Starting phenix.real_space_refine
on Tue Mar  3 18:03:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w7v_32349/03_2026/7w7v_32349.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w7v_32349/03_2026/7w7v_32349.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w7v_32349/03_2026/7w7v_32349.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w7v_32349/03_2026/7w7v_32349.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w7v_32349/03_2026/7w7v_32349.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w7v_32349/03_2026/7w7v_32349.map"
  }
  resolution = 3.0
  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=   0.009
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: 7
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      58      5.16       5
     Be      1      3.05       5
     C    4984      2.51       5
     N    1305      2.21       5
     O    1471      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7823
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1012, 7818
          Classifications: {'peptide': 1012}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 45, 'TRANS': 966}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 5
          Unusual residues: {' MG': 1, 'BEF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.92, per 1000 atoms: 0.25
  Number of scatterers: 7823
  At special positions: 0
  Unit cell: (88.395, 98.355, 141.93, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      58     16.00
     Mg      1     11.99
     F       3      9.00
     O    1471      8.00
     N    1305      7.00
     C    4984      6.00
     Be      1      4.00
    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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 269.8 milliseconds
  

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1896

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 6 sheets defined
      54.6% alpha, 14.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 7
    Processing helix  chain 'A' and resid 8 through 17
      removed outlier: 3.623A  pdb=" N   PHE A  16 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 37
    Processing helix  chain 'A' and resid 48 through 56
    Processing helix  chain 'A' and resid 59 through 79
    Processing helix  chain 'A' and resid 84 through 87
      removed outlier: 3.854A  pdb=" N   ALA A  87 " --> pdb=" O   THR A  84 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 84 through 87'
    Processing helix  chain 'A' and resid 88 through 117
      removed outlier: 3.935A  pdb=" N   PHE A  92 " --> pdb=" O   PHE A  88 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   ILE A  94 " --> pdb=" O   GLU A  90 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU A  95 " --> pdb=" O   PRO A  91 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU A  96 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   ILE A  97 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   ALA A 102 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   GLU A 109 " --> pdb=" O   GLY A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 120
      No H-bonds generated for 'chain 'A' and resid 118 through 120'
    Processing helix  chain 'A' and resid 143 through 145
      No H-bonds generated for 'chain 'A' and resid 143 through 145'
    Processing helix  chain 'A' and resid 177 through 182
    Processing helix  chain 'A' and resid 226 through 229
    Processing helix  chain 'A' and resid 230 through 242
    Processing helix  chain 'A' and resid 247 through 276
    Processing helix  chain 'A' and resid 277 through 281
      removed outlier: 4.009A  pdb=" N   ASN A 280 " --> pdb=" O   GLY A 277 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ASP A 281 " --> pdb=" O   HIS A 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 277 through 281'
    Processing helix  chain 'A' and resid 291 through 307
    Processing helix  chain 'A' and resid 310 through 329
    Processing helix  chain 'A' and resid 335 through 340
    Processing helix  chain 'A' and resid 403 through 406
      removed outlier: 3.656A  pdb=" N   GLN A 406 " --> pdb=" O   ASN A 403 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 403 through 406'
    Processing helix  chain 'A' and resid 407 through 421
      removed outlier: 3.942A  pdb=" N   ASN A 421 " --> pdb=" O   CYS A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 452
    Processing helix  chain 'A' and resid 463 through 468
      removed outlier: 4.059A  pdb=" N   ALA A 468 " --> pdb=" O   LYS A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 478
      removed outlier: 3.534A  pdb=" N   SER A 473 " --> pdb=" O   ASN A 469 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   VAL A 474 " --> pdb=" O   ALA A 470 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU A 478 " --> pdb=" O   VAL A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 523
    Processing helix  chain 'A' and resid 537 through 554
      removed outlier: 3.710A  pdb=" N   LYS A 541 " --> pdb=" O   THR A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 586
      removed outlier: 4.090A  pdb=" N   ILE A 584 " --> pdb=" O   SER A 580 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   LYS A 585 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 616
      removed outlier: 3.609A  pdb=" N   SER A 609 " --> pdb=" O   GLU A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 639
    Processing helix  chain 'A' and resid 654 through 660
    Processing helix  chain 'A' and resid 661 through 672
      removed outlier: 3.916A  pdb=" N   ASP A 667 " --> pdb=" O   SER A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 692
    Processing helix  chain 'A' and resid 703 through 705
      No H-bonds generated for 'chain 'A' and resid 703 through 705'
    Processing helix  chain 'A' and resid 706 through 713
    Processing helix  chain 'A' and resid 723 through 730
    Processing helix  chain 'A' and resid 740 through 781
    Processing helix  chain 'A' and resid 787 through 807
      removed outlier: 4.331A  pdb=" N   ASP A 799 " --> pdb=" O   ASN A 795 " (cutoff:3.500A)
      Proline residue:  A 802  - end of helix
    Processing helix  chain 'A' and resid 829 through 857
    Processing helix  chain 'A' and resid 887 through 891
    Processing helix  chain 'A' and resid 892 through 913
      removed outlier: 4.546A  pdb=" N   MET A 896 " --> pdb=" O   SER A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 925 through 928
