Starting phenix.real_space_refine
on Fri Jun  6 14:12:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w7v_32349/06_2025/7w7v_32349.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w7v_32349/06_2025/7w7v_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w7v_32349/06_2025/7w7v_32349.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w7v_32349/06_2025/7w7v_32349.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w7v_32349/06_2025/7w7v_32349.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w7v_32349/06_2025/7w7v_32349.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.22, per 1000 atoms: 0.80
  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: 2.77
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.70
  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: 4.35

  Time building geometry restraints manager: 3.20 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:                  0.010
  Normalize map: mean=0, sd=1:             111.770
  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:             0.040
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     30.420
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:39.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  182.330
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (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
 TRP   0.010   0.001   TRP A 831 
 HIS   0.009   0.001   HIS A 278 
 PHE   0.024   0.001   PHE A 759 
 TYR   0.007   0.001   TYR A 842 
 ARG   0.004   0.000   ARG A 666 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14476 (  417)
  hydrogen bonds       : angle       6.70791 ( 1239)
  covalent geometry    : bond        0.00256 ( 7968)
  covalent geometry    : angle       0.55503 (10813)
  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  : 0.926 
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: 0.8148 (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: 0.3243 (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: 1.3979
  time to fit residues: 244.2662
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  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.0980
   chunk 76 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 51 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:   10.0000
   chunk 58 optimal weight:    8.9990
   chunk 91 optimal weight:   10.0000
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 111 ASN
A 380 ASN
A 428 ASN
A 477 GLN
A 918 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.201761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.157849 restraints weight = 8226.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3793 rms_B_bonded: 1.66
r_work: 0.3614 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3478 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.1654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7969  Z= 0.137
  Angle     :  0.552  10.712  10813  Z= 0.288
  Chirality :  0.043   0.172   1269
  Planarity :  0.005   0.076   1378
  Dihedral  :  3.981  19.857   1070
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 10.88 %
    Favored  : 86.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.27), residues: 1006
  helix:  1.23 (0.24), residues: 504
  sheet: -0.53 (0.51), residues: 93
  loop : -0.34 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 927 
 HIS   0.006   0.001   HIS A 405 
 PHE   0.030   0.001   PHE A 367 
 TYR   0.013   0.001   TYR A 497 
 ARG   0.005   0.001   ARG A 324 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04264 (  417)
  hydrogen bonds       : angle       4.67781 ( 1239)
  covalent geometry    : bond        0.00307 ( 7968)
  covalent geometry    : angle       0.55242 (10813)
  Misc. bond           : bond        0.00016 (    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
  143 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 1.309 
Fit side-chains
REVERT: A    2 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7387 (pm20)
REVERT: A   33 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7048 (tptp)
REVERT: A  157 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7300 (m-30)
REVERT: A  218 LYS cc_start: 0.8379 (ttmt) cc_final: 0.7925 (ttmt)
REVERT: A  238 GLU cc_start: 0.7561 (tt0) cc_final: 0.7284 (tt0)
REVERT: A  243 GLU cc_start: 0.6924 (tp30) cc_final: 0.6717 (pm20)
REVERT: A  259 GLN cc_start: 0.5992 (mt0) cc_final: 0.5629 (mt0)
REVERT: A  361 MET cc_start: 0.8547 (tpp) cc_final: 0.8200 (tpp)
REVERT: A  399 ASP cc_start: 0.7619 (m-30) cc_final: 0.7385 (m-30)
REVERT: A  413 LEU cc_start: 0.8145 (tp) cc_final: 0.7632 (tt)
