Starting phenix.real_space_refine on Wed Jun 11 22:43:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w7j_37339/06_2025/8w7j_37339.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w7j_37339/06_2025/8w7j_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/cci-nas-00/data/ceres_data/8w7j_37339/06_2025/8w7j_37339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w7j_37339/06_2025/8w7j_37339.map" model { file = "/net/cci-nas-00/data/ceres_data/8w7j_37339/06_2025/8w7j_37339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w7j_37339/06_2025/8w7j_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.66, per 1000 atoms: 0.64 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: 3.39 Conformation dependent library (CDL) restraints added in 3.2 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: 1.37 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: 6.82 Time building geometry restraints manager: 4.11 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: 124.020 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 38.690 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 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: 0.020 Load rotamer database and sin/cos tables:4.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.400 ------------------------------------------------------------------------------- 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= 0.250 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 Details of bonding type rmsd hydrogen bonds : bond 0.16731 ( 426) hydrogen bonds : angle 6.92841 ( 1239) covalent geometry : bond 0.00494 (13759) covalent geometry : angle 1.10159 (18618) *********************** 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 : 1.831 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: 0.2370 time to fit residues: 80.2443 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 : 1.829 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.139262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.113551 restraints weight = 34268.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.114948 restraints weight = 20184.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.116804 restraints weight = 14186.508| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 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= 0.201 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 : 10.83 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 Details of bonding type rmsd hydrogen bonds : bond 0.04666 ( 426) hydrogen bonds : angle 5.22554 ( 1239) covalent geometry : bond 0.00442 (13759) covalent geometry : angle 0.72922 (18618) *********************** 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 : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 TYR cc_start: 0.8446 (m-10) cc_final: 0.8193 (m-80) REVERT: A 568 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7215 (pm20) REVERT: A 593 TYR cc_start: 0.8578 (t80) cc_final: 0.8332 (t80) REVERT: A 747 THR cc_start: 0.8639 (p) cc_final: 0.8398 (p) REVERT: B 26 TYR cc_start: 0.7086 (m-10) cc_final: 0.6886 (m-80) REVERT: B 80 CYS cc_start: 0.9014 (m) cc_final: 0.8715 (m) REVERT: B 324 LYS cc_start: 0.5323 (mmtt) cc_final: 0.4862 (mmtp) REVERT: B 678 ASN cc_start: 0.7253 (t0) cc_final: 0.6987 (t0) REVERT: B 744 TYR cc_start: 0.7335 (m-80) cc_final: 0.6799 (m-10) outliers start: 27 outliers final: 17 residues processed: 178 average time/residue: 0.2032 time to fit residues: 56.9700 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 : 1.616 ------------------------------------------------------------------------------- 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 80 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 159 optimal weight: 4.9990 chunk 3 optimal weight: 0.3980 chunk 45 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 100 optimal weight: 40.0000 chunk 68 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 B 46 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.144270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.117575 restraints weight = 36992.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.120551 restraints weight = 21440.