    Processing helix  chain 'A' and resid 929 through 948
      removed outlier: 3.575A  pdb=" N   VAL A 933 " --> pdb=" O   ASN A 929 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 951 through 956
    Processing helix  chain 'A' and resid 962 through 974
    Processing helix  chain 'A' and resid 974 through 990
      removed outlier: 3.861A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1016 through 1031
      removed outlier: 3.589A  pdb=" N   LEU A1021 " --> pdb=" O   PRO A1017 " (cutoff:3.500A)
      Proline residue:  A1024  - end of helix
      removed outlier: 4.690A  pdb=" N   TRP A1028 " --> pdb=" O   PRO A1024 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   SER A1031 " --> pdb=" O   ILE A1027 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 141
      removed outlier: 6.159A  pdb=" N   SER A 136 " --> pdb=" O   ARG A 131 " (cutoff:3.500A)
      removed outlier: 5.359A  pdb=" N   ARG A 131 " --> pdb=" O   SER A 136 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   LYS A 128 " --> pdb=" O   GLU A 152 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ILE A 150 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
      removed outlier: 5.786A  pdb=" N   VAL A 222 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   LEU A 165 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   VAL A 224 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   ILE A 163 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 189
      removed outlier: 4.594A  pdb=" N   LEU A 173 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASN A 213 " --> pdb=" O   ASP A 176 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 333
      removed outlier: 6.387A  pdb=" N   GLY A 716 " --> pdb=" O   MET A 732 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   LEU A 734 " --> pdb=" O   GLY A 716 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ALA A 718 " --> pdb=" O   LEU A 734 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   THR A 697 " --> pdb=" O   ILE A 715 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   ILE A 717 " --> pdb=" O   THR A 697 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   MET A 699 " --> pdb=" O   ILE A 717 " (cutoff:3.500A)
      removed outlier: 7.738A  pdb=" N   MET A 719 " --> pdb=" O   MET A 699 " (cutoff:3.500A)
      removed outlier: 7.548A  pdb=" N   GLY A 701 " --> pdb=" O   MET A 719 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   VAL A 347 " --> pdb=" O   ALA A 698 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   THR A 700 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   CYS A 349 " --> pdb=" O   THR A 700 " (cutoff:3.500A)
      removed outlier: 8.480A  pdb=" N   PHE A 675 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   MET A 622 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396
      removed outlier: 7.470A  pdb=" N   THR A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 5.145A  pdb=" N   VAL A 372 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 4.941A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 5.217A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   CYS A 595 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.572A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.347A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 16.417A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 5.126A  pdb=" N   PHE A 592 " --> pdb=" O   THR A 565 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   THR A 565 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   MET A 598 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   SER A 493 " --> pdb=" O   PHE A 487 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   PHE A 487 " --> pdb=" O   SER A 493 " (cutoff:3.500A)
      removed outlier: 5.425A  pdb=" N   THR A 499 " --> pdb=" O   LYS A 481 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   LYS A 481 " --> pdb=" O   THR A 499 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396
      removed outlier: 7.470A  pdb=" N   THR A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 5.145A  pdb=" N   VAL A 372 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 4.941A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 5.217A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   CYS A 595 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.572A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.347A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 16.417A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   HIS A 526 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 8.738A  pdb=" N   GLY A 594 " --> pdb=" O   HIS A 526 " (cutoff:3.500A)
      removed outlier: 9.554A  pdb=" N   ARG A 528 " --> pdb=" O   GLY A 594 " (cutoff:3.500A)
      removed outlier: 13.134A  pdb=" N   VAL A 596 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 428

    428 hydrogen bonds defined for protein.
    1239 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.40

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2554
        1.34 -     1.46: 1500
        1.46 -     1.58: 3824
        1.58 -     1.70: 0
        1.70 -     1.82: 90
  Bond restraints: 7968
  Sorted by residual:
  bond pdb=" F2  BEF A2001 "
       pdb="BE   BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.560 -0.084 2.00e-02 2.50e+03 1.78e+01
  bond pdb=" F3  BEF A2001 "
       pdb="BE   BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.546 -0.070 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" F1  BEF A2001 "
       pdb="BE   BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.534 -0.058 2.00e-02 2.50e+03 8.32e+00
  bond pdb=" C   MET A1023 "
       pdb=" N   PRO A1024 "
    ideal  model  delta    sigma   weight residual
    1.337  1.351 -0.014 9.80e-03 1.04e+04 2.18e+00
  bond pdb=" CB  GLU A 748 "
       pdb=" CG  GLU A 748 "
    ideal  model  delta    sigma   weight residual
    1.520  1.490  0.030 3.00e-02 1.11e+03 9.79e-01
  ... (remaining 7963 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.73: 10745
        2.73 -     5.46: 63
        5.46 -     8.20: 3
        8.20 -    10.93: 1
       10.93 -    13.66: 1
  Bond angle restraints: 10813
  Sorted by residual:
  angle pdb=" F2  BEF A2001 "
        pdb="BE   BEF A2001 "
        pdb=" F3  BEF A2001 "
      ideal   model   delta    sigma   weight residual
     119.96  106.30   13.66 3.00e+00 1.11e-01 2.07e+01
  angle pdb=" F1  BEF A2001 "
        pdb="BE   BEF A2001 "
        pdb=" F3  BEF A2001 "