REVERT: A  437 VAL cc_start: 0.7137 (m) cc_final: 0.6860 (t)
REVERT: A  439 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7028 (tm-30)
REVERT: A  466 GLU cc_start: 0.7475 (pm20) cc_final: 0.6455 (tp30)
REVERT: A  487 PHE cc_start: 0.6533 (t80) cc_final: 0.6158 (t80)
REVERT: A  508 MET cc_start: 0.5086 (tmm) cc_final: 0.3388 (tpp)
REVERT: A  536 MET cc_start: 0.4268 (mmp) cc_final: 0.2990 (tpp)
REVERT: A  575 MET cc_start: 0.3912 (mmp) cc_final: 0.3224 (mmt)
REVERT: A  650 LYS cc_start: 0.8413 (mttt) cc_final: 0.8205 (mtpp)
REVERT: A  670 LEU cc_start: 0.7642 (mm) cc_final: 0.7166 (mt)
REVERT: A  699 MET cc_start: 0.8547 (tpt) cc_final: 0.6363 (tpt)
REVERT: A  731 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7267 (mt-10)
REVERT: A  756 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7508 (mmt)
REVERT: A  824 LYS cc_start: 0.7275 (mmtt) cc_final: 0.6668 (mmpt)
REVERT: A 1023 MET cc_start: 0.3214 (tmt) cc_final: 0.2394 (ptt)
  outliers start: 22
  outliers final: 9
  residues processed: 137
  average time/residue: 1.3205
  time to fit residues: 192.7765
Evaluate side-chains
  118 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue  157 ASP
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  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 83 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 60 optimal weight:    0.1980
   chunk 41 optimal weight:    2.9990
   chunk 91 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 44 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   chunk 99 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.4165 r_free = 0.4165 target = 0.200652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.156263 restraints weight = 8358.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 1.71
r_work: 0.3596 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3458 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7255
moved from start:          0.1989

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= 0.118
  Angle     :  0.498   6.567  10813  Z= 0.263
  Chirality :  0.042   0.170   1269
  Planarity :  0.005   0.063   1378
  Dihedral  :  3.904  19.291   1070
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 13.43 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.26), residues: 1006
  helix:  1.50 (0.24), residues: 491
  sheet: -0.76 (0.50), residues: 93
  loop : -0.39 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 927 
 HIS   0.003   0.001   HIS A 566 
 PHE   0.027   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 497 
 ARG   0.004   0.000   ARG A 324 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03955 (  417)
  hydrogen bonds       : angle       4.36979 ( 1239)
  covalent geometry    : bond        0.00263 ( 7968)
  covalent geometry    : angle       0.49821 (10813)
  Misc. bond           : bond        0.00058 (    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
  150 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 122
  time to evaluate  : 0.848 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6161 (tpp) cc_final: 0.5791 (tpp)
REVERT: A   33 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7108 (tptp)
REVERT: A  179 ILE cc_start: 0.7831 (mp) cc_final: 0.7436 (mp)
REVERT: A  205 LYS cc_start: 0.8665 (mttm) cc_final: 0.8377 (mtpp)
REVERT: A  218 LYS cc_start: 0.8342 (ttmt) cc_final: 0.7960 (ttmt)
REVERT: A  228 VAL cc_start: 0.8228 (t) cc_final: 0.7985 (m)
REVERT: A  238 GLU cc_start: 0.7531 (tt0) cc_final: 0.7295 (tt0)
REVERT: A  243 GLU cc_start: 0.6874 (tp30) cc_final: 0.6476 (pm20)
REVERT: A  259 GLN cc_start: 0.6014 (mt0) cc_final: 0.5696 (mt0)
REVERT: A  399 ASP cc_start: 0.7624 (m-30) cc_final: 0.7378 (m-30)
REVERT: A  413 LEU cc_start: 0.8003 (tp) cc_final: 0.7515 (tt)
REVERT: A  437 VAL cc_start: 0.7175 (m) cc_final: 0.6941 (t)
REVERT: A  439 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7039 (tm-30)
REVERT: A  466 GLU cc_start: 0.7540 (pm20) cc_final: 0.6426 (tp30)
REVERT: A  487 PHE cc_start: 0.6546 (t80) cc_final: 0.6131 (t80)
REVERT: A  508 MET cc_start: 0.4884 (tmm) cc_final: 0.3068 (tpp)
REVERT: A  518 GLU cc_start: 0.6445 (pm20) cc_final: 0.5897 (mm-30)
REVERT: A  536 MET cc_start: 0.4168 (mmp) cc_final: 0.3098 (tpt)
REVERT: A  559 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7473 (mtm110)
REVERT: A  575 MET cc_start: 0.3848 (mmp) cc_final: 0.2414 (ppp)
REVERT: A  731 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7283 (mt-10)
REVERT: A  824 LYS cc_start: 0.7229 (mmtt) cc_final: 0.6640 (mmpt)
REVERT: A  968 MET cc_start: 0.7724 (tpt) cc_final: 0.7504 (tpt)
