Starting phenix.real_space_refine on Wed Aug 5 17:49:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xgb_66842/08_2026/9xgb_66842.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xgb_66842/08_2026/9xgb_66842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xgb_66842/08_2026/9xgb_66842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xgb_66842/08_2026/9xgb_66842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xgb_66842/08_2026/9xgb_66842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xgb_66842/08_2026/9xgb_66842.map" } resolution = 3.3 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= 0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 6874 2.51 5 N 1812 2.21 5 O 2048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10786 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2336 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 277} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 583 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 7867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7867 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 48, 'TRANS': 941} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 2.51, per 1000 atoms: 0.23 Number of scatterers: 10786 At special positions: 0 Unit cell: (106.656, 95.344, 121.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 2048 8.00 N 1812 7.00 C 6874 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: 0.97 Conformation dependent library (CDL) restraints added in 454.8 milliseconds 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 9 sheets defined 47.0% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'B' and resid 4524 through 4535 removed outlier: 4.406A pdb=" N LYS B4534 " --> pdb=" O ALA B4530 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU B4535 " --> pdb=" O VAL B4531 " (cutoff:3.500A) Processing helix chain 'B' and resid 4559 through 4565 Processing helix chain 'B' and resid 4571 through 4588 removed outlier: 3.841A pdb=" N ALA B4575 " --> pdb=" O SER B4571 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR B4584 " --> pdb=" O GLN B4580 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B4587 " --> pdb=" O VAL B4583 " (cutoff:3.500A) Processing helix chain 'B' and resid 4687 through 4699 removed outlier: 3.887A pdb=" N VAL B4691 " --> pdb=" O SER B4687 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN B4696 " --> pdb=" O LEU B4692 " (cutoff:3.500A) Processing helix chain 'B' and resid 4703 through 4708 removed outlier: 3.660A pdb=" N GLU B4708 " --> pdb=" O TYR B4705 " (cutoff:3.500A) Processing helix chain 'B' and resid 4717 through 4738 removed outlier: 3.842A pdb=" N GLN B4733 " --> pdb=" O GLY B4729 " (cutoff:3.500A) Processing helix chain 'B' and resid 4740 through 4746 removed outlier: 3.590A pdb=" N ILE B4744 " --> pdb=" O MET B4740 " (cutoff:3.500A) Processing helix chain 'B' and resid 4748 through 4750 No H-bonds generated for 'chain 'B' and resid 4748 through 4750' Processing helix chain 'B' and resid 4751 through 4762 Processing helix chain 'B' and resid 4764 through 4780 removed outlier: 3.643A pdb=" N ALA B4768 " --> pdb=" O VAL B4764 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN B4779 " --> pdb=" O ALA B4775 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR B4780 " --> pdb=" O ASP B4776 " (cutoff:3.500A) Processing helix chain 'B' and resid 4786 through 4811 removed outlier: 3.793A pdb=" N ALA B4796 " --> pdb=" O HIS B4792 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B4809 " --> pdb=" O ARG B4805 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 37 through 41 removed outlier: 3.522A pdb=" N GLN C 41 " --> pdb=" O PRO C 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 97 through 103 removed outlier: 3.531A pdb=" N GLY A 102 " --> pdb=" O TRP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 115 removed outlier: 3.694A pdb=" N VAL A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 removed outlier: 3.639A pdb=" N VAL A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N HIS A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 154 removed outlier: 3.514A pdb=" N ASP A 152 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS A 153 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 Processing helix chain 'A' and resid 253 through 257 removed outlier: 3.579A pdb=" N LEU A 256 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 removed outlier: 4.032A pdb=" N LYS A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 340 removed outlier: 3.725A pdb=" N GLU A 324 " --> pdb=" O GLU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 365 Processing helix chain 'A' and resid 372 through 382 Processing helix chain 'A' and resid 387 through 408 Processing helix chain 'A' and resid 421 through 426 removed outlier: 3.963A pdb=" N VAL A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 433 through 437 removed outlier: 3.631A pdb=" N LEU A 437 " --> pdb=" O GLU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 451 removed outlier: 3.874A pdb=" N CYS A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 Processing helix chain 'A' and resid 469 through 483 removed outlier: 3.677A pdb=" N LYS A 477 " --> pdb=" O CYS A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.540A