Starting phenix.real_space_refine
on Sun Jul 27 02:13:40 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/7pu7_13654/07_2025/7pu7_13654.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pu7_13654/07_2025/7pu7_13654.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pu7_13654/07_2025/7pu7_13654.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pu7_13654/07_2025/7pu7_13654.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pu7_13654/07_2025/7pu7_13654.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pu7_13654/07_2025/7pu7_13654.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 6
    Type Number    sf(0)   Gaussians
     Zn      3      6.06       5
     P      33      5.49       5
     S      37      5.16       5
     C    5565      2.51       5
     N    1587      2.21       5
     O    1765      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8990
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1070, 8267
          Classifications: {'peptide': 1070}
          Link IDs: {'PTRANS': 53, 'TRANS': 1016}
          Chain breaks: 1
    Chain: "T"
      Number of atoms: 400
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 400
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
    Chain: "P"
      Number of atoms: 280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 280
          Classifications: {'DNA': 14}
          Link IDs: {'rna3p': 13}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 43
          Unusual residues: {' ZN': 3, '82W': 1}
          Classifications: {'undetermined': 4, 'water': 3}
          Link IDs: {None: 6}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1148  SG  CYS A 158      64.073  79.106  65.092  1.00 45.51           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C1  82W A1204 " occ=0.00
      ... (35 atoms not shown)
      pdb=" O7  82W A1204 " occ=0.00
  Time building chain proxies: 6.13, per 1000 atoms: 0.68
  Number of scatterers: 8990
  At special positions: 0
  Unit cell: (101.322, 108.25, 112.58, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      3     29.99
     S      37     16.00
     P      33     15.00
     O    1765      8.00
     N    1587      7.00
     C    5565      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: 2.46
  Conformation dependent library (CDL) restraints added in 853.6 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1201 "
        pdb="ZN    ZN A1201 " - pdb=" SG  CYS A 158 "
        pdb="ZN    ZN A1201 " - pdb=" ND1 HIS A 107 "
      pdb="  ZN A1202 "
        pdb="ZN    ZN A1202 " - pdb=" NE2 HIS A  14 "
        pdb="ZN    ZN A1202 " - pdb=" NE2 HIS A  16 "
      pdb="  ZN A1203 "
        pdb="ZN    ZN A1203 " - pdb=" NE2 HIS A 228 "
        pdb="ZN    ZN A1203 " - pdb=" NE2 HIS A  48 "


  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1954

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 7 sheets defined
      56.6% alpha, 11.3% beta
      13 base pairs and 26 stacking pairs defined.
    Time for finding SS restraints: 3.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 38
    Processing helix  chain 'A' and resid 53 through 65
    Processing helix  chain 'A' and resid 99 through 104
    Processing helix  chain 'A' and resid 114 through 132
      removed outlier: 3.546A  pdb=" N   SER A 129 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 148
      removed outlier: 3.633A  pdb=" N   ALA A 146 " --> pdb=" O   ALA A 142 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   GLU A 147 " --> pdb=" O   GLU A 143 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   HIS A 148 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 170
    Processing helix  chain 'A' and resid 171 through 187
    Processing helix  chain 'A' and resid 200 through 218
      removed outlier: 4.148A  pdb=" N   VAL A 206 " --> pdb=" O   ILE A 202 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   ASP A 208 " --> pdb=" O   ARG A 204 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   GLY A 209 " --> pdb=" O   ARG A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 233
      No H-bonds generated for 'chain 'A' and resid 231 through 233'
    Processing helix  chain 'A' and resid 234 through 247
      removed outlier: 3.586A  pdb=" N   ALA A 240 " --> pdb=" O   HIS A 236 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   CYS A 243 " --> pdb=" O   GLU A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 277
      removed outlier: 3.560A  pdb=" N   ILE A 274 " --> pdb=" O   GLU A 270 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   ASP A 277 " --> pdb=" O   GLN A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 293
      removed outlier: 4.135A  pdb=" N   THR A 286 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   LEU A 287 " --> pdb=" O   CYS A 283 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ARG A 292 " --> pdb=" O   LEU A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 301
    Processing helix  chain 'A' and resid 316 through 333
    Processing helix  chain 'A' and resid 340 through 355
    Processing helix  chain 'A' and resid 357 through 375
      removed outlier: 3.965A  pdb=" N   PHE A 361 " --> pdb=" O   PHE A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 387
      removed outlier: 3.847A  pdb=" N   GLY A 387 " --> pdb=" O   SER A 384 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 384 through 387'
    Processing helix  chain 'A' and resid 388 through 395
    Processing helix  chain 'A' and resid 400 through 405