REVERT: A 1023 MET cc_start: 0.3387 (tmt) cc_final: 0.2455 (ptt)
  outliers start: 28
  outliers final: 14
  residues processed: 143
  average time/residue: 1.1090
  time to fit residues: 168.9565
Evaluate side-chains
  130 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
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  188 ILE
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  369 LEU
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 68 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 91 optimal weight:    6.9990
   chunk 46 optimal weight:    0.4980
   chunk 29 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 85 optimal weight:    5.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A   3 ASN
A 380 ASN
A 918 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.196756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.153994 restraints weight = 8292.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 1.75
r_work: 0.3538 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3401 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7969  Z= 0.170
  Angle     :  0.554   6.281  10813  Z= 0.294
  Chirality :  0.044   0.177   1269
  Planarity :  0.005   0.059   1378
  Dihedral  :  4.188  23.427   1070
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 15.05 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.26), residues: 1006
  helix:  1.23 (0.24), residues: 494
  sheet: -0.54 (0.49), residues: 95
  loop : -0.45 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 927 
 HIS   0.005   0.001   HIS A 566 
 PHE   0.030   0.002   PHE A 367 
 TYR   0.013   0.002   TYR A 762 
 ARG   0.003   0.001   ARG A 750 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04441 (  417)
  hydrogen bonds       : angle       4.52533 ( 1239)
  covalent geometry    : bond        0.00399 ( 7968)
  covalent geometry    : angle       0.55440 (10813)
  Misc. bond           : bond        0.00114 (    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
  149 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 117
  time to evaluate  : 0.890 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6258 (tpp) cc_final: 0.5920 (tpp)
REVERT: A   33 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7207 (tptp)
REVERT: A  157 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7362 (m-30)
REVERT: A  179 ILE cc_start: 0.7888 (mp) cc_final: 0.7553 (mp)
REVERT: A  205 LYS cc_start: 0.8640 (mttm) cc_final: 0.8439 (mtpp)
REVERT: A  218 LYS cc_start: 0.8360 (ttmt) cc_final: 0.7999 (ttmt)
REVERT: A  228 VAL cc_start: 0.8396 (t) cc_final: 0.8191 (m)
REVERT: A  238 GLU cc_start: 0.7524 (tt0) cc_final: 0.7238 (tt0)
REVERT: A  259 GLN cc_start: 0.5865 (mt0) cc_final: 0.5578 (mt0)
REVERT: A  384 ILE cc_start: 0.8349 (mm) cc_final: 0.7931 (mp)
REVERT: A  399 ASP cc_start: 0.7648 (m-30) cc_final: 0.7433 (m-30)
REVERT: A  413 LEU cc_start: 0.8137 (tp) cc_final: 0.7661 (tt)
REVERT: A  435 GLU cc_start: 0.7708 (mp0) cc_final: 0.6857 (mp0)
REVERT: A  437 VAL cc_start: 0.7524 (m) cc_final: 0.7319 (t)
REVERT: A  439 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7356 (tm-30)
REVERT: A  466 GLU cc_start: 0.7715 (pm20) cc_final: 0.6545 (tp30)
REVERT: A  487 PHE cc_start: 0.6577 (t80) cc_final: 0.6116 (t80)
REVERT: A  508 MET cc_start: 0.5092 (tmm) cc_final: 0.3239 (tpp)
REVERT: A  536 MET cc_start: 0.4237 (mmp) cc_final: 0.3318 (tpt)
REVERT: A  559 ARG cc_start: 0.7976 (mtp85) cc_final: 0.7549 (mtm110)
REVERT: A  575 MET cc_start: 0.3478 (mmp) cc_final: 0.2261 (ppp)
REVERT: A  731 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7083 (mt-10)
REVERT: A  824 LYS cc_start: 0.7358 (mmtt) cc_final: 0.6747 (mmpt)
REVERT: A  970 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7605 (mp)
REVERT: A 1023 MET cc_start: 0.3913 (tmt) cc_final: 0.2886 (ptt)
  outliers start: 32
  outliers final: 18
  residues processed: 139
  average time/residue: 1.1745
  time to fit residues: 173.9201
Evaluate side-chains
  133 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
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  339 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  439 GLU
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  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 60 optimal weight:    0.9990
   chunk 51 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 84 optimal weight:    0.7980
   chunk 94 optimal weight:    0.0770
   chunk 61 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.6940

