Starting phenix.real_space_refine on Sat Aug 23 16:30:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w7j_37339/08_2025/8w7j_37339.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w7j_37339/08_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_37339/08_2025/8w7j_37339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w7j_37339/08_2025/8w7j_37339.map" model { file = "/net/cci-nas-00/data/ceres_data/8w7j_37339/08_2025/8w7j_37339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w7j_37339/08_2025/8w7j_37339.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.31, per 1000 atoms: 0.17 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: 0.92 Conformation dependent library (CDL) restraints added in 585.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.46 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: 1.69 Time building geometry restraints manager: 1.28 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: 1.090 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.810 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.490 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.013 0.001 ARG A 84 TYR 0.035 0.002 TYR B 656 PHE 0.048 0.002 PHE A 573 TRP 0.021 0.002 TRP A 395 HIS 0.015 0.002 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00494 (13759) covalent geometry : angle 1.10159 (18618) hydrogen bonds : bond 0.16731 ( 426) hydrogen bonds : angle 6.92841 ( 1239) *********************** 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 : 0.510 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: 0.0952 time to fit residues: 32.2600 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 : 0.543 ------------------------------------------------------------------------------- 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 98 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 379 ASN A 432 GLN A 737 GLN B 33 ASN B 345 HIS B 450 HIS B 509 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN B 683 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.136828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.112277 restraints weight = 34540.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.112583 restraints weight = 22380.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.113827 restraints weight = 17210.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.114298 restraints weight = 14048.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.114582 restraints weight = 12396.759| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 13759 Z= 0.252 Angle : 0.790 9.701 18618 Z= 0.418 Chirality : 0.048 0.208 2006 Planarity : 0.005 0.062 2359 Dihedral : 7.952 115.067 1803 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.50 % Allowed : 11.56 % Favored : 87.95 % Rotamer: Outliers : 2.41 % Allowed : 12.32 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.96 (0.19), residues: 1601 helix: -0.62 (0.21), residues: 609 sheet: -1.72 (0.61), residues: 74 loop : -3.11 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 396 TYR 0.037 0.002 TYR B 656 PHE 0.021 0.002 PHE A 503 TRP 0.025 0.002 TRP A 395 HIS 0.012 0.002 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00558 (13759) covalent geometry : angle 0.79002 (18618) hydrogen bonds : bond 0.05147 ( 426) hydrogen bonds : angle 5.43846 ( 1239) *********************** 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 188 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7378 (pm20) REVERT: A 585 LYS cc_start: 0.7806 (tttp) cc_final: 0.7604 (tttm) REVERT: A 593 TYR cc_start: 0.8543 (t80) cc_final: 0.8253 (t80) REVERT: A 747 THR cc_start: 0.8687 (p) cc_final: 0.8467 (p) REVERT: B 80 CYS cc_start: 0.8968 (m) cc_final: 0.8653 (m) REVERT: B 324 LYS cc_start: 0.5386 (mmtt) cc_final: 0.4878 (mmtp) REVERT: B 742 LEU cc_start: 0.8215 (mp) cc_final: 0.7942 (mp) REVERT: B 744 TYR cc_start: 0.7308 (m-80) cc_final: 0.6760 (m-80) outliers start: 35 outliers final: 23 residues processed: 176 average time/residue: 0.0909 time to fit residues: 25.6322 Evaluate side-chains 163 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 432 GLN 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 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 420 VAL Chi-restraints excluded: chain B residue 465 CYS Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 537 LEU 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 8 optimal weight: 4.9990 chunk 85 optimal weight: 40.0000 chunk 93 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 HIS B 450 HIS B 509 GLN B 564 GLN ** B 567 ASN ** 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 = 0.4112 r_free = 0.4112 target = 0.138918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.113403 restraints weight = 37616.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.114362 restraints weight = 23742.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.116383 restraints weight = 16756.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.116820 restraints weight = 13027.