      removed outlier: 4.243A  pdb=" N   HIS A 404 " --> pdb=" O   ASP A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 412
      removed outlier: 4.197A  pdb=" N   PHE A 411 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 443
      removed outlier: 3.932A  pdb=" N   MET A 434 " --> pdb=" O   ARG A 430 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL A 435 " --> pdb=" O   ARG A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 471
      removed outlier: 3.664A  pdb=" N   LYS A 463 " --> pdb=" O   LYS A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 483
    Processing helix  chain 'A' and resid 496 through 501
      removed outlier: 3.592A  pdb=" N   ILE A 499 " --> pdb=" O   LEU A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 509
    Processing helix  chain 'A' and resid 510 through 520
    Processing helix  chain 'A' and resid 520 through 533
      removed outlier: 3.534A  pdb=" N   THR A 529 " --> pdb=" O   THR A 525 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   GLY A 532 " --> pdb=" O   GLN A 528 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU A 533 " --> pdb=" O   THR A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 553 through 557
    Processing helix  chain 'A' and resid 574 through 581
      removed outlier: 3.991A  pdb=" N   ILE A 581 " --> pdb=" O   ALA A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 608
    Processing helix  chain 'A' and resid 613 through 617
      removed outlier: 3.591A  pdb=" N   VAL A 617 " --> pdb=" O   LEU A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 631
      removed outlier: 3.794A  pdb=" N   TYR A 625 " --> pdb=" O   ASP A 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 652
      removed outlier: 3.706A  pdb=" N   ASP A 646 " --> pdb=" O   GLY A 642 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 665
      removed outlier: 3.785A  pdb=" N   VAL A 659 " --> pdb=" O   GLY A 655 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ILE A 663 " --> pdb=" O   VAL A 659 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ALA A 664 " --> pdb=" O   VAL A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 675 through 684
      removed outlier: 3.521A  pdb=" N   ALA A 680 " --> pdb=" O   HIS A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 693 through 697
      removed outlier: 3.741A  pdb=" N   GLU A 697 " --> pdb=" O   PRO A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 726
      removed outlier: 3.586A  pdb=" N   ILE A 717 " --> pdb=" O   TYR A 713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 742
      removed outlier: 3.540A  pdb=" N   ILE A 734 " --> pdb=" O   ALA A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 762
      removed outlier: 3.626A  pdb=" N   GLU A 752 " --> pdb=" O   GLU A 748 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 764 through 776
      removed outlier: 3.547A  pdb=" N   TRP A 772 " --> pdb=" O   ILE A 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 784 through 805
      removed outlier: 3.638A  pdb=" N   ALA A 788 " --> pdb=" O   ASN A 784 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   VAL A 794 " --> pdb=" O   GLY A 790 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 805 through 817
      removed outlier: 3.628A  pdb=" N   GLY A 812 " --> pdb=" O   GLU A 808 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   SER A 816 " --> pdb=" O   GLY A 812 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   VAL A 817 " --> pdb=" O   LEU A 813 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 835
      removed outlier: 3.575A  pdb=" N   VAL A 826 " --> pdb=" O   ASP A 822 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ARG A 832 " --> pdb=" O   LEU A 828 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 864
    Processing helix  chain 'A' and resid 868 through 882
    Processing helix  chain 'A' and resid 887 through 895
    Processing helix  chain 'A' and resid 896 through 900
    Processing helix  chain 'A' and resid 901 through 912
    Processing helix  chain 'A' and resid 920 through 940
      removed outlier: 4.470A  pdb=" N   SER A 929 " --> pdb=" O   PHE A 925 " (cutoff:3.500A)
      removed outlier: 5.155A  pdb=" N   ASP A 930 " --> pdb=" O   LEU A 926 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ASP A 933 " --> pdb=" O   SER A 929 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 987
    Processing helix  chain 'A' and resid 998 through 1006
      removed outlier: 3.884A  pdb=" N   GLN A1005 " --> pdb=" O   LEU A1001 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1009 through 1016
      removed outlier: 3.635A  pdb=" N   ILE A1013 " --> pdb=" O   ALA A1009 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1061 through 1069
      removed outlier: 3.501A  pdb=" N   SER A1067 " --> pdb=" O   HIS A1063 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1070 through 1072
      No H-bonds generated for 'chain 'A' and resid 1070 through 1072'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 48
      removed outlier: 6.695A  pdb=" N   VAL A  43 " --> pdb=" O   ILE A  69 " (cutoff:3.500A)
      removed outlier: 8.253A  pdb=" N   GLY A  71 " --> pdb=" O   VAL A  43 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   MET A  45 " --> pdb=" O   GLY A  71 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   GLU A  73 " --> pdb=" O   MET A  45 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ASP A  47 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 7.388A  pdb=" N   TYR A  75 " --> pdb=" O   ASP A  47 " (cutoff:3.500A)