      ideal   model   delta    sigma   weight residual
     120.12  109.90   10.22 3.00e+00 1.11e-01 1.16e+01
  angle pdb=" N   GLY A 291 "
        pdb=" CA  GLY A 291 "
        pdb=" C   GLY A 291 "
      ideal   model   delta    sigma   weight residual
     115.66  110.50    5.16 1.56e+00 4.11e-01 1.09e+01
  angle pdb=" F1  BEF A2001 "
        pdb="BE   BEF A2001 "
        pdb=" F2  BEF A2001 "
      ideal   model   delta    sigma   weight residual
     119.91  112.04    7.87 3.00e+00 1.11e-01 6.88e+00
  angle pdb=" C   GLN A 758 "
        pdb=" N   PHE A 759 "
        pdb=" CA  PHE A 759 "
      ideal   model   delta    sigma   weight residual
     121.14  116.57    4.57 1.75e+00 3.27e-01 6.81e+00
  ... (remaining 10808 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.45: 4388
       17.45 -    34.91: 365
       34.91 -    52.36: 54
       52.36 -    69.81: 8
       69.81 -    87.27: 10
  Dihedral angle restraints: 4825
    sinusoidal: 1901
      harmonic: 2924
  Sorted by residual:
  dihedral pdb=" CA  MET A 536 "
           pdb=" C   MET A 536 "
           pdb=" N   THR A 537 "
           pdb=" CA  THR A 537 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.40   18.60     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CB  GLU A 439 "
           pdb=" CG  GLU A 439 "
           pdb=" CD  GLU A 439 "
           pdb=" OE1 GLU A 439 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.67  -86.67     1      3.00e+01 1.11e-03 1.00e+01
  dihedral pdb=" CA  GLU A 950 "
           pdb=" C   GLU A 950 "
           pdb=" N   PRO A 951 "
           pdb=" CA  PRO A 951 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.86  -15.14     0      5.00e+00 4.00e-02 9.16e+00
  ... (remaining 4822 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 862
       0.036 -    0.072: 288
       0.072 -    0.109: 95
       0.109 -    0.145: 22
       0.145 -    0.181: 2
  Chirality restraints: 1269
  Sorted by residual:
  chirality pdb=" CA  PHE A 759 "
            pdb=" N   PHE A 759 "
            pdb=" C   PHE A 759 "
            pdb=" CB  PHE A 759 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.21e-01
  chirality pdb=" CA  GLU A  90 "
            pdb=" N   GLU A  90 "
            pdb=" C   GLU A  90 "
            pdb=" CB  GLU A  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.29e-01
  chirality pdb=" CA  LEU A 974 "
            pdb=" N   LEU A 974 "
            pdb=" C   LEU A 974 "
            pdb=" CB  LEU A 974 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.27e-01
  ... (remaining 1266 not shown)

  Planarity restraints: 1378
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 534 "   -0.065 5.00e-02 4.00e+02   9.88e-02 1.56e+01
        pdb=" N   PRO A 535 "    0.171 5.00e-02 4.00e+02
        pdb=" CA  PRO A 535 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO A 535 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 796 "    0.009 2.00e-02 2.50e+03   1.71e-02 2.94e+00
        pdb=" C   LEU A 796 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   LEU A 796 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL A 797 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 759 "   -0.011 2.00e-02 2.50e+03   1.04e-02 1.90e+00
        pdb=" CG  PHE A 759 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 759 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 759 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 759 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 759 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 759 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1375 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 69
        2.59 -     3.17: 6785
        3.17 -     3.74: 12824
        3.74 -     4.32: 16942
        4.32 -     4.90: 27900
  Nonbonded interactions: 64520
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 351 "
            pdb=" F3  BEF A2001 "
     model   vdw
     2.010 2.990
  nonbonded pdb=" OD2 ASP A 351 "
            pdb="MG    MG A2002 "
     model   vdw
     2.064 2.170
  nonbonded pdb=" O   THR A 353 "
            pdb="MG    MG A2002 "
     model   vdw
     2.064 2.170
  nonbonded pdb=" OD1 ASP A 702 "
            pdb="MG    MG A2002 "
     model   vdw
     2.076 2.170
  nonbonded pdb=" OE2 GLU A 373 "
            pdb=" OG1 THR A 376 "
     model   vdw
     2.130 3.040
  ... (remaining 64515 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             0.450
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.910
  Find NCS groups from input model:        0.040
  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:             0.000
  Load rotamer database and sin/cos tables:8.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6942
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   0.879   7969  Z= 0.993
  Angle     :  0.555  13.660  10813  Z= 0.299
  Chirality :  0.041   0.181   1269
  Planarity :  0.004   0.099   1378
  Dihedral  : 13.316  87.266   2929
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.27), residues: 1006
  helix:  1.34 (0.24), residues: 483
  sheet: -0.15 (0.51), residues: 97
  loop : -0.44 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 666 
 TYR   0.007   0.001   TYR A 842 
 PHE   0.024   0.001   PHE A 759 
 TRP   0.010   0.001   TRP A 831 
 HIS   0.009   0.001   HIS A 278 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 7968)
  covalent geometry    : angle       0.55503 (10813)
  hydrogen bonds       : bond        0.14476 (  417)
  hydrogen bonds       : angle       6.70791 ( 1239)
  Misc. bond           : bond        0.87917 (    1)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 THR cc_start: 0.7687 (p) cc_final: 0.7479 (t)
REVERT: A  207 MET cc_start: 0.8443 (mmm) cc_final: 0.7943 (mmm)
REVERT: A  218 LYS cc_start: 0.8225 (ttmt) cc_final: 0.7872 (ttmt)
REVERT: A  238 GLU cc_start: 0.6968 (tt0) cc_final: 0.6700 (tt0)
REVERT: A  259 GLN cc_start: 0.5474 (mt0) cc_final: 0.5268 (mt0)
REVERT: A  361 MET cc_start: 0.8147 (tpp) cc_final: 0.7754 (tpp)
REVERT: A  437 VAL cc_start: 0.6945 (m) cc_final: 0.6724 (t)
REVERT: A  452 MET cc_start: 0.8382 (ptt) cc_final: 0.8095 (ptt)
REVERT: A  466 GLU cc_start: 0.6981 (pm20) cc_final: 0.6280 (tp30)
REVERT: A  487 PHE cc_start: 0.6587 (t80) cc_final: 0.6231 (t80)
REVERT: A  508 MET cc_start: 0.5266 (tmm) cc_final: 0.3693 (tpp)
REVERT: A  536 MET cc_start: 0.3242 (mmp) cc_final: 0.2114 (tpp)
REVERT: A  670 LEU cc_start: 0.7702 (mm) cc_final: 0.7441 (mt)