pdb=" N ASN A 507 " --> pdb=" O SER A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 removed outlier: 3.889A pdb=" N ILE A 517 " --> pdb=" O PRO A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 533 removed outlier: 3.520A pdb=" N LYS A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 551 removed outlier: 3.549A pdb=" N GLU A 550 " --> pdb=" O PRO A 547 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A 551 " --> pdb=" O THR A 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 547 through 551' Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 570 through 584 Processing helix chain 'A' and resid 623 through 630 Processing helix chain 'A' and resid 633 through 650 removed outlier: 3.784A pdb=" N THR A 637 " --> pdb=" O ALA A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 663 Processing helix chain 'A' and resid 665 through 675 removed outlier: 3.726A pdb=" N LYS A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 691 removed outlier: 3.871A pdb=" N VAL A 685 " --> pdb=" O GLY A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 712 Processing helix chain 'A' and resid 712 through 722 Processing helix chain 'A' and resid 751 through 769 removed outlier: 3.532A pdb=" N ALA A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 778 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 819 through 834 Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 879 through 889 removed outlier: 3.586A pdb=" N ARG A 885 " --> pdb=" O PHE A 881 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 886 " --> pdb=" O LYS A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 914 removed outlier: 3.680A pdb=" N LYS A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 979 Processing helix chain 'A' and resid 1000 through 1005 removed outlier: 3.558A pdb=" N LEU A1005 " --> pdb=" O HIS A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1014 Processing sheet with id=AA1, first strand: chain 'B' and resid 4537 through 4540 removed outlier: 7.133A pdb=" N ILE B4608 " --> pdb=" O ASP B4602 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 4543 through 4545 Processing sheet with id=AA3, first strand: chain 'C' and resid 12 through 16 Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.955A pdb=" N HIS A 63 " --> pdb=" O CYS A 156 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N VAL A 158 " --> pdb=" O HIS A 63 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE A 65 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THR A 160 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N SER A 67 " --> pdb=" O THR A 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA6, first strand: chain 'A' and resid 260 through 262 removed outlier: 5.432A pdb=" N ILE A 250 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLY A 285 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLY A 286 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 541 removed outlier: 5.808A pdb=" N ILE A 493 " --> pdb=" O ASP A 539 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N HIS A 541 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 495 " --> pdb=" O HIS A 541 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 463 " --> pdb=" O THR A 494 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N THR A 496 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU A 465 " --> pdb=" O THR A 496 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 565 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE A 564 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N SER A 591 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A 566 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N THR A 593 " --> pdb=" O THR A 566 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS A 924 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL A 602 " --> pdb=" O LYS A 922 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LYS A 922 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 944 through 947 removed outlier: 6.545A pdb=" N ILE A 950 " --> pdb=" O ILE A 946 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.264A pdb=" N TRP A 958 " --> pdb=" O ARG A1044 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR A1046 " --> pdb=" O TRP A 958 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 960 " --> pdb=" O TYR A1046 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET A 985 " --> pdb=" O SER A1027 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLN A 988 " --> pdb=" O MET A 992 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N MET A 992 " --> pdb=" O GLN A 988 " (cutoff:3.500A) 491 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1840 1.31 - 1.44: 2811 1.44 - 1.56: 6301 1.56 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 11028 Sorted by residual: bond pdb=" C SER B4638 " pdb=" N SER B4639 " ideal model delta sigma weight residual 1.331 1.263 0.068 1.59e-02 3.96e+03 1.84e+01 bond pdb=" N SER A 388 " pdb=" CA SER A 388 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.69e+00 bond pdb=" N GLU B4678 " pdb=" CA GLU B4678 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.03e+00 bond pdb=" CA PRO A1041 " pdb=" C PRO A1041 " ideal model delta sigma weight residual 1.517 1.535 -0.018 6.70e-03 2.23e+04 7.39e+00 bond pdb=" C PRO A1041 " pdb=" O PRO A1041 " ideal model delta sigma weight residual 1.243 1.220 0.023 8.50e-03 1.38e+04 7.24e+00 ... (remaining 11023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 14483 2.17 - 4.34: 417 4.34 - 6.51: 41 6.51 - 8.68: 9 8.68 - 10.85: 2 Bond angle restraints: 14952 Sorted by residual: angle pdb=" N ARG B4713 " pdb=" CA ARG B4713 " pdb=" C ARG B4713 " ideal model delta sigma weight residual 111.14 103.95 7.19 1.08e+00 8.57e-01 4.44e+01 angle pdb=" N ALA B4569 " pdb=" CA ALA B4569 " pdb=" C ALA B4569 " ideal model delta sigma weight residual 113.19 106.17 7.02 1.19e+00 7.06e-01 3.48e+01 angle pdb=" C ILE A 930 " pdb=" N PRO A 931 " pdb=" CA PRO A 931 " ideal model delta sigma weight residual 127.00 137.85 -10.85 2.40e+00 1.74e-01 2.04e+01 angle pdb=" C ILE A 930 " pdb=" N PRO A 931 " pdb=" CD PRO A 931 " ideal model delta sigma weight residual 120.60 111.45 9.15 2.20e+00 2.07e-01 1.73e+01 angle pdb=" CA GLU A1036 " pdb=" C GLU A1036 " pdb=" O GLU A1036 " ideal model delta sigma weight residual 122.63 117.60 5.03 1.29e+00 6.01e-01 1.52e+01 ... (remaining 14947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.12: 6498 16.12 - 32.24: 136 32.24 - 48.36: 38 48.36 - 64.48: 9 64.48 - 80.61: 3 Dihedral angle restraints: 6684 sinusoidal: 2692 harmonic: 3992 Sorted by residual: dihedral pdb=" CA ASN B4656 " pdb=" C ASN B4656 " pdb=" N PRO B4657 " pdb=" CA PRO B4657 " ideal model delta harmonic sigma weight residual 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA SER A 411 " pdb=" C SER A 411 " pdb=" N PRO A 412 " pdb=" CA PRO A 412 " ideal model delta harmonic sigma weight residual -180.00 -158.36 -21.64 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA LYS B4550 " pdb=" C LYS B4550 " pdb=" N LEU B4551 " pdb=" CA LEU B4551 " ideal model delta harmonic sigma weight residual 180.00 -159.09 -20.91 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 6681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1186 0.048 - 0.095: 384 0.095 - 0.142: 99 0.142 - 0.190: 10 0.190 - 0.237: 4 Chirality restraints: 1683 Sorted by residual: chirality pdb=" CB ILE A 538 " pdb=" CA ILE A 538 " pdb=" CG1 ILE A 538 " pdb=" CG2 ILE A 538 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ILE A 622 " pdb=" N ILE A 622 " pdb=" C ILE A 622 " pdb=" CB ILE A 622 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CG LEU C 50 " pdb=" CB LEU C 50 " pdb=" CD1 LEU C 50 " pdb=" CD2 LEU C 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1680 not shown) Planarity restraints: 1931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B4712 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.12e+00 pdb=" C GLU B4712 " -0.049 2.00e-02 2.50e+03 pdb=" O GLU B4712 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG B4713 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1036 " -0.013 2.00e-02 2.50e+03 2.71e-02 7.36e+00 pdb=" C GLU A1036 " 0.047 2.00e-02 2.50e+03 pdb=" O GLU A1036 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP A1037 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 59 " -0.005 2.00e-02 2.50e+03 1.90e-02 7.20e+00 pdb=" CG TYR C 59 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR C 59 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR C 59 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR C 59 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 59 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 59 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 59 " 0.003 2.00e-02 2.50e+03 ... (remaining 1928 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 107 2.55 - 3.14: 8478 3.14 - 3.72: 17200 3.72 - 4.31: 24718 4.31 - 4.90: 39462 Nonbonded interactions: 89965 Sorted by model distance: nonbonded pdb=" O SER A 798 " pdb=" CG ASN A 799 " model vdw 1.961 3.270 nonbonded pdb=" O ASN A 234 " pdb=" OD1 ASN A 234 " model vdw 1.986 3.040 nonbonded pdb=" OH TYR A 49 " pdb=" O PHE A 881 " model vdw 2.261 3.040 nonbonded pdb=" O TYR A 576 " pdb=" OG SER A 579 " model vdw 2.297 3.040 nonbonded pdb=" O ASP A 879 " pdb=" OG1 THR A 883 " model vdw 2.298 3.040 ... (remaining 89960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.710 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4697 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 11028 Z= 0.406 Angle : 0.886 10.847 14952 Z= 0.525 Chirality : 0.050 0.237 1683 Planarity : 0.007 0.062 1931 Dihedral : 8.696 80.606 4092 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.05 % Favored : 95.88 % Rotamer: Outliers : 0.67 % Allowed : 1.00 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.08 % 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 are not related in a simple way. whole: -2.76 (0.19), residues: 1358 helix: -2.87 (0.14), residues: 529 sheet: -0.69 (0.35), residues: 217 loop : -1.06 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A1044 TYR 0.042 0.003 TYR C 59 PHE 0.026 0.003 PHE A 410 TRP 0.031 0.004 TRP A 660 HIS 0.023 0.002 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00808 / 0.41 (11028) covalent geometry : angle 0.88624 / 0.53 (14952) hydrogen bonds : bond 0.26849 / 17.49 ( 491) hydrogen bonds : angle 9.18112 / 6.51 ( 1392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 