      removed outlier: 14.325A  pdb=" N   SER A 138 " --> pdb=" O   GLY A  71 " (cutoff:3.500A)
      removed outlier: 9.606A  pdb=" N   GLU A  73 " --> pdb=" O   SER A 138 " (cutoff:3.500A)
      removed outlier: 8.838A  pdb=" N   MET A 140 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   TYR A  75 " --> pdb=" O   MET A 140 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 48
      removed outlier: 6.695A  pdb=" N   VAL A  43 " --> pdb=" O   ILE A  69 " (cutoff:3.500A)
      removed outlier: 8.253A  pdb=" N   GLY A  71 " --> pdb=" O   VAL A  43 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   MET A  45 " --> pdb=" O   GLY A  71 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   GLU A  73 " --> pdb=" O   MET A  45 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ASP A  47 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 7.388A  pdb=" N   TYR A  75 " --> pdb=" O   ASP A  47 " (cutoff:3.500A)
      removed outlier: 5.007A  pdb=" N   ILE A  70 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   THR A 109 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
      removed outlier: 9.055A  pdb=" N   PHE A 192 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ILE A 154 " --> pdb=" O   PHE A 192 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   GLU A 194 " --> pdb=" O   ILE A 154 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 427
      removed outlier: 6.631A  pdb=" N   ILE A 424 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   LEU A 591 " --> pdb=" O   ILE A 424 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   PHE A 426 " --> pdb=" O   LEU A 591 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 451 through 455
      removed outlier: 4.143A  pdb=" N   ASN A 539 " --> pdb=" O   GLY A 454 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 560 through 562
    Processing sheet with id=AA6, first strand: chain 'A' and resid 837 through 839
      removed outlier: 3.542A  pdb=" N   ALA A 851 " --> pdb=" O   ARG A 858 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1023 through 1029
      removed outlier: 6.938A  pdb=" N   LEU A1079 " --> pdb=" O   LEU A1098 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   LEU A1098 " --> pdb=" O   LEU A1079 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   ASN A1081 " --> pdb=" O   ASN A1096 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   GLU A1057 " --> pdb=" O   LEU A1093 " (cutoff:3.500A)
      removed outlier: 7.368A  pdb=" N   ALA A1095 " --> pdb=" O   GLU A1057 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   MET A1059 " --> pdb=" O   ALA A1095 " (cutoff:3.500A)
      removed outlier: 7.755A  pdb=" N   ASP A1097 " --> pdb=" O   MET A1059 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   GLN A1048 " --> pdb=" O   SER A1032 " (cutoff:3.500A)
      removed outlier: 5.537A  pdb=" N   SER A1032 " --> pdb=" O   GLN A1048 " (cutoff:3.500A)

    401 hydrogen bonds defined for protein.
    1149 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      32 hydrogen bonds
      64 hydrogen bond angles
      0 basepair planarities
      13 basepair parallelities
      26 stacking parallelities
  Total time for adding SS restraints: 4.14

  Time building geometry restraints manager: 2.85 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 1903
        1.33 -     1.46: 2682
        1.46 -     1.58: 4532
        1.58 -     1.70: 64
        1.70 -     1.82: 65
  Bond restraints: 9246
  Sorted by residual:
  bond pdb=" C4  82W A1204 "
       pdb=" C5  82W A1204 "
    ideal  model  delta    sigma   weight residual
    1.510  1.356  0.154 2.00e-02 2.50e+03 5.93e+01
  bond pdb=" C1  82W A1204 "
       pdb=" C2  82W A1204 "
    ideal  model  delta    sigma   weight residual
    1.532  1.381  0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" C1' 82W A1204 "
       pdb=" C2' 82W A1204 "
    ideal  model  delta    sigma   weight residual
    1.451  1.314  0.137 2.00e-02 2.50e+03 4.72e+01
  bond pdb=" C13 82W A1204 "
       pdb=" C14 82W A1204 "
    ideal  model  delta    sigma   weight residual
    1.510  1.374  0.136 2.00e-02 2.50e+03 4.63e+01
  bond pdb=" C6  82W A1204 "
       pdb=" C7  82W A1204 "
    ideal  model  delta    sigma   weight residual
    1.500  1.367  0.133 2.00e-02 2.50e+03 4.40e+01
  ... (remaining 9241 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 11489
        2.24 -     4.48: 1127
        4.48 -     6.71: 58
        6.71 -     8.95: 5
        8.95 -    11.19: 2
  Bond angle restraints: 12681
  Sorted by residual:
  angle pdb=" N   LYS A 743 "
        pdb=" CA  LYS A 743 "
        pdb=" C   LYS A 743 "
      ideal   model   delta    sigma   weight residual
     109.59   98.76   10.83 1.47e+00 4.63e-01 5.43e+01
  angle pdb=" N   PRO A 670 "
        pdb=" CA  PRO A 670 "
        pdb=" C   PRO A 670 "
      ideal   model   delta    sigma   weight residual
     112.47  123.66  -11.19 2.06e+00 2.36e-01 2.95e+01
  angle pdb=" C   ALA A1009 "
        pdb=" N   ILE A1010 "
        pdb=" CA  ILE A1010 "
      ideal   model   delta    sigma   weight residual
     120.24  123.52   -3.28 6.30e-01 2.52e+00 2.71e+01
  angle pdb=" N   ALA A1045 "
        pdb=" CA  ALA A1045 "
        pdb=" C   ALA A1045 "
      ideal   model   delta    sigma   weight residual
     109.23  117.21   -7.98 1.55e+00 4.16e-01 2.65e+01
  angle pdb=" C   MET A 671 "
        pdb=" N   GLY A 672 "
        pdb=" CA  GLY A 672 "