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.200254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.156298 restraints weight = 8196.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 1.73
r_work: 0.3603 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3465 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.2502

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= 0.115
  Angle     :  0.498   6.616  10813  Z= 0.263
  Chirality :  0.042   0.164   1269
  Planarity :  0.004   0.053   1378
  Dihedral  :  3.968  19.973   1070
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 16.44 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.27), residues: 1006
  helix:  1.60 (0.24), residues: 486
  sheet: -0.95 (0.49), residues: 90
  loop : -0.40 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 927 
 HIS   0.003   0.001   HIS A 405 
 PHE   0.028   0.001   PHE A 759 
 TYR   0.009   0.001   TYR A 762 
 ARG   0.003   0.000   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03822 (  417)
  hydrogen bonds       : angle       4.31313 ( 1239)
  covalent geometry    : bond        0.00257 ( 7968)
  covalent geometry    : angle       0.49780 (10813)
  Misc. bond           : bond        0.00058 (    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
  151 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 120
  time to evaluate  : 0.899 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6042 (tpp) cc_final: 0.5658 (tpp)
REVERT: A   33 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7176 (tptp)
REVERT: A  218 LYS cc_start: 0.8355 (ttmt) cc_final: 0.7983 (ttmt)
REVERT: A  238 GLU cc_start: 0.7525 (tt0) cc_final: 0.7207 (tt0)
REVERT: A  243 GLU cc_start: 0.6965 (tp30) cc_final: 0.6615 (pm20)
REVERT: A  259 GLN cc_start: 0.6084 (mt0) cc_final: 0.5790 (mt0)
REVERT: A  399 ASP cc_start: 0.7653 (m-30) cc_final: 0.7427 (m-30)
REVERT: A  413 LEU cc_start: 0.8189 (tp) cc_final: 0.7735 (tt)
REVERT: A  435 GLU cc_start: 0.7548 (mp0) cc_final: 0.6915 (mp0)
REVERT: A  437 VAL cc_start: 0.7397 (m) cc_final: 0.7187 (t)
REVERT: A  466 GLU cc_start: 0.7729 (pm20) cc_final: 0.6578 (tp30)
REVERT: A  508 MET cc_start: 0.5116 (tmm) cc_final: 0.3179 (tpp)
REVERT: A  518 GLU cc_start: 0.6284 (pm20) cc_final: 0.5783 (mm-30)
REVERT: A  536 MET cc_start: 0.4117 (mmp) cc_final: 0.3264 (tpt)
REVERT: A  559 ARG cc_start: 0.7977 (mtp85) cc_final: 0.7607 (mtm110)
REVERT: A  575 MET cc_start: 0.3288 (mmp) cc_final: 0.2095 (ppp)
REVERT: A  731 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7308 (mt-10)
REVERT: A  824 LYS cc_start: 0.7297 (mmtt) cc_final: 0.6719 (mmpt)
REVERT: A 1023 MET cc_start: 0.3773 (tmt) cc_final: 0.2788 (ptt)
REVERT: A 1039 MET cc_start: 0.3338 (mmm) cc_final: 0.2950 (mmm)
  outliers start: 31
  outliers final: 13
  residues processed: 143
  average time/residue: 1.1764
  time to fit residues: 178.6788
Evaluate side-chains
  131 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
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  185 VAL
Chi-restraints excluded: chain A residue  188 ILE
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  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  915 LEU
Chi-restraints excluded: chain A residue  916 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 58 optimal weight:    5.9990
   chunk 8 optimal weight:    0.2980
   chunk 92 optimal weight:    1.9990
   chunk 85 optimal weight:    0.6980
   chunk 86 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 29 optimal weight:    0.4980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4157 r_free = 0.4157 target = 0.199962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.154117 restraints weight = 8203.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3700 rms_B_bonded: 1.80
r_work: 0.3509 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3373 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7969  Z= 0.113
  Angle     :  0.497   6.640  10813  Z= 0.261
  Chirality :  0.041   0.167   1269
  Planarity :  0.004   0.049   1378
  Dihedral  :  3.879  19.806   1070
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 17.36 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.27), residues: 1006
  helix:  1.69 (0.24), residues: 489
  sheet: -0.95 (0.49), residues: 90
  loop : -0.42 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 927 
 HIS   0.004   0.001   HIS A 405 
 PHE   0.028   0.001   PHE A 759 
 TYR   0.009   0.001   TYR A 990 
 ARG   0.002   0.000   ARG A 324 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03715 (  417)
  hydrogen bonds       : angle       4.22449 ( 1239)
  covalent geometry    : bond        0.00251 ( 7968)