263 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4560 MET cc_start: 0.4981 (ttp) cc_final: 0.4706 (ttp) REVERT: B 4568 ASP cc_start: 0.6016 (m-30) cc_final: 0.5590 (t70) REVERT: B 4588 SER cc_start: 0.4974 (m) cc_final: 0.4506 (p) REVERT: B 4623 ASN cc_start: 0.6037 (m-40) cc_final: 0.5711 (m-40) REVERT: B 4627 GLU cc_start: 0.5501 (tt0) cc_final: 0.5296 (mt-10) REVERT: B 4654 ARG cc_start: 0.6363 (ttt180) cc_final: 0.6159 (ttt180) REVERT: B 4678 GLU cc_start: 0.3424 (OUTLIER) cc_final: 0.3195 (tm-30) REVERT: B 4790 MET cc_start: 0.3045 (mmm) cc_final: 0.2836 (mmm) REVERT: B 4805 ARG cc_start: 0.6963 (ttm170) cc_final: 0.5979 (ttp80) REVERT: A 109 GLU cc_start: 0.6488 (mt-10) cc_final: 0.6022 (mm-30) REVERT: A 139 SER cc_start: 0.7805 (p) cc_final: 0.7574 (t) REVERT: A 161 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7760 (mt-10) REVERT: A 202 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 204 GLU cc_start: 0.5787 (tt0) cc_final: 0.5217 (tp30) REVERT: A 215 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6686 (mt-10) REVERT: A 249 GLU cc_start: 0.6195 (mt-10) cc_final: 0.5808 (tt0) REVERT: A 304 ARG cc_start: 0.6047 (ttt180) cc_final: 0.5273 (mmp80) REVERT: A 339 TYR cc_start: 0.6399 (m-80) cc_final: 0.6034 (m-80) REVERT: A 442 ARG cc_start: 0.6516 (ptm160) cc_final: 0.6309 (ptm-80) REVERT: A 535 GLN cc_start: 0.5550 (mm-40) cc_final: 0.5288 (mp10) REVERT: A 552 ILE cc_start: 0.4891 (mt) cc_final: 0.4645 (mt) REVERT: A 578 ASP cc_start: 0.5777 (t70) cc_final: 0.5547 (t0) REVERT: A 594 MET cc_start: 0.4516 (tpp) cc_final: 0.3612 (tmm) REVERT: A 773 PHE cc_start: 0.4809 (p90) cc_final: 0.4540 (p90) REVERT: A 876 GLU cc_start: 0.6814 (tt0) cc_final: 0.6539 (mm-30) REVERT: A 889 LYS cc_start: 0.5812 (mttt) cc_final: 0.5452 (mmtt) REVERT: A 919 GLU cc_start: 0.7244 (mp0) cc_final: 0.6958 (mp0) REVERT: A 937 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6160 (mm-30) REVERT: A 940 GLU cc_start: 0.6375 (tt0) cc_final: 0.6036 (tt0) REVERT: A 943 LYS cc_start: 0.7343 (mttt) cc_final: 0.6506 (mptt) REVERT: A 945 LYS cc_start: 0.7040 (mttt) cc_final: 0.6641 (mtmm) REVERT: A 957 ARG cc_start: 0.6846 (ttp-170) cc_final: 0.6009 (ttm-80) REVERT: A 1020 LYS cc_start: 0.6294 (mttt) cc_final: 0.5584 (mmtm) REVERT: A 1038 LEU cc_start: 0.4508 (mt) cc_final: 0.4124 (mt) outliers start: 8 outliers final: 2 residues processed: 271 average time/residue: 0.1149 time to fit residues: 43.0677 Evaluate side-chains 158 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 155 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4678 GLU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 388 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B4580 GLN ** B4644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4661 ASN B4696 GLN B4758 HIS B4792 HIS C 60 ASN ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN A 234 ASN A 262 GLN A 284 HIS ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN A 713 HIS A 760 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.233641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.199059 restraints weight = 10676.836| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 1.34 r_work: 0.3751 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11028 Z= 0.125 Angle : 0.557 8.684 14952 Z= 0.297 Chirality : 0.042 0.175 1683 Planarity : 0.005 0.048 1931 Dihedral : 5.132 57.542 1453 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.09 % Allowed : 5.85 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.08 % 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 are not related in a simple way. whole: -0.82 (0.21), residues: 1358 helix: -0.38 (0.19), residues: 591 sheet: -0.09 (0.36), residues: 208 loop : -0.72 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 248 TYR 0.010 0.001 TYR C 59 PHE 0.016 0.001 PHE A 410 TRP 0.015 0.001 TRP A 660 HIS 0.009 0.001 HIS B4792 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (11028) covalent geometry : angle 0.55711 / 0.30 (14952) hydrogen bonds : bond 0.04624 / 3.02 ( 491) hydrogen bonds : angle 5.32201 / 3.79 ( 1392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: B 4588 SER cc_start: 0.8474 (m) cc_final: 0.8230 (p) REVERT: B 4779 GLN cc_start: 0.6196 (OUTLIER) cc_final: 0.5762 (mp10) REVERT: B 4805 ARG cc_start: 0.6781 (ttm170) cc_final: 0.6389 (ttp80) REVERT: A 352 GLU cc_start: 0.5957 (mt-10) cc_final: 0.5535 (pt0) REVERT: A 433 CYS cc_start: 0.7879 (t) cc_final: 0.7502 (m) REVERT: A 492 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.6844 (tmm) REVERT: A 602 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8814 (p) REVERT: A 724 LEU cc_start: 0.7960 (mp) cc_final: 0.7516 (tt) REVERT: A 889 LYS cc_start: 0.7907 (mttt) cc_final: 0.7535 (mmtt) REVERT: A 957 ARG cc_start: 0.8208 (ttp-170) cc_final: 0.7803 (ttm110) REVERT: A 1020 LYS cc_start: 0.7315 (mttt) cc_final: 0.6742 (mmtm) REVERT: A 1038 LEU cc_start: 0.7299 (mt) cc_final: 0.6962 (mt) outliers start: 25 outliers final: 13 residues processed: 191 average time/residue: 0.1123 time to fit residues: 29.8969 Evaluate side-chains 158 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4638 SER Chi-restraints excluded: chain B residue 4680 LYS Chi-restraints excluded: chain B residue 4779 GLN Chi-restraints excluded: chain B residue 4792 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1010 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 123 optimal weight: 0.0060 chunk 100 optimal weight: 9.9990 chunk 46 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B4644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN A 262 GLN A 415 GLN A 599 HIS A 614 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.234339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.208435 restraints weight = 10853.785| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 1.05 r_work: 0.3898 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11028 Z= 0.119 Angle : 0.509 6.994 14952 Z= 0.268 Chirality : 0.041 0.144 1683 Planarity : 0.004 0.044 1931 Dihedral : 4.418 31.124 1450 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.84 % Allowed : 6.93 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.08 % 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 are not related in a simple way. whole: -0.05 (0.22), residues: 1358 helix: 0.51 (0.21), residues: 588 sheet: -0.05 (0.36), residues: 195 loop : -0.46 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 439 TYR 0.020 0.001 TYR B4780 PHE 0.023 0.001 PHE A 711 TRP 0.012 0.001 TRP A 660 HIS 0.013 0.001 HIS B4792 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (11028) covalent geometry : angle 0.50918 / 0.27 (14952) hydrogen bonds : bond 0.03895 / 2.54 ( 491) hydrogen bonds : angle 4.76937 / 3.39 ( 1392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.409 Fit side-chains REVERT: B 4588 SER cc_start: 0.8637 (m) cc_final: 0.8388 (p) REVERT: B 4732 ARG cc_start: 0.7460 (mtt180) cc_final: 0.7089 (mtp180) REVERT: B 4805 ARG cc_start: 0.6912 (ttm170) cc_final: 0.6340 (ttp80) REVERT: C 1 MET cc_start: 0.2948 (ptt) cc_final: 0.2080 (tpt) REVERT: A 349 GLN cc_start: 0.5685 (tm-30) cc_final: 0.5175 (mm-40) REVERT: A 368 LYS cc_start: 0.7638 (tptp) cc_final: 0.6521 (mptt) REVERT: A 433 CYS cc_start: 0.8047 (t) cc_final: 0.7624 (m) REVERT: A 492 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.6874 (tmm) REVERT: A 527 ASP cc_start: 0.7817 (m-30) cc_final: 0.7612 (m-30) REVERT: A 578 ASP cc_start: 0.8566 (t70) cc_final: 0.8340 (t0) REVERT: A 724 LEU cc_start: 0.7987 (mp) cc_final: 0.7577 (tt) REVERT: A 844 MET cc_start: 0.7340 (mtt) cc_final: 0.6986 (mtt) REVERT: A 889 LYS cc_start: 0.7952 (mttt) cc_final: 0.7608 (mmtt) REVERT: A 957 ARG cc_start: 0.8299 (ttp-170) cc_final: 0.7847 (ttt90) REVERT: A 1009 MET cc_start: 0.7353 (mmt) cc_final: 0.7036 (mmt) REVERT: A 1020 LYS cc_start: 0.7332 (mttt) cc_final: 0.6732 (mmtm) outliers start: 22 outliers final: 14 residues processed: 171 average time/residue: 0.0991 time to fit residues: 24.3061 Evaluate side-chains 159 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4638 SER Chi-restraints excluded: chain B residue 4756 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 1010 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B4644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4743 GLN ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 HIS A 336 GLN A 614 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.198564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.156613 restraints weight = 10786.490| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.81 r_work: 0.3505 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11028 Z= 0.170 Angle : 0.564 11.142 14952 Z= 0.290 Chirality : 0.043 0.143 1683 Planarity : 0.004 0.043 1931 Dihedral : 4.408 21.956 1450 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.76 % Allowed : 7.02 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.08 % 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 are not related in a simple way. whole: 0.24 (0.22), residues: 1358 helix: 0.87 (0.21), residues: 577 sheet: -0.02 (0.36), residues: 204 loop : -0.39 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 442 TYR 0.020 0.002 TYR B4780 PHE 0.017 0.002 PHE A 464 TRP 0.016 0.002 TRP A 660 HIS 0.008 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (11028) covalent geometry : angle 0.56426 / 0.29 (14952) hydrogen bonds : bond 0.04107 / 2.68 ( 491) hydrogen bonds : angle 4.77176 / 3.40 ( 1392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: B 4728 ASP cc_start: 0.8032 (m-30) cc_final: 0.7783 (m-30) REVERT: C 1 MET cc_start: 0.2770 (ptt) cc_final: 0.1924 (tpt) REVERT: A 162 MET cc_start: 0.8182 (tpp) cc_final: 0.7976 (ttm) REVERT: A 253 MET cc_start: 0.6531 (OUTLIER) cc_final: 0.5785 (mtt) REVERT: A 307 LYS cc_start: 0.6939 (mtpp) cc_final: 0.6446 (mtmm) REVERT: A 349 GLN cc_start: 0.5589 (tm-30) cc_final: 0.5067 (mm-40) REVERT: A 492 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.6465 (tmm) REVERT: A 746 LYS cc_start: 0.6669 (tttt) cc_final: 0.6255 (tppt) REVERT: A 844 MET cc_start: 0.7782 (mtt) cc_final: 0.7468 (mtt) REVERT: A 889 LYS cc_start: 0.7922 (mttt) cc_final: 0.7502 (mmtt) REVERT: A 957 ARG cc_start: 0.8303 (ttp-170) cc_final: 0.7761 (ttt90) outliers start: 33 outliers final: 20 residues processed: 160 average time/residue: 0.0974 time to fit residues: 22.6261 Evaluate side-chains 149 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4560 