      ideal   model   delta    sigma   weight residual
     120.00  125.21   -5.21 1.10e+00 8.26e-01 2.24e+01
  ... (remaining 12676 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.65: 4999
       22.65 -    45.29: 417
       45.29 -    67.93: 102
       67.93 -    90.58: 8
       90.58 -   113.22: 1
  Dihedral angle restraints: 5527
    sinusoidal: 2468
      harmonic: 3059
  Sorted by residual:
  dihedral pdb=" CA  SER A  20 "
           pdb=" C   SER A  20 "
           pdb=" N   MET A  21 "
           pdb=" CA  MET A  21 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.42  -23.58     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" C   PHE A1061 "
           pdb=" N   PHE A1061 "
           pdb=" CA  PHE A1061 "
           pdb=" CB  PHE A1061 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.48   10.88     0      2.50e+00 1.60e-01 1.90e+01
  dihedral pdb=" C   THR A 774 "
           pdb=" N   THR A 774 "
           pdb=" CA  THR A 774 "
           pdb=" CB  THR A 774 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -132.04   10.04     0      2.50e+00 1.60e-01 1.61e+01
  ... (remaining 5524 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 900
       0.092 -    0.184: 389
       0.184 -    0.276: 89
       0.276 -    0.367: 21
       0.367 -    0.459: 3
  Chirality restraints: 1402
  Sorted by residual:
  chirality pdb=" CA  PRO A 670 "
            pdb=" N   PRO A 670 "
            pdb=" C   PRO A 670 "
            pdb=" CB  PRO A 670 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.26    0.46 2.00e-01 2.50e+01 5.27e+00
  chirality pdb=" C7  82W A1204 "
            pdb=" C12 82W A1204 "
            pdb=" C6  82W A1204 "
            pdb=" C8  82W A1204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.51   -0.41 2.00e-01 2.50e+01 4.24e+00
  chirality pdb=" CA  PHE A1061 "
            pdb=" N   PHE A1061 "
            pdb=" C   PHE A1061 "
            pdb=" CB  PHE A1061 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.54e+00
  ... (remaining 1399 not shown)

  Planarity restraints: 1543
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 490 "   -0.010 2.00e-02 2.50e+03   2.10e-02 4.40e+00
        pdb=" C   MET A 490 "    0.036 2.00e-02 2.50e+03
        pdb=" O   MET A 490 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ALA A 491 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 197 "    0.009 2.00e-02 2.50e+03   1.73e-02 3.00e+00
        pdb=" C   ASP A 197 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ASP A 197 "    0.011 2.00e-02 2.50e+03
        pdb=" N   HIS A 198 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 563 "    0.008 2.00e-02 2.50e+03   1.67e-02 2.80e+00
        pdb=" C   ARG A 563 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ARG A 563 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PRO A 564 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1540 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1909
        2.80 -     3.33: 8009
        3.33 -     3.85: 14131
        3.85 -     4.38: 17291
        4.38 -     4.90: 28396
  Nonbonded interactions: 69736
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  23 "
            pdb="ZN    ZN A1203 "
     model   vdw
     2.280 2.230
  nonbonded pdb=" O   PHE A 925 "
            pdb=" ND1 HIS A 928 "
     model   vdw
     2.372 3.120
  nonbonded pdb=" ND2 ASN A  15 "
            pdb=" O   GLY A  44 "
     model   vdw
     2.379 3.120
  nonbonded pdb=" OD1 ASP A 842 "
            pdb=" N   VAL A 843 "
     model   vdw
     2.481 3.120
  nonbonded pdb=" O   ALA A 112 "
            pdb=" OH  TYR A 296 "
     model   vdw
     2.483 3.040
  ... (remaining 69731 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=0.00 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:             1.570
  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:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     29.290
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
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      :  0.010   0.323   9252  Z= 0.561
  Angle     :  1.335  11.191  12681  Z= 0.916
  Chirality :  0.107   0.459   1402
  Planarity :  0.005   0.027   1543
  Dihedral  : 16.901 113.218   3573
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  8.59 %
    Favored  : 90.13 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.22), residues: 1066
  helix: -0.50 (0.20), residues: 474
  sheet:  0.14 (0.60), residues: 68
  loop : -1.42 (0.23), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP A 561 
 HIS   0.006   0.002   HIS A  48 
 PHE   0.021   0.003   PHE A 850 
 TYR   0.021   0.003   TYR A 392 
 ARG   0.006   0.001   ARG A 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.30119 (  433)
  hydrogen bonds       : angle       8.11730 ( 1213)
  metal coordination   : bond        0.23335 (    6)
  covalent geometry    : bond        0.00830 ( 9246)
  covalent geometry    : angle       1.33517 (12681)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A  196 MET cc_start: 0.8573 (ptm) cc_final: 0.8290 (ptm)
REVERT: A  197 ASP cc_start: 0.8560 (t0) cc_final: 0.8283 (t0)
REVERT: A  622 LYS cc_start: 0.7930 (tppt) cc_final: 0.7714 (ttpp)
REVERT: A  793 MET cc_start: 0.8507 (tpt) cc_final: 0.8239 (tpt)
REVERT: A  968 VAL cc_start: 0.8275 (t) cc_final: 0.7696 (t)
  outliers start: 11
  outliers final: 2
  residues processed: 128
  average time/residue: 1.3869
  time to fit residues: 188.4718
Evaluate side-chains