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.116949 restraints weight = 11959.472| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 13759 Z= 0.227 Angle : 0.733 8.254 18618 Z= 0.386 Chirality : 0.046 0.212 2006 Planarity : 0.005 0.058 2359 Dihedral : 7.742 115.657 1799 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.24 % Favored : 88.38 % Rotamer: Outliers : 3.10 % Allowed : 16.59 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.77 (0.20), residues: 1601 helix: -0.35 (0.21), residues: 609 sheet: -1.90 (0.61), residues: 74 loop : -3.07 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 396 TYR 0.033 0.002 TYR B 656 PHE 0.024 0.002 PHE A 573 TRP 0.019 0.002 TRP A 395 HIS 0.008 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00511 (13759) covalent geometry : angle 0.73279 (18618) hydrogen bonds : bond 0.04667 ( 426) hydrogen bonds : angle 5.28973 ( 1239) *********************** 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 196 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.6760 (m-10) cc_final: 0.6509 (m-80) REVERT: A 534 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.8005 (m-80) REVERT: B 80 CYS cc_start: 0.9004 (m) cc_final: 0.8680 (m) REVERT: B 83 MET cc_start: 0.8365 (pmm) cc_final: 0.8105 (pmm) REVERT: B 644 LYS cc_start: 0.9220 (pttp) cc_final: 0.9018 (mmmt) REVERT: B 744 TYR cc_start: 0.7314 (m-80) cc_final: 0.6875 (m-80) outliers start: 45 outliers final: 31 residues processed: 183 average time/residue: 0.1009 time to fit residues: 29.0914 Evaluate side-chains 163 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 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 534 PHE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 414 TYR Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 465 CYS Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 604 LEU 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 691 HIS Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 855 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 157 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 142 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 HIS A 530 GLN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 HIS B 564 GLN ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN B 812 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.139712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.114021 restraints weight = 37028.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.115273 restraints weight = 23067.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.116705 restraints weight = 16275.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.117111 restraints weight = 13415.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.117461 restraints weight = 12217.603| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 13759 Z= 0.183 Angle : 0.691 9.758 18618 Z= 0.361 Chirality : 0.045 0.246 2006 Planarity : 0.004 0.058 2359 Dihedral : 7.518 114.780 1799 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.81 % Favored : 87.88 % Rotamer: Outliers : 3.23 % Allowed : 18.72 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.69 (0.20), residues: 1601 helix: -0.19 (0.21), residues: 607 sheet: -2.02 (0.62), residues: 74 loop : -3.07 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 84 TYR 0.026 0.002 TYR B 656 PHE 0.028 0.002 PHE A 573 TRP 0.018 0.001 TRP A 395 HIS 0.008 0.001 HIS B 9 Details of bonding type rmsd covalent geometry : bond 0.00416 (13759) covalent geometry : angle 0.69084 (18618) hydrogen bonds : bond 0.04270 ( 426) hydrogen bonds : angle 5.08225 ( 1239) *********************** 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 189 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 CYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7982 (p) REVERT: A 232 TYR cc_start: 0.7209 (OUTLIER) cc_final: 0.6881 (m-80) REVERT: A 363 ASP cc_start: 0.7734 (t0) cc_final: 0.7404 (t0) REVERT: A 392 PHE cc_start: 0.6520 (m-10) cc_final: 0.6311 (m-80) REVERT: A 507 TYR cc_start: 0.8173 (t80) cc_final: 0.7967 (t80) REVERT: A 534 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: B 12 PHE cc_start: 0.5781 (OUTLIER) cc_final: 0.5475 (t80) REVERT: B 80 CYS cc_start: 0.9050 (m) cc_final: 0.8726 (m) REVERT: B 83 MET cc_start: 0.8327 (pmm) cc_final: 0.8054 (pmm) REVERT: B 154 LEU cc_start: 0.7776 (pt) cc_final: 0.7251 (tp) REVERT: B 644 LYS cc_start: 0.9231 (pttp) cc_final: 0.8995 (mmmt) REVERT: B 744 TYR cc_start: 0.7181 (m-10) cc_final: 0.6702 (m-80) outliers start: 47 outliers final: 29 residues processed: 176 average time/residue: 0.0870 time to fit residues: 24.4076 Evaluate side-chains 161 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 310 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 349 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 567 ASN Chi-restraints excluded: chain B residue 647 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 820 TYR Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 132 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 HIS ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS B 564 GLN ** 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 = 0.4095 r_free = 0.4095 target = 0.137614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.112848 restraints weight = 37407.