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.122533 restraints weight = 14818.214| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13759 Z= 0.133 Angle : 0.640 7.792 18618 Z= 0.336 Chirality : 0.044 0.197 2006 Planarity : 0.004 0.053 2359 Dihedral : 7.329 117.565 1799 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.68 % Favored : 89.94 % Rotamer: Outliers : 2.27 % Allowed : 15.28 % Favored : 82.45 % 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: -2.55 (0.20), residues: 1601 helix: -0.14 (0.21), residues: 607 sheet: -1.45 (0.62), residues: 72 loop : -2.99 (0.18), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 395 HIS 0.005 0.001 HIS A 9 PHE 0.028 0.001 PHE A 573 TYR 0.019 0.001 TYR B 414 ARG 0.003 0.000 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 426) hydrogen bonds : angle 4.85971 ( 1239) covalent geometry : bond 0.00295 (13759) covalent geometry : angle 0.64038 (18618) *********************** 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 189 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.7008 (mtt90) cc_final: 0.6794 (mtt90) REVERT: A 260 TYR cc_start: 0.8176 (m-10) cc_final: 0.7961 (m-80) REVERT: A 363 ASP cc_start: 0.7662 (t0) cc_final: 0.7334 (t0) REVERT: A 568 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7286 (pm20) REVERT: A 593 TYR cc_start: 0.8380 (t80) cc_final: 0.8126 (t80) REVERT: A 747 THR cc_start: 0.8415 (p) cc_final: 0.8190 (p) REVERT: B 80 CYS cc_start: 0.8921 (m) cc_final: 0.8613 (m) REVERT: B 744 TYR cc_start: 0.7248 (m-80) cc_final: 0.6761 (m-80) outliers start: 33 outliers final: 21 residues processed: 179 average time/residue: 0.2132 time to fit residues: 61.1037 Evaluate side-chains 154 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 PHE 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 820 TYR 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 754 LEU Chi-restraints excluded: chain B residue 779 ASP 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 65 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 159 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 481 HIS A 530 GLN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 HIS ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.136169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.111398 restraints weight = 33877.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.111643 restraints weight = 21783.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.112904 restraints weight = 16697.883| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 13759 Z= 0.239 Angle : 0.750 11.447 18618 Z= 0.390 Chirality : 0.046 0.210 2006 Planarity : 0.005 0.064 2359 Dihedral : 7.528 115.280 1798 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.12 % Favored : 87.57 % Rotamer: Outliers : 3.30 % Allowed : 17.48 % Favored : 79.22 % 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: -2.67 (0.20), residues: 1601 helix: -0.19 (0.21), residues: 609 sheet: -1.98 (0.61), residues: 74 loop : -3.05 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 395 HIS 0.016 0.001 HIS B 9 PHE 0.028 0.002 PHE B 13 TYR 0.044 0.002 TYR B 656 ARG 0.004 0.000 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 426) hydrogen bonds : angle 5.24461 ( 1239) covalent geometry : bond 0.00543 (13759) covalent geometry : angle 0.74952 (18618) *********************** 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 190 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7736 (tmm) cc_final: 0.7478 (ttm) REVERT: A 115 CYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8053 (p) REVERT: A 356 LEU cc_start: 0.8161 (mp) cc_final: 0.7841 (tp) REVERT: A 363 ASP cc_start: 0.7805 (t0) cc_final: 0.7538 (t0) REVERT: A 392 PHE cc_start: 0.6765 (m-10) cc_final: 0.6397 (m-80) REVERT: B 80 CYS cc_start: 0.9044 (m) cc_final: 0.8736 (m) REVERT: B 636 LEU cc_start: 0.8419 (pp) cc_final: 0.8206 (tp) REVERT: B 744 TYR cc_start: 0.7299 (m-10) cc_final: 0.6734 (m-80) REVERT: B 848 PHE cc_start: 0.7902 (t80) cc_final: 0.7685 (t80) outliers start: 48 outliers final: 33 residues processed: 175 average time/residue: 0.2534 time to fit residues: 71.0096 Evaluate side-chains 161 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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 254 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 568 GLU Chi-restraints excluded: chain A residue 591 LEU 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 B residue 9 HIS 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 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 Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 855 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 2 optimal weight: 0.0670 chunk 119 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 124 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 18 optimal weight: 0.0050 overall best weight: 0.4532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 HIS B 564 GLN B 683 ASN B 812 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.145132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.118536 restraints weight = 36939.