REVERT: A  699 MET cc_start: 0.8088 (tpt) cc_final: 0.5974 (tpt)
REVERT: A  824 LYS cc_start: 0.7183 (mmtt) cc_final: 0.6570 (mmpt)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.5852
  time to fit residues: 101.7621
Evaluate side-chains
  112 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0670
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   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 428 ASN
A 477 GLN
A 918 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.202865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.158651 restraints weight = 8274.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3787 rms_B_bonded: 1.69
r_work: 0.3613 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3475 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7969  Z= 0.123
  Angle     :  0.536  10.111  10813  Z= 0.279
  Chirality :  0.042   0.171   1269
  Planarity :  0.005   0.075   1378
  Dihedral  :  3.904  18.500   1070
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 11.11 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.27), residues: 1006
  helix:  1.29 (0.24), residues: 504
  sheet: -0.42 (0.51), residues: 92
  loop : -0.31 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 324 
 TYR   0.014   0.001   TYR A 497 
 PHE   0.027   0.001   PHE A 759 
 TRP   0.012   0.001   TRP A 927 
 HIS   0.007   0.001   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 7968)
  covalent geometry    : angle       0.53587 (10813)
  hydrogen bonds       : bond        0.04231 (  417)
  hydrogen bonds       : angle       4.67894 ( 1239)
  Misc. bond           : bond        0.00086 (    1)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A    2 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7303 (pm20)
REVERT: A   33 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.6984 (tptp)
REVERT: A  218 LYS cc_start: 0.8345 (ttmt) cc_final: 0.7920 (ttmm)
REVERT: A  238 GLU cc_start: 0.7552 (tt0) cc_final: 0.7285 (tt0)
REVERT: A  259 GLN cc_start: 0.5901 (mt0) cc_final: 0.5523 (mt0)
REVERT: A  361 MET cc_start: 0.8535 (tpp) cc_final: 0.8136 (tpp)
REVERT: A  399 ASP cc_start: 0.7618 (m-30) cc_final: 0.7369 (m-30)
REVERT: A  413 LEU cc_start: 0.8073 (tp) cc_final: 0.7572 (tt)
REVERT: A  439 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6761 (tm-30)
REVERT: A  466 GLU cc_start: 0.7437 (pm20) cc_final: 0.6385 (tp30)
REVERT: A  487 PHE cc_start: 0.6578 (t80) cc_final: 0.6181 (t80)
REVERT: A  508 MET cc_start: 0.5022 (tmm) cc_final: 0.3378 (tpp)
REVERT: A  536 MET cc_start: 0.4261 (mmp) cc_final: 0.2950 (tpp)
REVERT: A  600 ASP cc_start: 0.7715 (t70) cc_final: 0.7427 (t70)
REVERT: A  650 LYS cc_start: 0.8373 (mttt) cc_final: 0.8166 (mtpp)
REVERT: A  670 LEU cc_start: 0.7428 (mm) cc_final: 0.6964 (mt)
REVERT: A  699 MET cc_start: 0.8534 (tpt) cc_final: 0.6453 (tpt)
REVERT: A  714 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8256 (mp0)
REVERT: A  731 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7284 (mt-10)
REVERT: A  756 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7496 (mmt)
REVERT: A  761 ARG cc_start: 0.8124 (mtt180) cc_final: 0.7863 (mpp80)
REVERT: A  824 LYS cc_start: 0.7232 (mmtt) cc_final: 0.6633 (mmpt)
  outliers start: 19
  outliers final: 6
  residues processed: 134
  average time/residue: 0.5513
  time to fit residues: 78.2612
Evaluate side-chains
  117 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  669 CYS
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  756 MET
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue  916 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 50 optimal weight:    9.9990
   chunk 34 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 56 optimal weight:    8.9990
   chunk 57 optimal weight:    0.0770
   chunk 58 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
A 380 ASN
A 477 GLN
** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 918 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.201663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.157940 restraints weight = 8304.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3746 rms_B_bonded: 1.67
r_work: 0.3559 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3419 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7969  Z= 0.116
  Angle     :  0.496   6.453  10813  Z= 0.262
  Chirality :  0.041   0.167   1269
  Planarity :  0.004   0.059   1378
  Dihedral  :  3.893  19.036   1070
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 12.85 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.26), residues: 1006
  helix:  1.61 (0.24), residues: 485
  sheet: -0.65 (0.51), residues: 93
  loop : -0.34 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 324 
 TYR   0.010   0.001   TYR A 497 
 PHE   0.027   0.001   PHE A 759 
 TRP   0.012   0.001   TRP A 927 
 HIS   0.004   0.001   HIS A 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7968)
  covalent geometry    : angle       0.49649 (10813)
  hydrogen bonds       : bond        0.03905 (  417)
  hydrogen bonds       : angle       4.34638 ( 1239)
  Misc. bond           : bond        0.00072 (    1)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6194 (tpp) cc_final: 0.5966 (tpp)
REVERT: A    2 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7272 (pm20)
REVERT: A   33 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7114 (tptp)
REVERT: A  157 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7204 (m-30)
REVERT: A  179 ILE cc_start: 0.7831 (mp) cc_final: 0.7441 (mp)
REVERT: A  205 LYS cc_start: 0.8672 (mttm) cc_final: 0.8375 (mtpp)
REVERT: A  207 MET cc_start: 0.8525 (mmm) cc_final: 0.8145 (mmm)
REVERT: A  218 LYS cc_start: 0.8343 (ttmt) cc_final: 0.7984 (ttmm)
REVERT: A  228 VAL cc_start: 0.8194 (t) cc_final: 0.7948 (m)
REVERT: A  238 GLU cc_start: 0.7537 (tt0) cc_final: 0.7289 (tt0)
REVERT: A  259 GLN cc_start: 0.5960 (mt0) cc_final: 0.5646 (mt0)
REVERT: A  399 ASP cc_start: 0.7623 (m-30) cc_final: 0.7374 (m-30)
REVERT: A  413 LEU cc_start: 0.7987 (tp) cc_final: 0.7510 (tt)
REVERT: A  437 VAL cc_start: 0.7135 (m) cc_final: 0.6910 (t)
REVERT: A  439 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6995 (tm-30)
REVERT: A  466 GLU cc_start: 0.7531 (pm20) cc_final: 0.6417 (tp30)
REVERT: A  487 PHE cc_start: 0.6625 (t80) cc_final: 0.6197 (t80)
REVERT: A  508 MET cc_start: 0.4852 (tmm) cc_final: 0.3013 (tpp)
REVERT: A  536 MET cc_start: 0.4151 (mmp) cc_final: 0.3060 (tpp)
REVERT: A  559 ARG cc_start: 0.7896 (mtp85) cc_final: 0.7502 (mtm110)