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.113167 restraints weight = 23271.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.114182 restraints weight = 17996.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.114462 restraints weight = 15102.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.114624 restraints weight = 13595.900| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 13759 Z= 0.219 Angle : 0.719 9.095 18618 Z= 0.377 Chirality : 0.046 0.239 2006 Planarity : 0.005 0.057 2359 Dihedral : 7.577 115.001 1798 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.55 % Favored : 87.07 % Rotamer: Outliers : 4.34 % Allowed : 18.86 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.72 (0.20), residues: 1601 helix: -0.17 (0.21), residues: 609 sheet: -2.18 (0.57), residues: 80 loop : -3.11 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 517 TYR 0.024 0.002 TYR A 45 PHE 0.029 0.002 PHE A 573 TRP 0.018 0.002 TRP A 395 HIS 0.007 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00497 (13759) covalent geometry : angle 0.71876 (18618) hydrogen bonds : bond 0.04509 ( 426) hydrogen bonds : angle 5.23860 ( 1239) *********************** 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 203 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 140 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7681 (tmm) cc_final: 0.7387 (ttm) REVERT: A 232 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.6956 (m-80) REVERT: A 260 TYR cc_start: 0.8364 (m-80) cc_final: 0.8149 (m-80) REVERT: A 291 TRP cc_start: 0.6285 (OUTLIER) cc_final: 0.6019 (m-10) REVERT: A 363 ASP cc_start: 0.7823 (t0) cc_final: 0.7522 (t0) REVERT: A 392 PHE cc_start: 0.6580 (m-80) cc_final: 0.6318 (m-80) REVERT: A 534 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.8067 (m-80) REVERT: B 80 CYS cc_start: 0.9022 (m) cc_final: 0.8680 (m) REVERT: B 83 MET cc_start: 0.8284 (pmm) cc_final: 0.7939 (pmm) REVERT: B 154 LEU cc_start: 0.7790 (pt) cc_final: 0.7219 (tp) REVERT: B 509 GLN cc_start: 0.7948 (mp-120) cc_final: 0.7692 (mp10) REVERT: B 559 TYR cc_start: 0.9007 (m-80) cc_final: 0.8798 (m-80) REVERT: B 644 LYS cc_start: 0.9208 (pttp) cc_final: 0.8977 (mmmt) REVERT: B 704 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7212 (tt) REVERT: B 744 TYR cc_start: 0.7281 (m-10) cc_final: 0.6768 (m-80) REVERT: B 865 ILE cc_start: 0.5525 (OUTLIER) cc_final: 0.5125 (mt) outliers start: 63 outliers final: 44 residues processed: 185 average time/residue: 0.0807 time to fit residues: 23.8313 Evaluate side-chains 178 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 291 TRP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 689 TYR Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 414 TYR Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 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 688 LEU Chi-restraints excluded: chain B residue 691 HIS Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 865 ILE Chi-restraints excluded: chain B residue 866 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 124 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 0.0050 chunk 6 optimal weight: 0.4980 chunk 67 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN B 676 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.143133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.115954 restraints weight = 36698.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.119053 restraints weight = 20908.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.121073 restraints weight = 14381.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.122400 restraints weight = 11337.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.123124 restraints weight = 9679.426| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13759 Z= 0.113 Angle : 0.632 8.917 18618 Z= 0.325 Chirality : 0.043 0.189 2006 Planarity : 0.004 0.055 2359 Dihedral : 7.033 109.879 1798 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.87 % Favored : 89.76 % Rotamer: Outliers : 2.68 % Allowed : 21.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.39 (0.20), residues: 1601 helix: 0.11 (0.21), residues: 603 sheet: -1.77 (0.61), residues: 74 loop : -2.93 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 84 TYR 0.018 0.001 TYR B 414 PHE 0.034 0.001 PHE A 573 TRP 0.020 0.001 TRP B 590 HIS 0.008 0.001 HIS B 9 Details of bonding type rmsd covalent geometry : bond 0.00250 (13759) covalent geometry : angle 0.63236 (18618) hydrogen bonds : bond 0.03537 ( 426) hydrogen bonds : angle 4.63651 ( 1239) *********************** 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 191 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 CYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7632 (p) REVERT: A 232 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.6670 (m-80) REVERT: A 363 ASP cc_start: 0.7717 (t0) cc_final: 0.7478 (t0) REVERT: A 392 PHE cc_start: 0.6516 (m-80) cc_final: 0.6288 (m-80) REVERT: A 859 