  covalent geometry    : angle       0.49682 (10813)
  Misc. bond           : bond        0.00054 (    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
  148 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.903 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5727 (tpp) cc_final: 0.5498 (tpp)
REVERT: A    2 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7296 (pm20)
REVERT: A   33 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7124 (tptp)
REVERT: A   88 PHE cc_start: 0.6016 (m-80) cc_final: 0.5699 (m-80)
REVERT: A  218 LYS cc_start: 0.8273 (ttmt) cc_final: 0.7840 (ttmt)
REVERT: A  238 GLU cc_start: 0.7540 (tt0) cc_final: 0.7275 (tt0)
REVERT: A  243 GLU cc_start: 0.6855 (tp30) cc_final: 0.6390 (pm20)
REVERT: A  259 GLN cc_start: 0.5983 (mt0) cc_final: 0.5707 (mt0)
REVERT: A  399 ASP cc_start: 0.7672 (m-30) cc_final: 0.7408 (m-30)
REVERT: A  413 LEU cc_start: 0.7936 (tp) cc_final: 0.7506 (tt)
REVERT: A  435 GLU cc_start: 0.7545 (mp0) cc_final: 0.6876 (mp0)
REVERT: A  466 GLU cc_start: 0.7620 (pm20) cc_final: 0.6494 (tp30)
REVERT: A  508 MET cc_start: 0.5014 (tmm) cc_final: 0.3069 (tpp)
REVERT: A  518 GLU cc_start: 0.6180 (pm20) cc_final: 0.5680 (mm-30)
REVERT: A  536 MET cc_start: 0.4144 (mmp) cc_final: 0.3395 (tpt)
REVERT: A  559 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7553 (mtm110)
REVERT: A  575 MET cc_start: 0.3496 (mmp) cc_final: 0.2298 (ppp)
REVERT: A  731 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7102 (mt-10)
REVERT: A  824 LYS cc_start: 0.7221 (mmtt) cc_final: 0.6653 (mmpt)
REVERT: A  974 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7332 (mm)
REVERT: A 1023 MET cc_start: 0.3567 (tmt) cc_final: 0.2557 (ptt)
REVERT: A 1039 MET cc_start: 0.3357 (mmm) cc_final: 0.2919 (mmm)
  outliers start: 29
  outliers final: 16
  residues processed: 141
  average time/residue: 1.1039
  time to fit residues: 166.3522
Evaluate side-chains
  132 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
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  185 VAL
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  611 LYS
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  670 LEU
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  974 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    0.1980
   chunk 99 optimal weight:    0.4980
   chunk 88 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 49 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0040
   overall best weight:    0.4392

-------------------------------------------------------------------------------
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 = 0.4167 r_free = 0.4167 target = 0.201052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.155446 restraints weight = 8241.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 1.79
r_work: 0.3525 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3381 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7969  Z= 0.105
  Angle     :  0.490   6.729  10813  Z= 0.257
  Chirality :  0.041   0.168   1269
  Planarity :  0.004   0.046   1378
  Dihedral  :  3.821  18.930   1070
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 16.67 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.27), residues: 1006
  helix:  1.79 (0.24), residues: 489
  sheet: -0.96 (0.50), residues: 90
  loop : -0.40 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 927 
 HIS   0.004   0.001   HIS A 405 
 PHE   0.029   0.001   PHE A 759 
 TYR   0.007   0.001   TYR A 762 
 ARG   0.002   0.000   ARG A 324 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03531 (  417)
  hydrogen bonds       : angle       4.13850 ( 1239)
  covalent geometry    : bond        0.00229 ( 7968)
  covalent geometry    : angle       0.49001 (10813)
  Misc. bond           : bond        0.00046 (    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
  152 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 119
  time to evaluate  : 0.892 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5662 (tpp) cc_final: 0.5321 (tpp)
REVERT: A   10 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7209 (mp0)
REVERT: A   33 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7073 (tptp)
REVERT: A   88 PHE cc_start: 0.5899 (m-80) cc_final: 0.5599 (m-80)
REVERT: A  218 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7745 (ttmt)
REVERT: A  238 GLU cc_start: 0.7565 (tt0) cc_final: 0.7316 (tt0)
REVERT: A  243 GLU cc_start: 0.6814 (tp30) cc_final: 0.6411 (pm20)
REVERT: A  259 GLN cc_start: 0.5987 (mt0) cc_final: 0.5705 (mt0)
REVERT: A  399 ASP cc_start: 0.7648 (m-30) cc_final: 0.7383 (m-30)