REVERT: A  575 MET cc_start: 0.3740 (mmp) cc_final: 0.2393 (ppp)
REVERT: A  731 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7303 (mt-10)
REVERT: A  824 LYS cc_start: 0.7264 (mmtt) cc_final: 0.6667 (mmpt)
REVERT: A 1023 MET cc_start: 0.3372 (tmt) cc_final: 0.2395 (ptm)
  outliers start: 30
  outliers final: 14
  residues processed: 148
  average time/residue: 0.5144
  time to fit residues: 80.7942
Evaluate side-chains
  131 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  595 CYS
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue  916 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 57 optimal weight:    7.9990
   chunk 100 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 85 optimal weight:    0.0770
   chunk 21 optimal weight:    6.9990
   chunk 68 optimal weight:    0.4980
   chunk 67 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   overall best weight:    0.8540

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

Flipped N/Q/H residues before XYZ refinement:
A 250 GLN
A 380 ASN
A 477 GLN
A 918 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.199192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.155922 restraints weight = 8376.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 1.69
r_work: 0.3533 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3395 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7969  Z= 0.123
  Angle     :  0.499   6.466  10813  Z= 0.263
  Chirality :  0.042   0.171   1269
  Planarity :  0.004   0.055   1378
  Dihedral  :  3.892  20.379   1070
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 14.47 %
    Favored  : 82.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.27), residues: 1006
  helix:  1.57 (0.24), residues: 491
  sheet: -0.46 (0.49), residues: 95
  loop : -0.37 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 666 
 TYR   0.010   0.001   TYR A 762 
 PHE   0.027   0.001   PHE A 759 
 TRP   0.011   0.001   TRP A 927 
 HIS   0.003   0.001   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7968)
  covalent geometry    : angle       0.49854 (10813)
  hydrogen bonds       : bond        0.03884 (  417)
  hydrogen bonds       : angle       4.29597 ( 1239)
  Misc. bond           : bond        0.00067 (    1)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 116
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6162 (tpp) cc_final: 0.5754 (tpp)
REVERT: A   33 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7137 (tptp)
REVERT: A  157 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7249 (m-30)
REVERT: A  179 ILE cc_start: 0.7871 (mp) cc_final: 0.7510 (mp)
REVERT: A  205 LYS cc_start: 0.8633 (mttm) cc_final: 0.8379 (mtpp)
REVERT: A  218 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7839 (ttmm)
REVERT: A  228 VAL cc_start: 0.8247 (t) cc_final: 0.8020 (m)
REVERT: A  238 GLU cc_start: 0.7533 (tt0) cc_final: 0.7304 (tt0)
REVERT: A  259 GLN cc_start: 0.5964 (mt0) cc_final: 0.5686 (mt0)
REVERT: A  399 ASP cc_start: 0.7629 (m-30) cc_final: 0.7397 (m-30)
REVERT: A  413 LEU cc_start: 0.8012 (tp) cc_final: 0.7552 (tt)
REVERT: A  437 VAL cc_start: 0.7258 (m) cc_final: 0.7051 (t)
REVERT: A  466 GLU cc_start: 0.7584 (pm20) cc_final: 0.6411 (tp30)
REVERT: A  487 PHE cc_start: 0.6610 (t80) cc_final: 0.6158 (t80)
REVERT: A  508 MET cc_start: 0.4932 (tmm) cc_final: 0.3089 (tpp)
REVERT: A  536 MET cc_start: 0.4324 (mmp) cc_final: 0.3385 (tpt)
REVERT: A  559 ARG cc_start: 0.7900 (mtp85) cc_final: 0.7519 (mtm110)
REVERT: A  575 MET cc_start: 0.3704 (mmp) cc_final: 0.2602 (ppp)
REVERT: A  731 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7334 (mt-10)
REVERT: A  756 MET cc_start: 0.7881 (mtp) cc_final: 0.7218 (mtp)
REVERT: A  761 ARG cc_start: 0.8182 (mtt180) cc_final: 0.7942 (mpp80)
REVERT: A  824 LYS cc_start: 0.7248 (mmtt) cc_final: 0.6657 (mmpt)
REVERT: A  970 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7277 (mp)
REVERT: A 1023 MET cc_start: 0.3810 (tmt) cc_final: 0.2785 (ptt)
  outliers start: 30
  outliers final: 16
  residues processed: 139
  average time/residue: 0.5303
  time to fit residues: 78.3113
Evaluate side-chains
  133 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  595 CYS
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  970 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 13 optimal weight:    6.9990
   chunk 95 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 86 optimal weight:    0.6980
   chunk 94 optimal weight:    6.9990
   chunk 96 optimal weight:    3.9990
   chunk 99 optimal weight:    0.5980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 380 ASN
A 477 GLN
A 918 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.196718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.153316 restraints weight = 8352.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3783 rms_B_bonded: 1.70
r_work: 0.3584 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3449 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7969  Z= 0.150
  Angle     :  0.528   6.201  10813  Z= 0.278
  Chirality :  0.043   0.172   1269
  Planarity :  0.004   0.052   1378
  Dihedral  :  4.061  22.662   1070
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 14.81 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.27), residues: 1006
  helix:  1.44 (0.24), residues: 489
  sheet: -0.62 (0.51), residues: 92
  loop : -0.37 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 666 
 TYR   0.012   0.002   TYR A 762 
 PHE   0.028   0.002   PHE A 759 
 TRP   0.018   0.001   TRP A 927 
 HIS   0.003   0.001   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 7968)
  covalent geometry    : angle       0.52764 (10813)
  hydrogen bonds       : bond        0.04178 (  417)
  hydrogen bonds       : angle       4.39002 ( 1239)
  Misc. bond           : bond        0.00103 (    1)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 121
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A   33 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7232 (tptp)
REVERT: A  157 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7349 (m-30)
REVERT: A  218 LYS cc_start: 0.8396 (ttmt) cc_final: 0.7956 (ttmm)
REVERT: A  238 GLU cc_start: 0.7523 (tt0) cc_final: 0.7236 (tt0)
REVERT: A  259 GLN cc_start: 0.5955 (mt0) cc_final: 0.5665 (mt0)
REVERT: A  381 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7759 (mm-30)
REVERT: A  399 ASP cc_start: 0.7652 (m-30) cc_final: 0.7414 (m-30)
REVERT: A  413 LEU cc_start: 0.8164 (tp) cc_final: 0.7707 (tt)