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7268 (pmm) REVERT: B 80 CYS cc_start: 0.8997 (m) cc_final: 0.8663 (m) REVERT: B 83 MET cc_start: 0.8229 (pmm) cc_final: 0.7973 (pmm) REVERT: B 154 LEU cc_start: 0.7739 (pt) cc_final: 0.7155 (tp) REVERT: B 405 TRP cc_start: 0.7401 (t60) cc_final: 0.7170 (t60) REVERT: B 559 TYR cc_start: 0.8785 (m-80) cc_final: 0.8578 (m-80) REVERT: B 644 LYS cc_start: 0.9260 (pttp) cc_final: 0.9017 (mmmt) REVERT: B 744 TYR cc_start: 0.7175 (m-10) cc_final: 0.6761 (m-80) outliers start: 39 outliers final: 26 residues processed: 177 average time/residue: 0.0867 time to fit residues: 24.1598 Evaluate side-chains 157 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain B residue 44 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 567 ASN Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 691 HIS Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 820 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 149 optimal weight: 40.0000 chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 HIS ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN B 410 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.136499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.110557 restraints weight = 36574.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.112302 restraints weight = 22773.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.113692 restraints weight = 14759.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.114169 restraints weight = 12961.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.114165 restraints weight = 12061.710| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 13759 Z= 0.247 Angle : 0.770 11.939 18618 Z= 0.395 Chirality : 0.047 0.220 2006 Planarity : 0.005 0.056 2359 Dihedral : 7.469 114.213 1798 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.37 % Allowed : 13.37 % Favored : 86.26 % Rotamer: Outliers : 3.92 % Allowed : 21.82 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.71 (0.20), residues: 1601 helix: -0.17 (0.21), residues: 611 sheet: -2.17 (0.57), residues: 80 loop : -3.11 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 99 TYR 0.027 0.002 TYR A 45 PHE 0.029 0.002 PHE A 573 TRP 0.027 0.002 TRP B 43 HIS 0.008 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00563 (13759) covalent geometry : angle 0.76995 (18618) hydrogen bonds : bond 0.04652 ( 426) hydrogen bonds : angle 5.26300 ( 1239) *********************** 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 191 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 134 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7704 (tmm) cc_final: 0.7422 (ttm) REVERT: A 98 MET cc_start: 0.8554 (tpp) cc_final: 0.8280 (tpp) REVERT: A 115 CYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7983 (p) REVERT: A 166 GLU cc_start: 0.5968 (OUTLIER) cc_final: 0.5729 (pm20) REVERT: A 232 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.6887 (m-80) REVERT: A 363 ASP cc_start: 0.7812 (t0) cc_final: 0.7553 (t0) REVERT: A 392 PHE cc_start: 0.6698 (m-80) cc_final: 0.6306 (m-80) REVERT: A 640 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7423 (pp20) REVERT: A 859 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7566 (pmm) REVERT: B 12 PHE cc_start: 0.5961 (OUTLIER) cc_final: 0.5566 (t80) REVERT: B 80 CYS cc_start: 0.8989 (m) cc_final: 0.8695 (m) REVERT: B 154 LEU cc_start: 0.7774 (pt) cc_final: 0.7202 (tp) REVERT: B 286 TRP cc_start: 0.7833 (t60) cc_final: 0.6908 (t60) REVERT: B 295 PHE cc_start: 0.7462 (m-10) cc_final: 0.7119 (m-10) REVERT: B 568 GLU cc_start: 0.9314 (OUTLIER) cc_final: 0.8634 (pm20) REVERT: B 636 LEU cc_start: 0.8417 (pp) cc_final: 0.8114 (tp) REVERT: B 744 TYR cc_start: 0.7369 (m-10) cc_final: 0.6794 (m-80) outliers start: 57 outliers final: 42 residues processed: 173 average time/residue: 0.0760 time to fit residues: 21.2592 Evaluate side-chains 172 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 123 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 383 VAL 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 506 THR Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 730 ASN Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 12 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 435 ILE 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 688 LEU Chi-restraints excluded: chain B residue 691 HIS Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 865 ILE Chi-restraints excluded: chain B residue 866 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 123 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 125 optimal weight: 0.5980 chunk 161 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 HIS A 676 GLN B 509 GLN B 544 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 = 0.4124 r_free = 0.4124 target = 0.139764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.113224 restraints weight = 36140.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.115771 restraints weight = 22258.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.117083 restraints weight = 14260.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.117619 restraints weight = 11894.