REVERT: A  413 LEU cc_start: 0.7943 (tp) cc_final: 0.7450 (tt)
REVERT: A  435 GLU cc_start: 0.7448 (mp0) cc_final: 0.6673 (mp0)
REVERT: A  466 GLU cc_start: 0.7610 (pm20) cc_final: 0.6460 (tp30)
REVERT: A  508 MET cc_start: 0.4868 (tmm) cc_final: 0.2965 (tpp)
REVERT: A  518 GLU cc_start: 0.6126 (pm20) cc_final: 0.5649 (mm-30)
REVERT: A  536 MET cc_start: 0.4020 (mmp) cc_final: 0.3325 (tpt)
REVERT: A  559 ARG cc_start: 0.7926 (mtp85) cc_final: 0.7490 (mtm110)
REVERT: A  575 MET cc_start: 0.3581 (mmp) cc_final: 0.2290 (ppp)
REVERT: A  731 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7085 (mt-10)
REVERT: A  824 LYS cc_start: 0.7206 (mmtt) cc_final: 0.6632 (mmpt)
REVERT: A  970 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7044 (mp)
REVERT: A  974 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7168 (mm)
REVERT: A 1023 MET cc_start: 0.3670 (tmt) cc_final: 0.2663 (ptt)
REVERT: A 1039 MET cc_start: 0.2903 (mmm) cc_final: 0.2552 (mmm)
  outliers start: 33
  outliers final: 17
  residues processed: 146
  average time/residue: 1.1231
  time to fit residues: 174.9903
Evaluate side-chains
  135 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
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  110 ARG
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  669 CYS
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  915 LEU
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  970 LEU
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 7 optimal weight:    0.9990
   chunk 90 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0030
   chunk 18 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   chunk 72 optimal weight:    4.9990
   chunk 8 optimal weight:    0.4980
   chunk 75 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 13 optimal weight:   10.0000
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.8394

-------------------------------------------------------------------------------
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 = 0.4149 r_free = 0.4149 target = 0.199023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.153474 restraints weight = 8275.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 1.78
r_work: 0.3503 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3363 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.2770

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= 0.124
  Angle     :  0.521   6.259  10813  Z= 0.271
  Chirality :  0.042   0.211   1269
  Planarity :  0.004   0.045   1378
  Dihedral  :  3.890  20.994   1070
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 17.59 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.27), residues: 1006
  helix:  1.58 (0.24), residues: 495
  sheet: -0.96 (0.49), residues: 89
  loop : -0.38 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 927 
 HIS   0.003   0.001   HIS A 405 
 PHE   0.030   0.001   PHE A 759 
 TYR   0.009   0.001   TYR A 762 
 ARG   0.003   0.000   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03811 (  417)
  hydrogen bonds       : angle       4.21997 ( 1239)
  covalent geometry    : bond        0.00284 ( 7968)
  covalent geometry    : angle       0.52116 (10813)
  Misc. bond           : bond        0.00069 (    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
  147 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 118
  time to evaluate  : 0.844 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5550 (tpp) cc_final: 0.5279 (tpp)
REVERT: A   33 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7082 (tptp)
REVERT: A   88 PHE cc_start: 0.5934 (m-80) cc_final: 0.5654 (m-80)
REVERT: A  218 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7753 (ttmt)
REVERT: A  238 GLU cc_start: 0.7530 (tt0) cc_final: 0.7275 (tt0)
REVERT: A  243 GLU cc_start: 0.6840 (tp30) cc_final: 0.6371 (pm20)
REVERT: A  259 GLN cc_start: 0.5941 (mt0) cc_final: 0.5626 (mt0)
REVERT: A  324 ARG cc_start: 0.6609 (mtp85) cc_final: 0.6325 (mtp85)
REVERT: A  399 ASP cc_start: 0.7656 (m-30) cc_final: 0.7367 (m-30)
REVERT: A  413 LEU cc_start: 0.7963 (tp) cc_final: 0.7465 (tt)
REVERT: A  435 GLU cc_start: 0.7539 (mp0) cc_final: 0.6806 (mp0)
REVERT: A  466 GLU cc_start: 0.7625 (pm20) cc_final: 0.6477 (tp30)
REVERT: A  508 MET cc_start: 0.4476 (tmm) cc_final: 0.3163 (tpp)
REVERT: A  518 GLU cc_start: 0.6269 (pm20) cc_final: 0.5797 (mm-30)
REVERT: A  559 ARG cc_start: 0.7949 (mtp85) cc_final: 0.7528 (mtm110)
REVERT: A  575 MET cc_start: 0.3463 (mmp) cc_final: 0.2974 (mmt)
REVERT: A  598 MET cc_start: 0.8518 (ptp) cc_final: 0.7545 (ptp)
REVERT: A  731 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6866 (mt-10)