REVERT: A  435 GLU cc_start: 0.7695 (mp0) cc_final: 0.6840 (mp0)
REVERT: A  466 GLU cc_start: 0.7715 (pm20) cc_final: 0.6570 (tp30)
REVERT: A  487 PHE cc_start: 0.6638 (t80) cc_final: 0.6180 (t80)
REVERT: A  508 MET cc_start: 0.5117 (tmm) cc_final: 0.3255 (tpp)
REVERT: A  536 MET cc_start: 0.4060 (mmp) cc_final: 0.3340 (tpt)
REVERT: A  559 ARG cc_start: 0.8011 (mtp85) cc_final: 0.7592 (mtm110)
REVERT: A  575 MET cc_start: 0.3506 (mmp) cc_final: 0.2297 (ppp)
REVERT: A  731 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7041 (mt-10)
REVERT: A  756 MET cc_start: 0.7925 (mtp) cc_final: 0.7672 (mtp)
REVERT: A  824 LYS cc_start: 0.7390 (mmtt) cc_final: 0.6787 (mmpt)
REVERT: A  919 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7664 (mm-40)
REVERT: A  970 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7706 (mp)
REVERT: A 1023 MET cc_start: 0.3808 (tmt) cc_final: 0.2798 (ptt)
REVERT: A 1039 MET cc_start: 0.3325 (mmm) cc_final: 0.2954 (mmm)
  outliers start: 33
  outliers final: 21
  residues processed: 145
  average time/residue: 0.5391
  time to fit residues: 82.8639
Evaluate side-chains
  140 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  595 CYS
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  748 GLU
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  970 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 91 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 67 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 87 optimal weight:    8.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 380 ASN
A 918 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.197545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.154141 restraints weight = 8380.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 1.74
r_work: 0.3574 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3435 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.2714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7969  Z= 0.156
  Angle     :  0.543   6.185  10813  Z= 0.286
  Chirality :  0.043   0.172   1269
  Planarity :  0.004   0.049   1378
  Dihedral  :  4.121  22.665   1070
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 15.51 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.26), residues: 1006
  helix:  1.24 (0.24), residues: 497
  sheet: -0.95 (0.49), residues: 88
  loop : -0.49 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 750 
 TYR   0.011   0.001   TYR A 762 
 PHE   0.028   0.002   PHE A 759 
 TRP   0.021   0.001   TRP A 927 
 HIS   0.003   0.001   HIS A 943 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 7968)
  covalent geometry    : angle       0.54328 (10813)
  hydrogen bonds       : bond        0.04227 (  417)
  hydrogen bonds       : angle       4.42054 ( 1239)
  Misc. bond           : bond        0.00093 (    1)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 114
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5711 (tpp) cc_final: 0.5368 (tpp)
REVERT: A   33 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7229 (tptp)
REVERT: A   88 PHE cc_start: 0.6005 (m-80) cc_final: 0.5691 (m-80)
REVERT: A  157 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7409 (m-30)
REVERT: A  218 LYS cc_start: 0.8404 (ttmt) cc_final: 0.7968 (ttmm)
REVERT: A  238 GLU cc_start: 0.7527 (tt0) cc_final: 0.7242 (tt0)
REVERT: A  259 GLN cc_start: 0.6187 (mt0) cc_final: 0.5810 (mt0)
REVERT: A  399 ASP cc_start: 0.7651 (m-30) cc_final: 0.7438 (m-30)
REVERT: A  413 LEU cc_start: 0.8210 (tp) cc_final: 0.7759 (tt)
REVERT: A  435 GLU cc_start: 0.7697 (mp0) cc_final: 0.6992 (mp0)
REVERT: A  466 GLU cc_start: 0.7747 (pm20) cc_final: 0.6673 (tp30)
REVERT: A  508 MET cc_start: 0.5208 (tmm) cc_final: 0.3222 (tpp)
REVERT: A  536 MET cc_start: 0.4089 (mmp) cc_final: 0.3348 (tpt)
REVERT: A  559 ARG cc_start: 0.8037 (mtp85) cc_final: 0.7631 (mtm110)
REVERT: A  575 MET cc_start: 0.3334 (mmp) cc_final: 0.2884 (mmt)
REVERT: A  731 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7062 (mt-10)
REVERT: A  824 LYS cc_start: 0.7409 (mmtt) cc_final: 0.6808 (mmpt)
REVERT: A  970 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7723 (mp)
REVERT: A 1023 MET cc_start: 0.3639 (tmt) cc_final: 0.2617 (ptt)
  outliers start: 42
  outliers final: 22
  residues processed: 145
  average time/residue: 0.5570
  time to fit residues: 85.4993
Evaluate side-chains
  134 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  329 LYS
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  595 CYS
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  748 GLU
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  970 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 51 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 17 optimal weight:    0.3980
   chunk 94 optimal weight:    0.0970
   chunk 8 optimal weight:    9.9990
   chunk 95 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 34 optimal weight:    0.3980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 380 ASN
A 918 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.199796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.157360 restraints weight = 8333.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 1.80
r_work: 0.3583 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3443 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7969  Z= 0.111
  Angle     :  0.497   6.551  10813  Z= 0.261
  Chirality :  0.041   0.168   1269
  Planarity :  0.004   0.045   1378
  Dihedral  :  3.946  19.845   1070
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 17.48 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.27), residues: 1006
  helix:  1.65 (0.24), residues: 488
  sheet: -0.97 (0.50), residues: 88
  loop : -0.47 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 761 
 TYR   0.010   0.001   TYR A 130 
 PHE   0.026   0.001   PHE A 759 
 TRP   0.021   0.001   TRP A 927 
 HIS   0.005   0.001   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 7968)
  covalent geometry    : angle       0.49735 (10813)
  hydrogen bonds       : bond        0.03759 (  417)
  hydrogen bonds       : angle       4.26096 ( 1239)
  Misc. bond           : bond        0.00053 (    1)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 114
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5738 (tpp) cc_final: 0.5479 (tpp)
REVERT: A   33 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7163 (tptp)
REVERT: A   88 PHE cc_start: 0.5967 (m-80) cc_final: 0.5533 (m-80)