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.121580 restraints weight = 21180.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.123547 restraints weight = 14784.399| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 13759 Z= 0.109 Angle : 0.623 8.500 18618 Z= 0.322 Chirality : 0.044 0.228 2006 Planarity : 0.004 0.053 2359 Dihedral : 7.004 115.314 1798 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.62 % Favored : 90.07 % Rotamer: Outliers : 1.86 % Allowed : 20.30 % Favored : 77.84 % 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: -2.32 (0.20), residues: 1601 helix: 0.17 (0.22), residues: 603 sheet: -1.59 (0.62), residues: 74 loop : -2.90 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 590 HIS 0.012 0.001 HIS B 9 PHE 0.030 0.001 PHE A 573 TYR 0.034 0.001 TYR B 656 ARG 0.007 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 426) hydrogen bonds : angle 4.60396 ( 1239) covalent geometry : bond 0.00239 (13759) covalent geometry : angle 0.62281 (18618) *********************** 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 184 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 CYS cc_start: 0.8164 (p) cc_final: 0.7826 (p) REVERT: A 232 TYR cc_start: 0.7058 (OUTLIER) cc_final: 0.6843 (m-80) REVERT: A 356 LEU cc_start: 0.7791 (mp) cc_final: 0.7475 (tp) REVERT: A 363 ASP cc_start: 0.7823 (t0) cc_final: 0.7523 (t0) REVERT: A 749 SER cc_start: 0.8682 (p) cc_final: 0.8221 (t) REVERT: B 12 PHE cc_start: 0.5263 (OUTLIER) cc_final: 0.4601 (t80) REVERT: B 80 CYS cc_start: 0.8980 (m) cc_final: 0.8643 (m) REVERT: B 154 LEU cc_start: 0.7762 (pt) cc_final: 0.7194 (tp) REVERT: B 509 GLN cc_start: 0.7772 (mp-120) cc_final: 0.7528 (mp10) REVERT: B 568 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.8976 (pm20) REVERT: B 590 TRP cc_start: 0.8709 (t60) cc_final: 0.8479 (t60) REVERT: B 744 TYR cc_start: 0.7107 (m-10) cc_final: 0.6673 (m-80) outliers start: 27 outliers final: 12 residues processed: 173 average time/residue: 0.2696 time to fit residues: 74.5587 Evaluate side-chains 153 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 426 THR 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 820 TYR Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 414 TYR Chi-restraints excluded: chain B residue 513 GLU 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 820 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 106 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 162 optimal weight: 0.3980 chunk 105 optimal weight: 20.0000 chunk 2 optimal weight: 0.0270 chunk 24 optimal weight: 6.9990 chunk 40 optimal weight: 0.1980 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 HIS B 355 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.143595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.116703 restraints weight = 33708.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.119776 restraints weight = 19302.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.121831 restraints weight = 13255.641| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13759 Z= 0.110 Angle : 0.620 12.068 18618 Z= 0.318 Chirality : 0.043 0.186 2006 Planarity : 0.004 0.052 2359 Dihedral : 6.767 109.419 1798 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.81 % Favored : 89.82 % Rotamer: Outliers : 2.27 % Allowed : 20.03 % Favored : 77.70 % 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: -2.22 (0.20), residues: 1601 helix: 0.26 (0.22), residues: 609 sheet: -1.64 (0.61), residues: 74 loop : -2.85 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 395 HIS 0.004 0.001 HIS A 89 PHE 0.034 0.001 PHE A 573 TYR 0.018 0.001 TYR B 414 ARG 0.007 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03247 ( 426) hydrogen bonds : angle 4.44208 ( 1239) covalent geometry : bond 0.00236 (13759) covalent geometry : angle 0.61976 (18618) *********************** 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 193 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 TYR cc_start: 0.7000 (OUTLIER) cc_final: 0.6712 (m-80) REVERT: A 363 ASP cc_start: 0.7834 (t0) cc_final: 0.7537 (t0) REVERT: A 507 TYR cc_start: 0.8134 (t80) cc_final: 0.7833 (t80) REVERT: A 593 TYR cc_start: 0.8525 (t80) cc_final: 0.8312 (t80) REVERT: A 749 SER cc_start: 0.8756 (p) cc_final: 0.8275 (t) REVERT: B 12 PHE cc_start: 0.5148 (OUTLIER) cc_final: 0.4889 (t80) REVERT: B 80 CYS cc_start: 0.8988 (m) cc_final: 0.8631 (m) REVERT: B 154 LEU cc_start: 0.7731 (pt) cc_final: 0.7171 (tp) REVERT: B 509 GLN cc_start: 0.7752 (mp-120) cc_final: 0.7434 (mp10) REVERT: B 510 TRP cc_start: 0.7090 (t-100) cc_final: 0.6447 (t-100) REVERT: B 559 TYR cc_start: 0.8883 (m-80) cc_final: 0.8647 (m-80) REVERT: B 568 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.8969 (pm20) REVERT: B 744 TYR cc_start: 0.7129 (m-10) cc_final: 0.6619 (m-80) outliers start: 33 outliers final: 21 residues processed: 182 average time/residue: 0.2703 time to fit residues: 76.0722 Evaluate side-chains 162 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 2.186 ------------------------------------------------------------------------------- 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 426 THR 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 820 TYR Chi-restraints excluded: chain A residue 826 ILE 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 513 GLU 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 745 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 820 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 92 optimal weight: 0.0020 chunk 7 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 105 optimal weight: 30.0000 chunk 149 optimal weight: 30.0000 chunk 72 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.143569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.117392 restraints weight = 36877.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.120509 restraints weight = 21911.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.121758 restraints weight = 13981.166| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13759 Z= 0.140 Angle : 0.647 8.506 18618 Z= 0.332 Chirality : 0.044 0.193 2006 Planarity : 0.004 0.051 2359 Dihedral : 6.869 114.524 1798 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.06 % Favored : 89.57 % Rotamer: Outliers : 2.75 % Allowed : 20.58 % Favored : 76.67 % 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: -2.21 (0.20), residues: 1601 helix: 0.24 (0.21), residues: 616 sheet: -1.82 (0.60), residues: 74 loop : -2.84 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 405 HIS 0.007 0.001 HIS A 9 PHE 0.015 0.001 PHE A 534 TYR 0.019 0.001 TYR B 406 ARG 0.006 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 426) hydrogen bonds : angle 4.62769 ( 1239) covalent geometry : bond 0.00324 (13759) covalent geometry : angle 0.64661 (18618) *********************** 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 181 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 TYR cc_start: 0.7030 (OUTLIER) cc_final: 0.6733 (m-80) REVERT: A 363 ASP cc_start: 0.7896 (t0) cc_final: 0.7602 (t0) REVERT: A 507 TYR cc_start: 0.8032 (t80) cc_final: 0.7683 (t80) REVERT: B 12 PHE cc_start: 0.5362 (OUTLIER) cc_final: 0.4892 (t80) REVERT: B 80 CYS cc_start: 0.8940 (m) cc_final: 0.8575 (m) REVERT: B 154 LEU cc_start: 0.7736 (pt) cc_final: 0.7164 (tp) REVERT: B 510 TRP cc_start: 0.7274 (t-100) cc_final: 0.6539 (t-100) REVERT: B 559 TYR cc_start: 0.8950 (m-80) cc_final: 0.8726 (m-80) REVERT: B 568 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.8909 (pm20) REVERT: B 744 TYR cc_start: 0.7276 (m-10) cc_final: 0.6734 (m-80) outliers start: 40 outliers final: 30 residues processed: 166 average time/residue: 0.2624 time to fit residues: 68.6478 Evaluate side-chains 163 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 1.586 ------------------------------------------------------------------------------- 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 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 356 LEU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 536 ASP 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 820 TYR Chi-restraints excluded: chain A residue 826 ILE 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 344 PHE 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 567 ASN 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 745 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 820 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 71 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 HIS ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.138133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.113062 restraints weight = 34418.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.113888 restraints weight = 21675.