  61 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  927 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    7.9990
   chunk 82 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 85 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 51 optimal weight:    0.4980
   chunk 63 optimal weight:    0.9990
   chunk 98 optimal weight:    0.0000
   overall best weight:    0.8788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  12 HIS
A 273 GLN
A 687 GLN
A 855 GLN
A 993 HIS
A1063 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.112194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.089680 restraints weight = 14872.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 3.13
r_work: 0.3120 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9252  Z= 0.156
  Angle     :  0.640   7.261  12681  Z= 0.351
  Chirality :  0.045   0.221   1402
  Planarity :  0.005   0.047   1543
  Dihedral  : 15.850 107.978   1631
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 12.54 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.24), residues: 1066
  helix:  1.32 (0.23), residues: 516
  sheet: -0.23 (0.49), residues: 91
  loop : -1.38 (0.25), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1044 
 HIS   0.005   0.001   HIS A1063 
 PHE   0.017   0.001   PHE A 754 
 TYR   0.035   0.002   TYR A 666 
 ARG   0.006   0.000   ARG A  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05500 (  433)
  hydrogen bonds       : angle       5.13677 ( 1213)
  metal coordination   : bond        0.00419 (    6)
  covalent geometry    : bond        0.00330 ( 9246)
  covalent geometry    : angle       0.64033 (12681)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 78
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 ARG cc_start: 0.7711 (mtm110) cc_final: 0.7350 (mtm110)
REVERT: A   95 LYS cc_start: 0.7742 (tmmt) cc_final: 0.7468 (tptp)
REVERT: A  524 ARG cc_start: 0.7620 (ttp-110) cc_final: 0.7249 (ttp-110)
REVERT: A 1084 VAL cc_start: 0.7384 (t) cc_final: 0.6983 (m)
  outliers start: 27
  outliers final: 10
  residues processed: 96
  average time/residue: 1.1866
  time to fit residues: 122.5046
Evaluate side-chains
  63 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 MET
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  915 ASP
Chi-restraints excluded: chain A residue  927 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 104 optimal weight:    9.9990
   chunk 18 optimal weight:    4.9990
   chunk 7 optimal weight:    7.9990
   chunk 42 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0670
   chunk 86 optimal weight:    6.9990
   chunk 73 optimal weight:    7.9990
   chunk 63 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.6518

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  12 HIS
A  15 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.113368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.091330 restraints weight = 15230.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 3.02
r_work: 0.3149 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9252  Z= 0.126
  Angle     :  0.560  12.496  12681  Z= 0.301
  Chirality :  0.042   0.226   1402
  Planarity :  0.004   0.060   1543
  Dihedral  : 15.363  99.502   1631
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 13.82 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.25), residues: 1066
  helix:  1.83 (0.23), residues: 510
  sheet: -0.99 (0.47), residues: 100
  loop : -1.16 (0.25), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 561 
 HIS   0.003   0.001   HIS A 504 
 PHE   0.014   0.001   PHE A 754 
 TYR   0.016   0.001   TYR A 666 
 ARG   0.005   0.000   ARG A  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04006 (  433)
  hydrogen bonds       : angle       4.59952 ( 1213)
  metal coordination   : bond        0.00303 (    6)
  covalent geometry    : bond        0.00270 ( 9246)
  covalent geometry    : angle       0.55970 (12681)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 71
  time to evaluate  : 0.990 
Fit side-chains
REVERT: A  524 ARG cc_start: 0.7529 (ttp-110) cc_final: 0.7107 (ttp-110)
REVERT: A  750 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7147 (mp0)
REVERT: A 1036 ARG cc_start: 0.5893 (mtt180) cc_final: 0.4905 (mmm-85)
REVERT: A 1084 VAL cc_start: 0.7350 (t) cc_final: 0.7007 (m)
  outliers start: 29
  outliers final: 8
  residues processed: 89
  average time/residue: 1.2808
  time to fit residues: 122.2547
Evaluate side-chains
  69 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 MET
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  464 ASP
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  927 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 52 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9990
   chunk 102 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 99 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0770
   overall best weight:    0.6938

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.113685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.091251 restraints weight = 15104.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 2.96
r_work: 0.3158 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.3001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9252  Z= 0.118
  Angle     :  0.524   9.871  12681  Z= 0.284
  Chirality :  0.041   0.262   1402
  Planarity :  0.004   0.056   1543
  Dihedral  : 15.166  91.428   1630
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 14.63 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.25), residues: 1066