REVERT: A  824 LYS cc_start: 0.7206 (mmtt) cc_final: 0.6624 (mmpt)
REVERT: A  916 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.8049 (m)
REVERT: A  970 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7247 (mp)
REVERT: A  974 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7306 (mm)
REVERT: A 1023 MET cc_start: 0.3793 (tmt) cc_final: 0.2831 (ptt)
REVERT: A 1039 MET cc_start: 0.3211 (mmm) cc_final: 0.2669 (mmm)
  outliers start: 29
  outliers final: 18
  residues processed: 139
  average time/residue: 1.2069
  time to fit residues: 178.1227
Evaluate side-chains
  133 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
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  380 ASN
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  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
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 11 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 39 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.3990

-------------------------------------------------------------------------------
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 = 0.4121 r_free = 0.4121 target = 0.195944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.150893 restraints weight = 8373.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 1.82
r_work: 0.3455 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7969  Z= 0.161
  Angle     :  0.561   6.088  10813  Z= 0.295
  Chirality :  0.044   0.212   1269
  Planarity :  0.004   0.044   1378
  Dihedral  :  4.108  22.953   1070
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 18.17 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.26), residues: 1006
  helix:  1.34 (0.24), residues: 494
  sheet: -0.99 (0.49), residues: 90
  loop : -0.39 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 927 
 HIS   0.003   0.001   HIS A 405 
 PHE   0.031   0.002   PHE A 759 
 TYR   0.012   0.001   TYR A 762 
 ARG   0.004   0.001   ARG A 761 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04247 (  417)
  hydrogen bonds       : angle       4.37866 ( 1239)
  covalent geometry    : bond        0.00383 ( 7968)
  covalent geometry    : angle       0.56105 (10813)
  Misc. bond           : bond        0.00104 (    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: 30
    poor density    : 107
  time to evaluate  : 0.892 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5575 (tpp) cc_final: 0.5362 (tpp)
REVERT: A   33 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7194 (tptp)
REVERT: A  126 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7421 (tpp)
REVERT: A  218 LYS cc_start: 0.8306 (ttmt) cc_final: 0.7918 (ttmt)
REVERT: A  238 GLU cc_start: 0.7564 (tt0) cc_final: 0.7290 (tt0)
REVERT: A  243 GLU cc_start: 0.6943 (tp30) cc_final: 0.6419 (pm20)
REVERT: A  259 GLN cc_start: 0.6201 (mt0) cc_final: 0.5886 (mt0)
REVERT: A  324 ARG cc_start: 0.6653 (mtp85) cc_final: 0.6361 (mtp85)
REVERT: A  399 ASP cc_start: 0.7683 (m-30) cc_final: 0.7402 (m-30)
REVERT: A  413 LEU cc_start: 0.8043 (tp) cc_final: 0.7595 (tt)
REVERT: A  435 GLU cc_start: 0.7729 (mp0) cc_final: 0.6984 (mp0)
REVERT: A  466 GLU cc_start: 0.7692 (pm20) cc_final: 0.6594 (tp30)
REVERT: A  518 GLU cc_start: 0.6508 (pm20) cc_final: 0.5982 (mm-30)
REVERT: A  559 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7585 (mtm110)
REVERT: A  575 MET cc_start: 0.3562 (mmp) cc_final: 0.3072 (mmt)
REVERT: A  731 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6939 (mt-10)
REVERT: A  824 LYS cc_start: 0.7312 (mmtt) cc_final: 0.6722 (mmpt)
REVERT: A  916 SER cc_start: 0.8674 (OUTLIER) cc_final: 0.8085 (m)
REVERT: A  970 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7579 (mp)
REVERT: A 1023 MET cc_start: 0.3779 (tmt) cc_final: 0.2860 (ptt)
  outliers start: 30
  outliers final: 17
  residues processed: 131
  average time/residue: 1.2402
  time to fit residues: 172.3544
Evaluate side-chains
  132 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
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  261 SER
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  380 ASN
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  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  702 ASP
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 95 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 61 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 40 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.4135 r_free = 0.4135 target = 0.197513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.151816 restraints weight = 8366.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 1.80
