74 loop : -3.11 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 395 HIS 0.014 0.002 HIS B 9 PHE 0.033 0.003 PHE B 13 TYR 0.030 0.003 TYR A 45 ARG 0.006 0.001 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 136 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7708 (tmm) cc_final: 0.7390 (ttm) REVERT: A 115 CYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8103 (p) REVERT: A 232 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.6930 (m-80) REVERT: A 291 TRP cc_start: 0.6058 (OUTLIER) cc_final: 0.5624 (m-10) REVERT: A 363 ASP cc_start: 0.7826 (t0) cc_final: 0.7522 (t0) REVERT: A 585 LYS cc_start: 0.8159 (tttp) cc_final: 0.7752 (tttt) REVERT: A 640 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7439 (pp20) REVERT: A 747 THR cc_start: 0.8838 (p) cc_final: 0.8618 (p) REVERT: A 859 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7481 (pmm) REVERT: B 80 CYS cc_start: 0.9045 (m) cc_final: 0.8739 (m) REVERT: B 154 LEU cc_start: 0.7788 (pt) cc_final: 0.7221 (tp) REVERT: B 286 TRP cc_start: 0.7638 (t60) cc_final: 0.6867 (t60) REVERT: B 295 PHE cc_start: 0.7259 (m-10) cc_final: 0.7050 (m-10) REVERT: B 509 GLN cc_start: 0.7986 (mp-120) cc_final: 0.7714 (mp10) REVERT: B 568 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8468 (pm20) REVERT: B 575 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8225 (mtmm) REVERT: B 744 TYR cc_start: 0.7541 (m-10) cc_final: 0.6979 (m-80) REVERT: B 848 PHE cc_start: 0.8196 (t80) cc_final: 0.7913 (t80) outliers start: 60 outliers final: 40 residues processed: 178 average time/residue: 0.2165 time to fit residues: 60.2015 Evaluate side-chains 170 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 123 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 291 TRP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 689 TYR Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 414 TYR Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 460 TYR Chi-restraints excluded: chain B residue 465 CYS Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 575 LYS Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 691 HIS Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 866 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 0.3980 chunk 93 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 99 optimal weight: 30.0000 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13759 Z= 0.203 Angle : 0.681 12.771 18618 Z= 0.349 Chirality : 0.045 0.267 2006 Planarity : 0.004 0.055 2359 Dihedral : 7.157 107.317 1798 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.18 % Favored : 89.44 % Rotamer: Outliers : 2.89 % Allowed : 21.68 % Favored : 75.43 % 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: -2.50 (0.20), residues: 1601 helix: 0.03 (0.21), residues: 610 sheet: -2.13 (0.57), residues: 80 loop : -2.99 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 590 HIS 0.005 0.001 HIS A 89 PHE 0.028 0.001 PHE A 189 TYR 0.019 0.002 TYR B 414 ARG 0.004 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 1.581 Fit side-chains revert: symmetry clash REVERT: A 115 CYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7809 (p) REVERT: A 163 ARG cc_start: 0.7055 (mtt90) cc_final: 0.6769 (mtt90) REVERT: A 166 GLU cc_start: 0.5883 (OUTLIER) cc_final: 0.5644 (pm20) REVERT: A 232 TYR cc_start: 0.7275 (OUTLIER) cc_final: 0.6885 (m-80) REVERT: A 363 ASP cc_start: 0.7783 (t0) cc_final: 0.7418 (t0) REVERT: A 640 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7426 (pp20) REVERT: A 747 THR cc_start: 0.8543 (p) cc_final: 0.8298 (p) REVERT: A 859 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7485 (pmm) REVERT: B 80 CYS cc_start: 0.8945 (m) cc_final: 0.8602 (m) REVERT: B 83 MET cc_start: 0.8380 (pmm) cc_final: 0.8145 (pmm) REVERT: B 154 LEU cc_start: 0.7761 (pt) cc_final: 0.7174 (tp) REVERT: B 509 GLN cc_start: 0.7860 (mp-120) cc_final: 0.7612 (mp10) REVERT: B 568 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8972 (pm20) REVERT: B 744 TYR cc_start: 0.7459 (m-10) cc_final: 0.6952 (m-80) REVERT: B 848 PHE cc_start: 0.7713 (t80) cc_final: 0.7448 (t80) outliers start: 42 outliers final: 27 residues processed: 159 average time/residue: 0.2234 time to fit residues: 55.8685 Evaluate side-chains 156 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 414 TYR Chi-restraints excluded: chain B residue 460 TYR Chi-restraints excluded: chain B residue 465 CYS Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 595 PHE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 691 HIS Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain B residue 866 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 ASN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 13759 Z= 0.272 Angle : 0.710 9.707 18618 Z= 0.366 Chirality : 0.046 0.267 2006 Planarity : 0.004 0.055 2359 Dihedral : 7.216 108.180 1798 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.12 % Favored : 87.51 % Rotamer: Outliers : 2.89 % Allowed : 21.61 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.56 (0.20), residues: 1601 helix: -0.03 (0.21), residues: 610 sheet: -2.21 (0.56), residues: 80 loop : -3.02 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 395 HIS 0.005 0.001 HIS A 89 PHE 0.023 0.002 PHE A 189 TYR 0.021 0.002 TYR A 45 ARG 0.005 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 