  helix:  1.98 (0.23), residues: 508
  sheet: -1.02 (0.48), residues: 95
  loop : -1.15 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 561 
 HIS   0.004   0.001   HIS A 323 
 PHE   0.011   0.001   PHE A 778 
 TYR   0.018   0.001   TYR A 781 
 ARG   0.004   0.000   ARG A  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03584 (  433)
  hydrogen bonds       : angle       4.41663 ( 1213)
  metal coordination   : bond        0.00249 (    6)
  covalent geometry    : bond        0.00257 ( 9246)
  covalent geometry    : angle       0.52409 (12681)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 1.038 
Fit side-chains
REVERT: A  524 ARG cc_start: 0.7491 (ttp-110) cc_final: 0.7123 (ttp-110)
REVERT: A  756 ASP cc_start: 0.7633 (t0) cc_final: 0.7401 (t0)
REVERT: A 1036 ARG cc_start: 0.5781 (mtt180) cc_final: 0.4970 (mmm-85)
REVERT: A 1084 VAL cc_start: 0.7354 (t) cc_final: 0.7019 (m)
  outliers start: 24
  outliers final: 10
  residues processed: 88
  average time/residue: 1.6229
  time to fit residues: 153.5045
Evaluate side-chains
  69 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 1.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  464 ASP
Chi-restraints excluded: chain A residue  469 HIS
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue  965 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 96 optimal weight:    6.9990
   chunk 70 optimal weight:    6.9990
   chunk 38 optimal weight:    0.4980
   chunk 58 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 101 optimal weight:    9.9990
   chunk 22 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9980
   chunk 104 optimal weight:    9.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 198 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.110999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.088702 restraints weight = 15136.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 2.91
r_work: 0.3102 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9252  Z= 0.159
  Angle     :  0.568  10.410  12681  Z= 0.308
  Chirality :  0.044   0.267   1402
  Planarity :  0.005   0.056   1543
  Dihedral  : 15.210  81.834   1630
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 15.10 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.25), residues: 1066
  helix:  1.83 (0.23), residues: 506
  sheet: -1.32 (0.46), residues: 95
  loop : -1.23 (0.26), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 561 
 HIS   0.004   0.001   HIS A 323 
 PHE   0.014   0.001   PHE A 778 
 TYR   0.016   0.002   TYR A 989 
 ARG   0.003   0.000   ARG A  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04668 (  433)
  hydrogen bonds       : angle       4.53679 ( 1213)
  metal coordination   : bond        0.00557 (    6)
  covalent geometry    : bond        0.00366 ( 9246)
  covalent geometry    : angle       0.56782 (12681)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 60
  time to evaluate  : 0.853 
Fit side-chains
REVERT: A  490 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.5282 (mtt)
REVERT: A  756 ASP cc_start: 0.7690 (t0) cc_final: 0.7467 (t0)
REVERT: A 1084 VAL cc_start: 0.7345 (t) cc_final: 0.6982 (m)
  outliers start: 32
  outliers final: 12
  residues processed: 82
  average time/residue: 1.0493
  time to fit residues: 93.8200
Evaluate side-chains
  70 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 1.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  464 ASP
Chi-restraints excluded: chain A residue  469 HIS
Chi-restraints excluded: chain A residue  490 MET
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue  965 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 99 optimal weight:    0.6980
   chunk 42 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   overall best weight:    1.5388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.111276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.088745 restraints weight = 15104.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 2.94
r_work: 0.3110 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9252  Z= 0.148
  Angle     :  0.549  10.965  12681  Z= 0.297
  Chirality :  0.043   0.264   1402
  Planarity :  0.004   0.056   1543
  Dihedral  : 15.141  71.804   1630
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 15.68 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.25), residues: 1066
  helix:  1.72 (0.23), residues: 514
  sheet: -1.32 (0.48), residues: 90
  loop : -1.15 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 561 
 HIS   0.004   0.001   HIS A 323 
 PHE   0.012   0.001   PHE A 778 
 TYR   0.015   0.002   TYR A 989 
 ARG   0.003   0.000   ARG A  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04263 (  433)
  hydrogen bonds       : angle       4.46122 ( 1213)
  metal coordination   : bond        0.00517 (    6)
  covalent geometry    : bond        0.00339 ( 9246)
  covalent geometry    : angle       0.54860 (12681)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 59
  time to evaluate  : 1.065 
Fit side-chains
REVERT: A   85 ARG cc_start: 0.8167 (mtp180) cc_final: 0.7910 (mtm110)
REVERT: A  490 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.5207 (mtt)
REVERT: A  586 MET cc_start: 0.8594 (mmm) cc_final: 0.8361 (mtt)
REVERT: A  756 ASP cc_start: 0.7756 (t0) cc_final: 0.7537 (t0)
REVERT: A 1084 VAL cc_start: 0.7286 (t) cc_final: 0.6919 (m)
  outliers start: 25
  outliers final: 12
  residues processed: 77
  average time/residue: 2.0283
  time to fit residues: 167.1285