MET Chi-restraints excluded: chain B residue 4583 VAL Chi-restraints excluded: chain B residue 4638 SER Chi-restraints excluded: chain B residue 4756 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 1010 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 69 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 16 optimal weight: 0.0170 chunk 35 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B4644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4743 GLN ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.199663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.157019 restraints weight = 10708.136| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.83 r_work: 0.3522 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11028 Z= 0.126 Angle : 0.489 6.562 14952 Z= 0.252 Chirality : 0.041 0.138 1683 Planarity : 0.004 0.042 1931 Dihedral : 4.148 22.218 1449 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.01 % Allowed : 8.94 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.08 % 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 are not related in a simple way. whole: 0.58 (0.23), residues: 1358 helix: 1.20 (0.21), residues: 581 sheet: -0.16 (0.35), residues: 217 loop : -0.12 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 439 TYR 0.008 0.001 TYR A 339 PHE 0.015 0.001 PHE A 656 TRP 0.007 0.001 TRP A 660 HIS 0.005 0.001 HIS B4800 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (11028) covalent geometry : angle 0.48910 / 0.25 (14952) hydrogen bonds : bond 0.03492 / 2.29 ( 491) hydrogen bonds : angle 4.55108 / 3.26 ( 1392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.2817 (ptt) cc_final: 0.1952 (tpt) REVERT: A 290 GLN cc_start: 0.6947 (tp40) cc_final: 0.6510 (tp-100) REVERT: A 349 GLN cc_start: 0.5510 (tm-30) cc_final: 0.5001 (mm-40) REVERT: A 492 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.6769 (tmm) REVERT: A 496 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8685 (t) REVERT: A 746 LYS cc_start: 0.6520 (tttt) cc_final: 0.6092 (tppt) REVERT: A 844 MET cc_start: 0.7716 (mtt) cc_final: 0.7370 (mtt) REVERT: A 889 LYS cc_start: 0.7856 (mttt) cc_final: 0.7450 (mmtt) REVERT: A 957 ARG cc_start: 0.8392 (ttp-170) cc_final: 0.7827 (ttt90) REVERT: A 998 MET cc_start: 0.7845 (mtp) cc_final: 0.7521 (mtp) outliers start: 24 outliers final: 14 residues processed: 148 average time/residue: 0.1017 time to fit residues: 21.5802 Evaluate side-chains 140 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4583 VAL Chi-restraints excluded: chain B residue 4638 SER Chi-restraints excluded: chain B residue 4756 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 1010 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 62 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B4644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4743 GLN ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** A 290 GLN ** 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 = 0.4124 r_free = 0.4124 target = 0.201580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.159538 restraints weight = 10656.578| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.83 r_work: 0.3546 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11028 Z= 0.098 Angle : 0.463 6.411 14952 Z= 0.238 Chirality : 0.040 0.153 1683 Planarity : 0.004 0.043 1931 Dihedral : 3.951 22.063 1449 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.59 % Allowed : 9.44 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.08 % 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 are not related in a simple way. whole: 0.90 (0.23), residues: 1358 helix: 1.56 (0.22), residues: 568 sheet: -0.05 (0.34), residues: 227 loop : -0.01 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B4577 TYR 0.009 0.001 TYR A 339 PHE 0.014 0.001 PHE A 656 TRP 0.006 0.001 TRP A 378 HIS 0.004 0.001 HIS B4800 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (11028) covalent geometry : angle 0.46319 / 0.24 (14952) hydrogen bonds : bond 0.03198 / 2.09 ( 491) hydrogen bonds : angle 4.39385 / 3.15 ( 1392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.2797 (ptt) cc_final: 0.1925 (tpt) REVERT: A 349 GLN cc_start: 0.5619 (tm-30) cc_final: 0.5130 (mm-40) REVERT: A 368 LYS cc_start: 0.7547 (tptp) cc_final: 0.6499 (mtmm) REVERT: A 492 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.6625 (tmm) REVERT: A 844 MET cc_start: 0.7723 (mtt) cc_final: 0.7311 (mtt) REVERT: A 889 LYS cc_start: 0.7866 (mttt) cc_final: 0.7478 (mmtt) REVERT: A 957 ARG cc_start: 0.8305 (ttp-170) cc_final: 0.7798 (ttt90) outliers start: 19 outliers final: 15 residues processed: 140 average time/residue: 0.1040 time to fit residues: 21.0218 Evaluate side-chains 141 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4560 MET Chi-restraints excluded: chain B residue 4583 VAL Chi-restraints excluded: chain B residue 4638 SER Chi-restraints excluded: chain B residue 4756 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 1010 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 33 optimal weight: 0.0470 chunk 49 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.227195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.199363 restraints weight = 