1.678 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.7647 (tmm) cc_final: 0.7291 (ttm) REVERT: A 115 CYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7976 (p) REVERT: A 163 ARG cc_start: 0.7075 (mtt90) cc_final: 0.6873 (mtt90) REVERT: A 232 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.6883 (m-80) REVERT: A 363 ASP cc_start: 0.7809 (t0) cc_final: 0.7494 (t0) REVERT: A 392 PHE cc_start: 0.6822 (m-80) cc_final: 0.6583 (m-80) REVERT: A 640 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7458 (pp20) REVERT: A 747 THR cc_start: 0.8639 (p) cc_final: 0.8401 (p) REVERT: A 859 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7598 (pmm) REVERT: B 80 CYS cc_start: 0.8912 (m) cc_final: 0.8611 (m) REVERT: B 83 MET cc_start: 0.8366 (pmm) cc_final: 0.8133 (pmm) REVERT: B 154 LEU cc_start: 0.7759 (pt) cc_final: 0.7176 (tp) REVERT: B 509 GLN cc_start: 0.7841 (mp-120) cc_final: 0.7572 (mp10) REVERT: B 568 GLU cc_start: 0.9294 (OUTLIER) cc_final: 0.8997 (pm20) REVERT: B 744 TYR cc_start: 0.7604 (m-10) cc_final: 0.7038 (m-80) REVERT: B 848 PHE cc_start: 0.7937 (t80) cc_final: 0.7659 (t80) outliers start: 42 outliers final: 31 residues processed: 157 average time/residue: 0.2119 time to fit residues: 53.0818 Evaluate side-chains 159 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 414 TYR Chi-restraints excluded: chain B residue 460 TYR Chi-restraints excluded: chain B residue 465 CYS Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 595 PHE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 691 HIS Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain B residue 866 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 149 optimal weight: 30.0000 chunk 129 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 99 optimal weight: 30.0000 chunk 79 optimal weight: 10.0000 chunk 102 optimal weight: 30.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 13759 Z= 0.299 Angle : 0.738 11.973 18618 Z= 0.378 Chirality : 0.046 0.234 2006 Planarity : 0.005 0.062 2359 Dihedral : 7.275 106.403 1798 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.30 % Favored : 87.32 % Rotamer: Outliers : 3.17 % Allowed : 21.75 % Favored : 75.09 % 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: -2.63 (0.20), residues: 1601 helix: -0.09 (0.21), residues: 608 sheet: -2.25 (0.56), residues: 80 loop : -3.05 (0.18), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 590 HIS 0.005 0.001 HIS B 89 PHE 0.022 0.002 PHE A 189 TYR 0.023 0.002 TYR A 45 ARG 0.006 0.000 ARG B 517 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.7636 (tmm) cc_final: 0.7325 (ttm) REVERT: A 115 CYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7949 (p) REVERT: A 163 ARG cc_start: 0.7056 (mtt90) cc_final: 0.6783 (mtt90) REVERT: A 166 GLU cc_start: 0.6010 (OUTLIER) cc_final: 0.5792 (pm20) REVERT: A 232 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.6895 (m-80) REVERT: A 363 ASP cc_start: 0.7834 (t0) cc_final: 0.7513 (t0) REVERT: A 392 PHE cc_start: 0.6879 (m-80) cc_final: 0.6625 (m-80) REVERT: A 640 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7445 (pp20) REVERT: A 747 THR cc_start: 0.8695 (p) cc_final: 0.8461 (p) REVERT: A 859 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7671 (pmm) REVERT: B 80 CYS cc_start: 0.8985 (m) cc_final: 0.8713 (m) REVERT: B 83 MET cc_start: 0.8374 (pmm) cc_final: 0.8152 (pmm) REVERT: B 154 LEU cc_start: 0.7781 (pt) cc_final: 0.7187 (tp) REVERT: B 509 GLN cc_start: 0.7899 (mp-120) cc_final: 0.7648 (mp10) REVERT: B 568 GLU cc_start: 0.9286 (OUTLIER) cc_final: 0.8979 (pm20) REVERT: B 744 TYR cc_start: 0.7568 (m-10) cc_final: 0.6994 (m-80) REVERT: B 848 PHE cc_start: 0.7968 (t80) cc_final: 0.7680 (t80) outliers start: 46 outliers final: 36 residues processed: 160 average time/residue: 0.2047 time to fit residues: 52.8293 Evaluate side-chains 166 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 414 TYR Chi-restraints excluded: chain B residue 460 TYR Chi-restraints excluded: chain B residue 465 CYS Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 691 HIS Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain B residue 866 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 129 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.141817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.114884 restraints weight = 36438.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.117807 restraints weight = 20783.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.119831 restraints weight = 14315.472| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13759 Z= 0.175 Angle : 0.663 9.491 18618 Z= 0.338 Chirality : 0.044 0.191 2006 Planarity : 0.004 0.056 2359 Dihedral : 6.931 105.809 1798 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.99 % Favored : 88.63 % Rotamer: Outliers : 2.55 % Allowed : 22.44 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.33 (0.20), residues: 1601 helix: 0.09 (0.21), residues: 614 sheet: -1.98 (0.60), residues: 74 loop : -2.85 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 590 HIS 0.005 0.001 HIS A 89 PHE 0.024 0.001 PHE A 189 TYR 0.020 0.001 TYR A 593 ARG 0.005 0.000 ARG B 517 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2459.19 seconds wall clock time: 46 minutes 31.28 seconds (2791.28 seconds total)