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.118017 restraints weight = 11257.905| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13759 Z= 0.149 Angle : 0.682 9.266 18618 Z= 0.349 Chirality : 0.045 0.282 2006 Planarity : 0.004 0.055 2359 Dihedral : 7.178 110.258 1798 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.49 % Favored : 89.13 % Rotamer: Outliers : 2.89 % Allowed : 23.33 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.20), residues: 1601 helix: 0.00 (0.21), residues: 614 sheet: -2.06 (0.57), residues: 80 loop : -2.99 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 99 TYR 0.018 0.001 TYR B 414 PHE 0.039 0.001 PHE A 573 TRP 0.034 0.002 TRP B 590 HIS 0.005 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00340 (13759) covalent geometry : angle 0.68236 (18618) hydrogen bonds : bond 0.03852 ( 426) hydrogen bonds : angle 4.84809 ( 1239) *********************** 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 174 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7679 (tmm) cc_final: 0.7340 (ttm) REVERT: A 115 CYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7780 (p) REVERT: A 166 GLU cc_start: 0.5880 (OUTLIER) cc_final: 0.5653 (pm20) REVERT: A 232 TYR cc_start: 0.7086 (OUTLIER) cc_final: 0.6833 (m-80) REVERT: A 363 ASP cc_start: 0.7789 (t0) cc_final: 0.7512 (t0) REVERT: A 392 PHE cc_start: 0.6568 (m-80) cc_final: 0.6280 (m-80) REVERT: A 640 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7348 (pp20) REVERT: A 859 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7566 (pmm) REVERT: B 12 PHE cc_start: 0.5447 (OUTLIER) cc_final: 0.5056 (t80) REVERT: B 80 CYS cc_start: 0.8931 (m) cc_final: 0.8594 (m) REVERT: B 154 LEU cc_start: 0.7770 (pt) cc_final: 0.7159 (tp) REVERT: B 509 GLN cc_start: 0.7794 (mp-120) cc_final: 0.7581 (mp10) REVERT: B 568 GLU cc_start: 0.9311 (OUTLIER) cc_final: 0.9061 (pm20) REVERT: B 590 TRP cc_start: 0.9130 (OUTLIER) cc_final: 0.8895 (t-100) REVERT: B 644 LYS cc_start: 0.9327 (pttp) cc_final: 0.9006 (tmtt) REVERT: B 744 TYR cc_start: 0.7290 (m-10) cc_final: 0.6837 (m-80) outliers start: 42 outliers final: 29 residues processed: 162 average time/residue: 0.0863 time to fit residues: 21.7972 Evaluate side-chains 161 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 12 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 435 ILE 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 590 TRP Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 691 HIS Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 820 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 126 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 148 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 HIS ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.142850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.116144 restraints weight = 36304.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.119114 restraints weight = 20825.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.121082 restraints weight = 14403.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.122289 restraints weight = 11335.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.122752 restraints weight = 9714.704| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13759 Z= 0.115 Angle : 0.654 10.921 18618 Z= 0.331 Chirality : 0.044 0.204 2006 Planarity : 0.004 0.055 2359 Dihedral : 6.859 108.359 1798 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.81 % Favored : 88.82 % Rotamer: Outliers : 2.55 % Allowed : 23.40 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.28 (0.20), residues: 1601 helix: 0.19 (0.21), residues: 616 sheet: -1.86 (0.60), residues: 74 loop : -2.87 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 99 TYR 0.018 0.001 TYR A 593 PHE 0.011 0.001 PHE B 848 TRP 0.044 0.002 TRP B 590 HIS 0.004 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00252 (13759) covalent geometry : angle 0.65441 (18618) hydrogen bonds : bond 0.03420 ( 426) hydrogen bonds : angle 4.56500 ( 1239) *********************** 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 175 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.7366 (ttmt) cc_final: 0.7138 (ptmt) REVERT: A 115 CYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7672 (p) REVERT: A 363 ASP cc_start: 0.7767 (t0) cc_final: 0.7514 (t0) REVERT: A 392 PHE cc_start: 0.6437 (m-80) cc_final: 0.6202 (m-80) REVERT: A 507 TYR cc_start: 0.7991 (t80) cc_final: 0.7721 (t80) REVERT: A 640 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7375 (pp20) REVERT: A 859 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7497 (pmm) REVERT: B 12 PHE cc_start: 0.5216 (OUTLIER) cc_final: 0.4801 (t80) REVERT: B 80 CYS cc_start: 0.8873 (m) cc_final: 0.8533 (m) REVERT: B 154 LEU cc_start: 0.7732 (pt) cc_final: 0.7135 (tp) REVERT: B 405 TRP cc_start: 0.7373 (t60) cc_final: 0.7098 (t60) REVERT: B 568 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.9037 (pm20) REVERT: B 644 LYS cc_start: 0.9294 (pttp) cc_final: 0.8960 (tmtt) REVERT: B 744 TYR cc_start: 0.7310 (m-10) cc_final: 0.6782 (m-80) outliers start: 37 outliers final: 26 residues processed: 162 average time/residue: 0.0847 time to fit residues: 21.8011 Evaluate side-chains 160 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 344 PHE 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 568 GLU Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 691 HIS Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 820 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 58 optimal weight: 0.7980 chunk 131 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 106 optimal weight: 30.0000 chunk 36 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 HIS 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.140302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.114790 restraints weight = 37102.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.116241 restraints weight = 22893.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.117755 restraints weight = 15887.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.118024 restraints weight = 12749.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.118344 restraints weight = 12091.204| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 13759 Z= 0.161 Angle : 0.682 9.174 18618 Z= 0.349 Chirality : 0.045 0.247 2006 Planarity : 0.004 0.055 2359 Dihedral : 6.977 107.942 1798 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.49 % Favored : 88.07 % Rotamer: Outliers : 2.62 % Allowed : 23.12 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.20), residues: 1601 helix: 0.13 (0.21), residues: 616 sheet: -1.93 (0.60), residues: 74 loop : -2.93 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 163 TYR 0.018 0.002 TYR A 45 PHE 0.018 0.001 PHE B 613 TRP 0.033 0.002 TRP B 590 HIS 0.005 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00368 (13759) covalent geometry : angle 0.68247 (18618) hydrogen bonds : bond 0.03791 ( 426) hydrogen bonds : angle 4.79434 ( 1239) ********************** 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 165 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7588 (tmm) cc_final: 0.7296 (ttm) REVERT: A 115 CYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7920 (p) REVERT: A 184 GLU cc_start: 0.8143 (tp30) cc_final: 0.7878 (tp30) REVERT: A 363 ASP cc_start: 0.7795 (t0) cc_final: 0.7514 (t0) REVERT: A 392 PHE cc_start: 0.6598 (m-80) cc_final: 0.6292 (m-80) REVERT: A 640 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7372 (pp20) REVERT: A 859 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7586 (pmm) REVERT: B 12 PHE cc_start: 0.5474 (OUTLIER) cc_final: 0.5044 (t80) REVERT: B 80 CYS cc_start: 0.8979 (m) cc_final: 0.8666 (m) REVERT: B 154 LEU cc_start: 0.7777 (pt) cc_final: 0.7172 (tp) REVERT: B 509 GLN cc_start: 0.8068 (mp-120) cc_final: 0.7692 (mp10) REVERT: B 568 GLU cc_start: 0.9315 (OUTLIER) cc_final: 0.9056 (pm20) REVERT: B 636 LEU cc_start: 0.8280 (pp) cc_final: 0.8066 (tp) REVERT: B 644 LYS cc_start: 0.9326 (pttp) cc_final: 0.8976 (tmtt) REVERT: B 744 TYR cc_start: 0.7423 (m-10) cc_final: 0.6837 (m-80) outliers start: 38 outliers final: 31 residues processed: 154 average time/residue: 0.0837 time to fit residues: 20.7938 Evaluate side-chains 160 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain B residue 12 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 435 ILE 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 668 CYS Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 691 HIS Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 820 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 18 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 HIS B 564 GLN ** 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 = 0.4164 r_free = 0.4164 target = 0.142412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.115638 restraints weight = 36214.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.118540 restraints weight = 20876.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.120401 restraints weight = 14466.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.121795 restraints weight = 11405.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.122653 restraints weight = 9732.496| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13759 Z= 0.120 Angle : 0.646 10.031 18618 Z= 0.328 Chirality : 0.044 0.191 2006 Planarity : 0.004 0.055 2359 Dihedral : 6.760 105.825 1798 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.99 % Favored : 88.57 % Rotamer: Outliers : 2.75 % Allowed : 22.99 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.20), residues: 1601 helix: 0.23 (0.21), residues: 612 sheet: -1.85 (0.60), residues: 74 loop : -2.86 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 99 TYR 0.018 0.001 TYR A 593 PHE 0.010 0.001 PHE B 848 TRP 0.037 0.002 TRP B 590 HIS 0.004 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00266 (13759) covalent geometry : angle 0.64639 (18618) hydrogen bonds : bond 0.03446 ( 426) hydrogen bonds : angle 4.58743 ( 1239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1839.76 seconds wall clock time: 32 minutes 47.98 seconds (1967.98 seconds total)