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.114955 restraints weight = 16276.113| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 13759 Z= 0.171 Angle : 0.683 9.028 18618 Z= 0.351 Chirality : 0.045 0.199 2006 Planarity : 0.004 0.050 2359 Dihedral : 7.004 116.846 1798 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.06 % Favored : 88.51 % Rotamer: Outliers : 2.89 % Allowed : 20.58 % Favored : 76.53 % 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: -2.33 (0.20), residues: 1601 helix: 0.10 (0.21), residues: 618 sheet: -1.90 (0.60), residues: 74 loop : -2.87 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 590 HIS 0.009 0.001 HIS A 9 PHE 0.034 0.002 PHE A 573 TYR 0.020 0.002 TYR A 45 ARG 0.007 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 426) hydrogen bonds : angle 4.84372 ( 1239) covalent geometry : bond 0.00395 (13759) covalent geometry : angle 0.68259 (18618) *********************** 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 177 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 CYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7994 (p) REVERT: A 232 TYR cc_start: 0.6977 (OUTLIER) cc_final: 0.6685 (m-80) REVERT: A 356 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7326 (tt) REVERT: A 363 ASP cc_start: 0.7867 (t0) cc_final: 0.7527 (t0) REVERT: A 859 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7434 (pmm) REVERT: B 12 PHE cc_start: 0.5535 (OUTLIER) cc_final: 0.4974 (t80) REVERT: B 80 CYS cc_start: 0.8939 (m) cc_final: 0.8611 (m) REVERT: B 83 MET cc_start: 0.8445 (pmm) cc_final: 0.8202 (pmm) REVERT: B 154 LEU cc_start: 0.7790 (pt) cc_final: 0.7234 (tp) REVERT: B 510 TRP cc_start: 0.7366 (t-100) cc_final: 0.6563 (t-100) REVERT: B 559 TYR cc_start: 0.8924 (m-80) cc_final: 0.8718 (m-80) REVERT: B 568 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.8939 (pm20) REVERT: B 744 TYR cc_start: 0.7419 (m-10) cc_final: 0.6854 (m-80) outliers start: 42 outliers final: 29 residues processed: 163 average time/residue: 0.2587 time to fit residues: 66.8151 Evaluate side-chains 165 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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 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 356 LEU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 536 ASP 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 820 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain B residue 12 PHE 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 471 ILE Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 567 ASN 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 779 ASP Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 820 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 111 optimal weight: 0.0010 chunk 76 optimal weight: 0.8980 chunk 77 optimal weight: 0.0070 chunk 13 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 0.0770 chunk 113 optimal weight: 8.9990 overall best weight: 0.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.147032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.121201 restraints weight = 36203.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.124205 restraints weight = 20717.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.126227 restraints weight = 14240.153| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13759 Z= 0.112 Angle : 0.631 10.347 18618 Z= 0.321 Chirality : 0.044 0.182 2006 Planarity : 0.004 0.051 2359 Dihedral : 6.643 120.190 1798 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.74 % Favored : 89.94 % Rotamer: Outliers : 2.13 % Allowed : 21.68 % Favored : 76.19 % 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: -2.08 (0.21), residues: 1601 helix: 0.42 (0.22), residues: 601 sheet: -1.84 (0.60), residues: 74 loop : -2.75 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 590 HIS 0.004 0.001 HIS A 89 PHE 0.037 0.001 PHE A 573 TYR 0.022 0.001 TYR B 460 ARG 0.008 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 426) hydrogen bonds : angle 4.43690 ( 1239) covalent geometry : bond 0.00236 (13759) covalent geometry : angle 0.63088 (18618) *********************** 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 185 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 CYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7706 (p) REVERT: A 364 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8402 (mm-30) REVERT: A 507 TYR cc_start: 0.7987 (t80) cc_final: 0.7777 (t80) REVERT: A 859 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7302 (pmm) REVERT: B 80 CYS cc_start: 0.8894 (m) cc_final: 0.8542 (m) REVERT: B 83 MET cc_start: 0.8382 (pmm) cc_final: 0.8145 (pmm) REVERT: B 154 LEU cc_start: 0.7736 (pt) cc_final: 0.7153 (tp) REVERT: B 509 GLN cc_start: 0.7727 (mp-120) cc_final: 0.7476 (mp10) REVERT: B 510 TRP cc_start: 0.7229 (t-100) cc_final: 0.6403 (t-100) REVERT: B 568 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8900 (pm20) REVERT: B 744 TYR cc_start: 0.7362 (m-10) cc_final: 0.6858 (m-80) outliers start: 31 outliers final: 22 residues processed: 172 average time/residue: 0.2281 time