REVERT: A  218 LYS cc_start: 0.8344 (ttmt) cc_final: 0.8022 (ttmm)
REVERT: A  238 GLU cc_start: 0.7474 (tt0) cc_final: 0.7219 (tt0)
REVERT: A  259 GLN cc_start: 0.6121 (mt0) cc_final: 0.5767 (mt0)
REVERT: A  399 ASP cc_start: 0.7660 (m-30) cc_final: 0.7416 (m-30)
REVERT: A  413 LEU cc_start: 0.8116 (tp) cc_final: 0.7680 (tt)
REVERT: A  435 GLU cc_start: 0.7595 (mp0) cc_final: 0.6872 (mp0)
REVERT: A  466 GLU cc_start: 0.7725 (pm20) cc_final: 0.6558 (tp30)
REVERT: A  508 MET cc_start: 0.5009 (tmm) cc_final: 0.3021 (tpp)
REVERT: A  536 MET cc_start: 0.3922 (mmp) cc_final: 0.3271 (tpt)
REVERT: A  559 ARG cc_start: 0.7964 (mtp85) cc_final: 0.7587 (mtm110)
REVERT: A  575 MET cc_start: 0.3402 (mmp) cc_final: 0.2915 (mmt)
REVERT: A  731 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6981 (mt-10)
REVERT: A  748 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7154 (mt-10)
REVERT: A  824 LYS cc_start: 0.7378 (mmtt) cc_final: 0.6780 (mmpt)
REVERT: A  916 SER cc_start: 0.8672 (OUTLIER) cc_final: 0.8078 (m)
REVERT: A  974 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7306 (mm)
REVERT: A 1023 MET cc_start: 0.3549 (tmt) cc_final: 0.2548 (ptt)
  outliers start: 27
  outliers final: 14
  residues processed: 135
  average time/residue: 0.5251
  time to fit residues: 75.3696
Evaluate side-chains
  130 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  669 CYS
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  748 GLU
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  974 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 95 optimal weight:    0.0770
   chunk 87 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 76 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 85 optimal weight:    8.9990
   overall best weight:    1.3742

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

Flipped N/Q/H residues before XYZ refinement:
A 380 ASN
A 918 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.197302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.153836 restraints weight = 8349.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3739 rms_B_bonded: 1.74
r_work: 0.3539 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3399 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7969  Z= 0.157
  Angle     :  0.543   6.134  10813  Z= 0.287
  Chirality :  0.044   0.242   1269
  Planarity :  0.004   0.044   1378
  Dihedral  :  4.161  23.040   1070
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 17.01 %
    Favored  : 78.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.26), residues: 1006
  helix:  1.32 (0.24), residues: 493
  sheet: -0.91 (0.50), residues: 89
  loop : -0.47 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 761 
 TYR   0.012   0.002   TYR A 836 
 PHE   0.029   0.002   PHE A 759 
 TRP   0.020   0.001   TRP A 927 
 HIS   0.004   0.001   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 7968)
  covalent geometry    : angle       0.54312 (10813)
  hydrogen bonds       : bond        0.04238 (  417)
  hydrogen bonds       : angle       4.44212 ( 1239)
  Misc. bond           : bond        0.00094 (    1)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 109
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5840 (tpp) cc_final: 0.5548 (tpp)
REVERT: A   33 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7204 (tptp)
REVERT: A  126 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7345 (tpp)
REVERT: A  218 LYS cc_start: 0.8349 (ttmt) cc_final: 0.7867 (ttmm)
REVERT: A  238 GLU cc_start: 0.7422 (tt0) cc_final: 0.7152 (tt0)
REVERT: A  259 GLN cc_start: 0.6252 (mt0) cc_final: 0.5897 (mt0)
REVERT: A  399 ASP cc_start: 0.7646 (m-30) cc_final: 0.7414 (m-30)
REVERT: A  413 LEU cc_start: 0.8107 (tp) cc_final: 0.7661 (tt)
REVERT: A  435 GLU cc_start: 0.7649 (mp0) cc_final: 0.6906 (mp0)
REVERT: A  466 GLU cc_start: 0.7727 (pm20) cc_final: 0.6625 (tp30)
REVERT: A  508 MET cc_start: 0.4647 (tmm) cc_final: 0.3267 (tpp)
REVERT: A  536 MET cc_start: 0.3818 (mmp) cc_final: 0.3512 (tpt)
REVERT: A  559 ARG cc_start: 0.8001 (mtp85) cc_final: 0.7563 (mtm110)
REVERT: A  575 MET cc_start: 0.3521 (mmp) cc_final: 0.3025 (mmt)
REVERT: A  731 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6778 (mt-10)
REVERT: A  824 LYS cc_start: 0.7370 (mmtt) cc_final: 0.6755 (mmpt)
REVERT: A  916 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.8115 (m)
REVERT: A  974 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7322 (mm)
REVERT: A 1023 MET cc_start: 0.3850 (tmt) cc_final: 0.2887 (ptt)
  outliers start: 35
  outliers final: 21
  residues processed: 136
  average time/residue: 0.5057
  time to fit residues: 73.0640
Evaluate side-chains
  135 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  126 MET
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  595 CYS
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  748 GLU
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  974 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 72 optimal weight:    0.0870
   chunk 68 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
A 643 GLN
A 918 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.200708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.157758 restraints weight = 8304.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3800 rms_B_bonded: 1.68
r_work: 0.3613 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3475 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7969  Z= 0.114
  Angle     :  0.502   6.618  10813  Z= 0.264
  Chirality :  0.041   0.167   1269
  Planarity :  0.004   0.045   1378
  Dihedral  :  3.972  19.803   1070
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 17.82 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.27), residues: 1006
  helix:  1.65 (0.24), residues: 488
  sheet: -0.92 (0.50), residues: 90
  loop : -0.47 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 371 
 TYR   0.009   0.001   TYR A 836 
 PHE   0.028   0.001   PHE A 759 
 TRP   0.023   0.001   TRP A 927 
 HIS   0.003   0.001   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 7968)
  covalent geometry    : angle       0.50249 (10813)
  hydrogen bonds       : bond        0.03729 (  417)
  hydrogen bonds       : angle       4.24212 ( 1239)
  Misc. bond           : bond        0.00060 (    1)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5828 (tpp) cc_final: 0.5597 (tpp)
REVERT: A   33 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7177 (tptp)
REVERT: A  126 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7247 (tpp)