10728.200| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 1.06 r_work: 0.3804 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 11028 Z= 0.096 Angle : 0.456 6.080 14952 Z= 0.233 Chirality : 0.040 0.147 1683 Planarity : 0.004 0.043 1931 Dihedral : 3.853 21.900 1449 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.42 % Allowed : 9.61 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.08 % 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 are not related in a simple way. whole: 1.00 (0.23), residues: 1358 helix: 1.66 (0.22), residues: 574 sheet: 0.10 (0.37), residues: 193 loop : -0.04 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B4577 TYR 0.006 0.001 TYR A 576 PHE 0.015 0.001 PHE A 656 TRP 0.005 0.001 TRP A 378 HIS 0.004 0.001 HIS B4800 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (11028) covalent geometry : angle 0.45596 / 0.23 (14952) hydrogen bonds : bond 0.03092 / 2.02 ( 491) hydrogen bonds : angle 4.30455 / 3.09 ( 1392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.1997 (ptt) cc_final: 0.1782 (tpt) REVERT: A 304 ARG cc_start: 0.7629 (ttt180) cc_final: 0.7098 (mtp85) REVERT: A 349 GLN cc_start: 0.5462 (tm-30) cc_final: 0.5096 (mm-40) REVERT: A 368 LYS cc_start: 0.7570 (tptp) cc_final: 0.6704 (mtmm) REVERT: A 492 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.6268 (tmm) REVERT: A 844 MET cc_start: 0.7512 (mtt) cc_final: 0.7284 (mtt) REVERT: A 889 LYS cc_start: 0.7958 (mttt) cc_final: 0.7740 (mmtt) REVERT: A 957 ARG cc_start: 0.8034 (ttp-170) cc_final: 0.7797 (ttt90) outliers start: 17 outliers final: 14 residues processed: 143 average time/residue: 0.1076 time to fit residues: 21.8177 Evaluate side-chains 142 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4638 SER Chi-restraints excluded: chain B residue 4756 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1010 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 22 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 123 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 106 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.199622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.157029 restraints weight = 10685.064| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.78 r_work: 0.3534 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11028 Z= 0.118 Angle : 0.478 7.038 14952 Z= 0.243 Chirality : 0.041 0.141 1683 Planarity : 0.004 0.041 1931 Dihedral : 3.884 20.775 1449 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.50 % Allowed : 9.86 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.08 % 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 are not related in a simple way. whole: 1.01 (0.23), residues: 1358 helix: 1.70 (0.22), residues: 573 sheet: 0.12 (0.36), residues: 208 loop : -0.08 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 248 TYR 0.009 0.001 TYR A 576 PHE 0.015 0.001 PHE A 656 TRP 0.008 0.001 TRP A 660 HIS 0.004 0.001 HIS B4800 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (11028) covalent geometry : angle 0.47824 / 0.24 (14952) hydrogen bonds : bond 0.03307 / 2.18 ( 491) hydrogen bonds : angle 4.34239 / 3.13 ( 1392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: B 4728 ASP cc_start: 0.8014 (m-30) cc_final: 0.7782 (m-30) REVERT: C 1 MET cc_start: 0.2811 (ptt) cc_final: 0.1973 (tpt) REVERT: A 304 ARG cc_start: 0.7814 (ttt180) cc_final: 0.7257 (mtp85) REVERT: A 307 LYS cc_start: 0.6874 (mtpp) cc_final: 0.6413 (mtmm) REVERT: A 349 GLN cc_start: 0.5570 (tm-30) cc_final: 0.5160 (mm-40) REVERT: A 352 GLU cc_start: 0.6749 (tm-30) cc_final: 0.6029 (tp30) REVERT: A 368 LYS cc_start: 0.7430 (tptp) cc_final: 0.6455 (mtmm) REVERT: A 492 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.6649 (tmm) REVERT: A 844 MET cc_start: 0.7781 (mtt) cc_final: 0.7347 (mtt) REVERT: A 889 LYS cc_start: 0.7816 (mttt) cc_final: 0.7458 (mmtt) REVERT: A 957 ARG cc_start: 0.8425 (ttp-170) cc_final: 0.7859 (ttt90) outliers start: 18 outliers final: 14 residues processed: 136 average time/residue: 0.1016 time to fit residues: 19.8677 Evaluate side-chains 140 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4638 SER Chi-restraints excluded: chain B residue 4756 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 944 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 112 optimal weight: 0.0270 chunk 47 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 36 optimal weight: 0.4980 chunk 88 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.203347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.160620 restraints weight = 10591.780| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 1.77 r_work: 0.3557 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 11028 Z= 0.087 Angle : 0.450 7.153 14952 Z= 0.229 Chirality : 0.039 0.135 1683 Planarity : 0.004 0.042 1931 Dihedral : 3.732 22.226 1449 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.25 % Allowed : 10.53 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.08 % 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 are not related in a simple way. whole: 1.16 (0.23), residues: 1358 helix: 1.85 (0.22), residues: 576 sheet: 0.14 (0.37), residues: 193 loop : -0.02 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B4577 TYR 0.006 0.001 TYR A 282 PHE 