Evaluate side-chains
  70 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  464 ASP
Chi-restraints excluded: chain A residue  469 HIS
Chi-restraints excluded: chain A residue  490 MET
Chi-restraints excluded: chain A residue  775 ILE
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue  965 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 68 optimal weight:    8.9990
   chunk 88 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.111154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.088457 restraints weight = 15269.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 2.99
r_work: 0.3101 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.3302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9252  Z= 0.151
  Angle     :  0.552  11.419  12681  Z= 0.297
  Chirality :  0.043   0.263   1402
  Planarity :  0.004   0.057   1543
  Dihedral  : 15.132  59.906   1630
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 17.07 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.25), residues: 1066
  helix:  1.71 (0.23), residues: 514
  sheet: -1.52 (0.46), residues: 100
  loop : -1.12 (0.26), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 561 
 HIS   0.004   0.001   HIS A 323 
 PHE   0.012   0.001   PHE A 778 
 TYR   0.015   0.002   TYR A 989 
 ARG   0.003   0.000   ARG A  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04336 (  433)
  hydrogen bonds       : angle       4.43127 ( 1213)
  metal coordination   : bond        0.00535 (    6)
  covalent geometry    : bond        0.00345 ( 9246)
  covalent geometry    : angle       0.55162 (12681)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 60
  time to evaluate  : 0.881 
Fit side-chains
REVERT: A   21 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.7750 (mtm)
REVERT: A   85 ARG cc_start: 0.8174 (mtp180) cc_final: 0.7897 (mtm110)
REVERT: A  490 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.4871 (mtt)
REVERT: A  586 MET cc_start: 0.8588 (mmm) cc_final: 0.8341 (mtt)
REVERT: A  756 ASP cc_start: 0.7763 (t0) cc_final: 0.7537 (t0)
REVERT: A 1084 VAL cc_start: 0.7247 (t) cc_final: 0.6881 (m)
  outliers start: 23
  outliers final: 13
  residues processed: 76
  average time/residue: 1.0724
  time to fit residues: 88.2933
Evaluate side-chains
  71 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 MET
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  140 MET
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  464 ASP
Chi-restraints excluded: chain A residue  469 HIS
Chi-restraints excluded: chain A residue  490 MET
Chi-restraints excluded: chain A residue  775 ILE
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue  965 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 47 optimal weight:    0.2980
   chunk 59 optimal weight:    1.9990
   chunk 93 optimal weight:    7.9990
   chunk 90 optimal weight:    4.9990
   chunk 100 optimal weight:    9.9990
   chunk 9 optimal weight:    3.9990
   chunk 101 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 877 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.112882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.090335 restraints weight = 15407.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 3.02
r_work: 0.3136 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9252  Z= 0.116
  Angle     :  0.523  11.689  12681  Z= 0.280
  Chirality :  0.041   0.234   1402
  Planarity :  0.004   0.054   1543
  Dihedral  : 15.024  59.615   1630
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 17.89 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.25), residues: 1066
  helix:  1.86 (0.23), residues: 516
  sheet: -1.45 (0.47), residues: 100
  loop : -1.06 (0.26), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 561 
 HIS   0.003   0.001   HIS A 323 
 PHE   0.012   0.001   PHE A 754 
 TYR   0.015   0.001   TYR A 989 
 ARG   0.003   0.000   ARG A  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03443 (  433)
  hydrogen bonds       : angle       4.25786 ( 1213)
  metal coordination   : bond        0.00294 (    6)
  covalent geometry    : bond        0.00255 ( 9246)
  covalent geometry    : angle       0.52324 (12681)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.877 
Fit side-chains
REVERT: A   85 ARG cc_start: 0.8145 (mtp180) cc_final: 0.7574 (mtt180)
REVERT: A  271 MET cc_start: 0.7940 (mmt) cc_final: 0.7474 (mmm)
REVERT: A  586 MET cc_start: 0.8577 (mmm) cc_final: 0.8322 (mtt)
REVERT: A  756 ASP cc_start: 0.7791 (t0) cc_final: 0.7568 (t0)
REVERT: A  774 THR cc_start: 0.8615 (t) cc_final: 0.8112 (m)
REVERT: A 1084 VAL cc_start: 0.7150 (t) cc_final: 0.6802 (m)
  outliers start: 17
  outliers final: 14
  residues processed: 76
  average time/residue: 1.0538
  time to fit residues: 87.1800
Evaluate side-chains
  70 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  140 MET
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  464 ASP
Chi-restraints excluded: chain A residue  469 HIS
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  758 MET
Chi-restraints excluded: chain A residue  775 ILE
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue  965 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 58 optimal weight:    0.2980
   chunk 54 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 60 optimal weight:    0.0170
   chunk 46 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 71 optimal weight:    0.8980
   chunk 77 optimal weight:    5.9990
   overall best weight:    0.5618