REVERT: A  218 LYS cc_start: 0.8322 (ttmt) cc_final: 0.7952 (ttmm)
REVERT: A  238 GLU cc_start: 0.7463 (tt0) cc_final: 0.7222 (tt0)
REVERT: A  259 GLN cc_start: 0.6346 (mt0) cc_final: 0.6048 (mt0)
REVERT: A  399 ASP cc_start: 0.7645 (m-30) cc_final: 0.7424 (m-30)
REVERT: A  413 LEU cc_start: 0.8236 (tp) cc_final: 0.7732 (tt)
REVERT: A  435 GLU cc_start: 0.7583 (mp0) cc_final: 0.6864 (mp0)
REVERT: A  466 GLU cc_start: 0.7686 (pm20) cc_final: 0.6635 (tp30)
REVERT: A  536 MET cc_start: 0.3685 (mmp) cc_final: 0.3350 (tpt)
REVERT: A  559 ARG cc_start: 0.7986 (mtp85) cc_final: 0.7614 (mtm110)
REVERT: A  575 MET cc_start: 0.3271 (mmp) cc_final: 0.2811 (mmt)
REVERT: A  702 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.6586 (p0)
REVERT: A  731 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6924 (mt-10)
REVERT: A  748 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7135 (mt-10)
REVERT: A  824 LYS cc_start: 0.7392 (mmtt) cc_final: 0.6793 (mmpt)
REVERT: A  916 SER cc_start: 0.8575 (OUTLIER) cc_final: 0.8068 (m)
REVERT: A  974 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7234 (mm)
REVERT: A 1023 MET cc_start: 0.3767 (tmt) cc_final: 0.2835 (ptt)
  outliers start: 26
  outliers final: 16
  residues processed: 132
  average time/residue: 0.5019
  time to fit residues: 70.5073
Evaluate side-chains
  130 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  126 MET
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  748 GLU
Chi-restraints excluded: chain A residue  915 LEU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  974 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 50 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   chunk 77 optimal weight:    6.9990
   chunk 21 optimal weight:    0.0070
   chunk 35 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
A 918 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.199465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.153671 restraints weight = 8206.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 1.80
r_work: 0.3505 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3364 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7969  Z= 0.115
  Angle     :  0.519   6.525  10813  Z= 0.270
  Chirality :  0.042   0.166   1269
  Planarity :  0.004   0.045   1378
  Dihedral  :  3.924  19.947   1070
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.06 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.27), residues: 1006
  helix:  1.64 (0.24), residues: 492
  sheet: -0.91 (0.50), residues: 89
  loop : -0.43 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 371 
 TYR   0.011   0.001   TYR A 990 
 PHE   0.029   0.001   PHE A 759 
 TRP   0.019   0.001   TRP A 927 
 HIS   0.002   0.001   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7968)
  covalent geometry    : angle       0.51850 (10813)
  hydrogen bonds       : bond        0.03734 (  417)
  hydrogen bonds       : angle       4.24078 ( 1239)
  Misc. bond           : bond        0.00053 (    1)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5714 (tpp) cc_final: 0.5477 (tpp)
REVERT: A   10 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7234 (mp0)
REVERT: A   33 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7107 (tptp)
REVERT: A  126 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7231 (tpp)
REVERT: A  218 LYS cc_start: 0.8261 (ttmt) cc_final: 0.7831 (ttmm)
REVERT: A  238 GLU cc_start: 0.7553 (tt0) cc_final: 0.7300 (tt0)
REVERT: A  259 GLN cc_start: 0.6260 (mt0) cc_final: 0.5976 (mt0)
REVERT: A  370 ASP cc_start: 0.7532 (t0) cc_final: 0.7178 (t70)
REVERT: A  399 ASP cc_start: 0.7671 (m-30) cc_final: 0.7402 (m-30)
REVERT: A  413 LEU cc_start: 0.8107 (tp) cc_final: 0.7610 (tt)
REVERT: A  435 GLU cc_start: 0.7557 (mp0) cc_final: 0.6806 (mp0)
REVERT: A  466 GLU cc_start: 0.7662 (pm20) cc_final: 0.6515 (tp30)
REVERT: A  536 MET cc_start: 0.3439 (mmp) cc_final: 0.3239 (tpt)
REVERT: A  559 ARG cc_start: 0.7966 (mtp85) cc_final: 0.7547 (mtm110)
REVERT: A  575 MET cc_start: 0.3441 (mmp) cc_final: 0.3005 (mmt)
REVERT: A  731 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7080 (mt-10)
REVERT: A  748 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7301 (mt-10)
REVERT: A  824 LYS cc_start: 0.7338 (mmtt) cc_final: 0.6743 (mmpt)
REVERT: A  916 SER cc_start: 0.8521 (OUTLIER) cc_final: 0.8007 (m)
REVERT: A  974 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7155 (mm)
REVERT: A 1023 MET cc_start: 0.3672 (tmt) cc_final: 0.2768 (ptt)
  outliers start: 27
  outliers final: 17
  residues processed: 134
  average time/residue: 0.5306
  time to fit residues: 75.6108
Evaluate side-chains
  132 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  126 MET
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  611 LYS
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  748 GLU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  974 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 98 optimal weight:    0.1980
   chunk 39 optimal weight:    8.9990
   chunk 75 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 918 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.199190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.152673 restraints weight = 8184.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 1.75
r_work: 0.3518 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3377 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.2955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7969  Z= 0.119
  Angle     :  0.522   6.482  10813  Z= 0.273
  Chirality :  0.042   0.187   1269
  Planarity :  0.004   0.045   1378
  Dihedral  :  3.932  20.552   1070
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 19.21 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.27), residues: 1006
  helix:  1.59 (0.24), residues: 494
  sheet: -0.92 (0.50), residues: 89
  loop : -0.45 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 371 
 TYR   0.010   0.001   TYR A 836 
 PHE   0.030   0.001   PHE A 759 
 TRP   0.019   0.001   TRP A 927 
 HIS   0.002   0.001   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7968)
  covalent geometry    : angle       0.52189 (10813)
  hydrogen bonds       : bond        0.03805 (  417)
  hydrogen bonds       : angle       4.25470 ( 1239)
  Misc. bond           : bond        0.00062 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3128.00 seconds
wall clock time: 53 minutes 49.86 seconds (3229.86 seconds total)