0.015 0.001 PHE A 656 TRP 0.004 0.001 TRP A 378 HIS 0.004 0.001 HIS B4800 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.09 (11028) covalent geometry : angle 0.44976 / 0.23 (14952) hydrogen bonds : bond 0.02905 / 1.91 ( 491) hydrogen bonds : angle 4.22324 / 3.05 ( 1392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.2791 (ptt) cc_final: 0.1991 (tpt) REVERT: A 290 GLN cc_start: 0.6808 (tp-100) cc_final: 0.6590 (tp-100) REVERT: A 304 ARG cc_start: 0.7790 (ttt180) cc_final: 0.7282 (mtp85) REVERT: A 307 LYS cc_start: 0.6756 (mtpp) cc_final: 0.6310 (mtmm) REVERT: A 349 GLN cc_start: 0.5512 (tm-30) cc_final: 0.5072 (mm-40) REVERT: A 352 GLU cc_start: 0.6681 (tm-30) cc_final: 0.5976 (tp30) REVERT: A 368 LYS cc_start: 0.7364 (tptp) cc_final: 0.6462 (mtmm) REVERT: A 492 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.6578 (tmm) REVERT: A 844 MET cc_start: 0.7742 (mtt) cc_final: 0.7314 (mtt) REVERT: A 851 LYS cc_start: 0.8159 (pttt) cc_final: 0.7941 (pttp) REVERT: A 889 LYS cc_start: 0.7859 (mttt) cc_final: 0.7436 (mmtt) REVERT: A 957 ARG cc_start: 0.8380 (ttp-170) cc_final: 0.7816 (ttt90) outliers start: 15 outliers final: 14 residues processed: 138 average time/residue: 0.1128 time to fit residues: 22.2843 Evaluate side-chains 140 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4638 SER Chi-restraints excluded: chain B residue 4756 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 944 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 56 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 133 optimal weight: 0.0770 chunk 112 optimal weight: 50.0000 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B4743 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.200945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.158618 restraints weight = 10617.965| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 1.77 r_work: 0.3557 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11028 Z= 0.108 Angle : 0.472 7.226 14952 Z= 0.238 Chirality : 0.040 0.135 1683 Planarity : 0.004 0.041 1931 Dihedral : 3.753 20.316 1449 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.42 % Allowed : 10.61 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.08 % 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 are not related in a simple way. whole: 1.16 (0.23), residues: 1358 helix: 1.84 (0.22), residues: 574 sheet: 0.16 (0.36), residues: 208 loop : -0.01 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 439 TYR 0.008 0.001 TYR A 576 PHE 0.015 0.001 PHE A 656 TRP 0.006 0.001 TRP A 660 HIS 0.004 0.001 HIS B4800 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (11028) covalent geometry : angle 0.47161 / 0.24 (14952) hydrogen bonds : bond 0.03158 / 2.09 ( 491) hydrogen bonds : angle 4.25718 / 3.07 ( 1392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: B 4728 ASP cc_start: 0.8029 (m-30) cc_final: 0.7809 (m-30) REVERT: C 1 MET cc_start: 0.2761 (ptt) cc_final: 0.1914 (tpt) REVERT: A 304 ARG cc_start: 0.7804 (ttt180) cc_final: 0.7284 (mtp85) REVERT: A 307 LYS cc_start: 0.6712 (mtpp) cc_final: 0.6241 (mtmm) REVERT: A 349 GLN cc_start: 0.5633 (tm-30) cc_final: 0.5209 (mm-40) REVERT: A 352 GLU cc_start: 0.6803 (tm-30) cc_final: 0.6030 (tp30) REVERT: A 368 LYS cc_start: 0.7349 (tptp) cc_final: 0.6418 (mtmm) REVERT: A 492 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.6630 (tmm) REVERT: A 844 MET cc_start: 0.7751 (mtt) cc_final: 0.7289 (mtt) REVERT: A 889 LYS cc_start: 0.7880 (mttt) cc_final: 0.7461 (mmtt) REVERT: A 957 ARG cc_start: 0.8369 (ttp-170) cc_final: 0.7834 (ttt90) outliers start: 17 outliers final: 14 residues processed: 138 average time/residue: 0.1092 time to fit residues: 21.8715 Evaluate side-chains 141 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4638 SER Chi-restraints excluded: chain B residue 4756 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 944 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 126 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B4743 GLN ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.198022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.155688 restraints weight = 10740.457| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.84 r_work: 0.3530 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11028 Z= 0.137 Angle : 0.498 7.440 14952 Z= 0.253 Chirality : 0.041 0.138 1683 Planarity : 0.004 0.041 1931 Dihedral : 3.922 20.261 1449 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.34 % Allowed : 10.86 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.08 % 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 are not related in a simple way. whole: 1.05 (0.23), residues: 1358 helix: 1.68 (0.22), residues: 577 sheet: 0.07 (0.36), residues: 217 loop : 0.03 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 439 TYR 0.010 0.001 TYR A 576 PHE 0.016 0.001 PHE A 656 TRP 0.012 0.001 TRP A 660 HIS 0.005 0.001 HIS B4800 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (11028) covalent geometry : angle 0.49850 / 0.25 (14952) hydrogen bonds : bond 0.03498 / 2.32 ( 491) hydrogen bonds : angle 4.39071 / 3.17 ( 1392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2402.13 seconds wall clock time: 42 minutes 3.81 seconds (2523.81 seconds total)