r_work: 0.3479 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3338 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7969  Z= 0.128
  Angle     :  0.548   8.432  10813  Z= 0.283
  Chirality :  0.042   0.177   1269
  Planarity :  0.004   0.044   1378
  Dihedral  :  4.030  20.991   1070
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 19.10 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.27), residues: 1006
  helix:  1.46 (0.24), residues: 494
  sheet: -0.94 (0.49), residues: 90
  loop : -0.42 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 927 
 HIS   0.003   0.001   HIS A 405 
 PHE   0.031   0.001   PHE A 759 
 TYR   0.011   0.001   TYR A 990 
 ARG   0.002   0.000   ARG A 655 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03956 (  417)
  hydrogen bonds       : angle       4.29860 ( 1239)
  covalent geometry    : bond        0.00294 ( 7968)
  covalent geometry    : angle       0.54753 (10813)
  Misc. bond           : bond        0.00070 (    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
  136 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.826 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7266 (mp0)
REVERT: A   33 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7146 (tptp)
REVERT: A  218 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7845 (ttmt)
REVERT: A  238 GLU cc_start: 0.7546 (tt0) cc_final: 0.7323 (tt0)
REVERT: A  243 GLU cc_start: 0.6907 (tp30) cc_final: 0.6415 (pm20)
REVERT: A  259 GLN cc_start: 0.6273 (mt0) cc_final: 0.5963 (mt0)
REVERT: A  324 ARG cc_start: 0.6558 (mtp85) cc_final: 0.6267 (mtp85)
REVERT: A  399 ASP cc_start: 0.7663 (m-30) cc_final: 0.7375 (m-30)
REVERT: A  413 LEU cc_start: 0.7967 (tp) cc_final: 0.7546 (tt)
REVERT: A  435 GLU cc_start: 0.7665 (mp0) cc_final: 0.6917 (mp0)
REVERT: A  466 GLU cc_start: 0.7669 (pm20) cc_final: 0.6589 (tp30)
REVERT: A  518 GLU cc_start: 0.6494 (pm20) cc_final: 0.5979 (mm-30)
REVERT: A  559 ARG cc_start: 0.8012 (mtp85) cc_final: 0.7570 (mtm110)
REVERT: A  575 MET cc_start: 0.3396 (mmp) cc_final: 0.2889 (mmt)
REVERT: A  731 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7124 (mt-10)
REVERT: A  824 LYS cc_start: 0.7305 (mmtt) cc_final: 0.6706 (mmpt)
REVERT: A  916 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8049 (m)
REVERT: A 1023 MET cc_start: 0.3655 (tmt) cc_final: 0.2749 (ptt)
REVERT: A 1039 MET cc_start: 0.3526 (mmm) cc_final: 0.3157 (mmm)
  outliers start: 23
  outliers final: 19
  residues processed: 132
  average time/residue: 1.1716
  time to fit residues: 164.3805
Evaluate side-chains
  133 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
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  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  380 ASN
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  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  702 ASP
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 93 optimal weight:    0.9980
   chunk 49 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0980
   chunk 46 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 7 optimal weight:    0.4980
   chunk 50 optimal weight:    0.0980
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.4157 r_free = 0.4157 target = 0.200051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.154421 restraints weight = 8287.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 1.81
r_work: 0.3515 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3373 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   7969  Z= 0.111
  Angle     :  0.529   9.164  10813  Z= 0.272
  Chirality :  0.042   0.170   1269
  Planarity :  0.004   0.045   1378
  Dihedral  :  3.879  19.117   1070
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 18.75 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.27), residues: 1006
  helix:  1.74 (0.24), residues: 488
  sheet: -1.00 (0.49), residues: 91
  loop : -0.47 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 927 
 HIS   0.003   0.001   HIS A 405 
 PHE   0.030   0.001   PHE A 759 
 TYR   0.007   0.001   TYR A 762 
 ARG   0.002   0.000   ARG A 164 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03624 (  417)
  hydrogen bonds       : angle       4.17072 ( 1239)
  covalent geometry    : bond        0.00246 ( 7968)
  covalent geometry    : angle       0.52885 (10813)
  Misc. bond           : bond        0.00047 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7164.03 seconds
wall clock time: 124 minutes 11.83 seconds (7451.83 seconds total)