to fit residues: 60.3648 Evaluate side-chains 167 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 CYS 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 536 ASP 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 820 TYR Chi-restraints excluded: chain A residue 826 ILE 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 471 ILE Chi-restraints excluded: chain B residue 513 GLU 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 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 46 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 47 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 HIS A 481 HIS ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.139651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.114530 restraints weight = 33778.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.116299 restraints weight = 20414.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.117540 restraints weight = 13806.720| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13759 Z= 0.163 Angle : 0.675 9.732 18618 Z= 0.346 Chirality : 0.044 0.195 2006 Planarity : 0.004 0.050 2359 Dihedral : 6.805 119.521 1798 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.12 % Favored : 89.44 % Rotamer: Outliers : 1.93 % Allowed : 21.82 % Favored : 76.26 % 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: -2.16 (0.21), residues: 1601 helix: 0.31 (0.22), residues: 607 sheet: -1.93 (0.59), residues: 74 loop : -2.78 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 395 HIS 0.005 0.001 HIS B 89 PHE 0.022 0.002 PHE B 12 TYR 0.020 0.002 TYR A 18 ARG 0.008 0.001 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 426) hydrogen bonds : angle 4.74075 ( 1239) covalent geometry : bond 0.00377 (13759) covalent geometry : angle 0.67533 (18618) ********************** 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 169 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 CYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7939 (p) REVERT: A 356 LEU cc_start: 0.7572 (mt) cc_final: 0.7301 (tp) REVERT: A 507 TYR cc_start: 0.8186 (t80) cc_final: 0.7887 (t80) REVERT: A 859 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7465 (pmm) REVERT: B 80 CYS cc_start: 0.8942 (m) cc_final: 0.8653 (m) REVERT: B 83 MET cc_start: 0.8344 (pmm) cc_final: 0.8114 (pmm) REVERT: B 510 TRP cc_start: 0.7185 (t-100) cc_final: 0.6819 (t-100) REVERT: B 568 GLU cc_start: 0.9296 (OUTLIER) cc_final: 0.8944 (pm20) REVERT: B 744 TYR cc_start: 0.7437 (m-10) cc_final: 0.6849 (m-80) outliers start: 28 outliers final: 23 residues processed: 159 average time/residue: 0.2170 time to fit residues: 54.3989 Evaluate side-chains 160 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 CYS 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 536 ASP Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 788 LEU 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 42 GLU 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 471 ILE Chi-restraints excluded: chain B residue 513 GLU 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 779 ASP Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 820 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 98 optimal weight: 0.0070 chunk 1 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 481 HIS ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN B 509 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.139753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.115576 restraints weight = 36731.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.116054 restraints weight = 22794.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.117200 restraints weight = 16231.975| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 13759 Z= 0.199 Angle : 0.720 9.320 18618 Z= 0.372 Chirality : 0.046 0.266 2006 Planarity : 0.004 0.050 2359 Dihedral : 7.012 117.609 1798 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.37 % Favored : 88.19 % Rotamer: Outliers : 2.20 % Allowed : 21.82 % Favored : 75.98 % 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: -2.44 (0.20), residues: 1601 helix: 0.04 (0.21), residues: 617 sheet: -2.18 (0.56), residues: 80 loop : -2.95 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 395 HIS 0.005 0.001 HIS B 9 PHE 0.033 0.002 PHE A 573 TYR 0.024 0.002 TYR A 45 ARG 0.009 0.001 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 426) hydrogen bonds : angle 5.04997 ( 1239) covalent geometry : bond 0.00458 (13759) covalent geometry : angle 0.72031 (18618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4514.93 seconds wall clock time: 81 minutes 50.76 seconds (4910.76 seconds total)