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 877 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.113824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.091239 restraints weight = 15320.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 3.01
r_work: 0.3154 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
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      :  0.003   0.057   9252  Z= 0.113
  Angle     :  0.531  11.975  12681  Z= 0.282
  Chirality :  0.041   0.226   1402
  Planarity :  0.004   0.053   1543
  Dihedral  : 14.976  59.950   1630
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 18.70 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.26), residues: 1066
  helix:  1.95 (0.23), residues: 512
  sheet: -1.34 (0.46), residues: 105
  loop : -1.02 (0.27), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 561 
 HIS   0.002   0.000   HIS A 323 
 PHE   0.013   0.001   PHE A 754 
 TYR   0.016   0.001   TYR A 989 
 ARG   0.003   0.000   ARG A  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03203 (  433)
  hydrogen bonds       : angle       4.16318 ( 1213)
  metal coordination   : bond        0.00221 (    6)
  covalent geometry    : bond        0.00250 ( 9246)
  covalent geometry    : angle       0.53090 (12681)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.892 
Fit side-chains
REVERT: A   85 ARG cc_start: 0.8127 (mtp180) cc_final: 0.7571 (mtt180)
REVERT: A  756 ASP cc_start: 0.7795 (t0) cc_final: 0.7577 (t0)
REVERT: A  967 LYS cc_start: 0.7369 (tppt) cc_final: 0.7063 (ptpp)
REVERT: A 1036 ARG cc_start: 0.5893 (mtt180) cc_final: 0.4963 (mmm-85)
REVERT: A 1084 VAL cc_start: 0.7176 (t) cc_final: 0.6849 (m)
  outliers start: 16
  outliers final: 12
  residues processed: 71
  average time/residue: 1.1399
  time to fit residues: 87.6415
Evaluate side-chains
  68 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  464 ASP
Chi-restraints excluded: chain A residue  469 HIS
Chi-restraints excluded: chain A residue  758 MET
Chi-restraints excluded: chain A residue  775 ILE
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue  965 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 92 optimal weight:    9.9990
   chunk 78 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 67 optimal weight:    4.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 877 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.110368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.088420 restraints weight = 15223.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.87
r_work: 0.3084 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.3440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9252  Z= 0.194
  Angle     :  0.613  11.944  12681  Z= 0.327
  Chirality :  0.046   0.226   1402
  Planarity :  0.005   0.053   1543
  Dihedral  : 15.203  59.940   1630
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 19.16 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.25), residues: 1066
  helix:  1.60 (0.23), residues: 515
  sheet: -1.40 (0.47), residues: 100
  loop : -1.15 (0.26), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 561 
 HIS   0.005   0.001   HIS A 323 
 PHE   0.018   0.002   PHE A 754 
 TYR   0.020   0.002   TYR A 989 
 ARG   0.003   0.000   ARG A 272 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04954 (  433)
  hydrogen bonds       : angle       4.45739 ( 1213)
  metal coordination   : bond        0.00720 (    6)
  covalent geometry    : bond        0.00456 ( 9246)
  covalent geometry    : angle       0.61343 (12681)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 55
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A  756 ASP cc_start: 0.7697 (t0) cc_final: 0.7489 (t0)
REVERT: A 1084 VAL cc_start: 0.7185 (t) cc_final: 0.6853 (m)
  outliers start: 17
  outliers final: 10
  residues processed: 66
  average time/residue: 1.3035
  time to fit residues: 93.3500
Evaluate side-chains
  62 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  464 ASP
Chi-restraints excluded: chain A residue  469 HIS
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue  965 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    8.9990
   chunk 32 optimal weight:    0.6980
   chunk 89 optimal weight:    6.9990
   chunk 79 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.110964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.088992 restraints weight = 15204.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 2.87
r_work: 0.3093 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9252  Z= 0.170
  Angle     :  0.598  12.996  12681  Z= 0.318
  Chirality :  0.045   0.244   1402
  Planarity :  0.004   0.055   1543
  Dihedral  : 15.178  59.990   1630
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 19.86 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.25), residues: 1066
  helix:  1.53 (0.23), residues: 515
  sheet: -1.41 (0.47), residues: 100
  loop : -1.20 (0.26), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 561 
 HIS   0.005   0.001   HIS A 323 
 PHE   0.018   0.001   PHE A 754 
 TYR   0.021   0.002   TYR A 989 
 ARG   0.003   0.000   ARG A 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04563 (  433)
  hydrogen bonds       : angle       4.44555 ( 1213)
  metal coordination   : bond        0.00618 (    6)
  covalent geometry    : bond        0.00398 ( 9246)
  covalent geometry    : angle       0.59784 (12681)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6155.80 seconds
wall clock time: 110 minutes 13.57 seconds (6613.57 seconds total)