Starting phenix.real_space_refine
on Wed Feb  4 07:01:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jg3_61449/02_2026/9jg3_61449.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jg3_61449/02_2026/9jg3_61449.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jg3_61449/02_2026/9jg3_61449.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jg3_61449/02_2026/9jg3_61449.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jg3_61449/02_2026/9jg3_61449.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jg3_61449/02_2026/9jg3_61449.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     174      5.49       5
     S      17      5.16       5
     C    5161      2.51       5
     N    1649      2.21       5
     O    2187      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9188
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 579, 4699
          Classifications: {'peptide': 579}
          Link IDs: {'PTRANS': 22, 'TRANS': 556}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 2938
          Classifications: {'RNA': 138}
          Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 64, 'rna3p_pyr': 60}
          Link IDs: {'rna2p': 14, 'rna3p': 123}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 546
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 546
          Classifications: {'DNA': 26}
          Link IDs: {'rna3p': 25}
    Chain: "D"
      Number of atoms: 203
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 203
          Classifications: {'DNA': 10}
          Link IDs: {'rna3p': 9}
    Chain: "E"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 802
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99}
  Time building chain proxies: 2.68, per 1000 atoms: 0.29
  Number of scatterers: 9188
  At special positions: 0
  Unit cell: (105.664, 105.664, 124.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      17     16.00
     P     174     15.00
     O    2187      8.00
     N    1649      7.00
     C    5161      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 550 " - pdb=" SG  CYS A 567 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  33 " - pdb=" SG  CYS E  36 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Conformation dependent library (CDL) restraints added in 255.5 milliseconds
  

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1286

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 7 sheets defined
      48.8% alpha, 14.3% beta
      68 base pairs and 98 stacking pairs defined.
    Time for finding SS restraints: 1.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 65
      removed outlier: 4.760A  pdb=" N   CYS A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 5.777A  pdb=" N   VAL A  42 " --> pdb=" O   HIS A  38 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   THR A  43 " --> pdb=" O   ASN A  39 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA A  46 " --> pdb=" O   VAL A  42 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU A  65 " --> pdb=" O   LYS A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 79
      removed outlier: 3.606A  pdb=" N   GLN A  71 " --> pdb=" O   PRO A  67 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   LEU A  72 " --> pdb=" O   GLU A  68 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   TYR A  77 " --> pdb=" O   VAL A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 96
      removed outlier: 3.578A  pdb=" N   LEU A  92 " --> pdb=" O   LYS A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 101
    Processing helix  chain 'A' and resid 182 through 186
      removed outlier: 3.855A  pdb=" N   PHE A 185 " --> pdb=" O   GLY A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 197
    Processing helix  chain 'A' and resid 198 through 209
    Processing helix  chain 'A' and resid 217 through 237
      removed outlier: 3.633A  pdb=" N   ILE A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 295
      removed outlier: 3.501A  pdb=" N   ASN A 295 " --> pdb=" O   VAL A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 332
      removed outlier: 3.521A  pdb=" N   LYS A 327 " --> pdb=" O   LEU A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 342
    Processing helix  chain 'A' and resid 345 through 365
      removed outlier: 3.521A  pdb=" N   GLU A 349 " --> pdb=" O   SER A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 428
      removed outlier: 4.056A  pdb=" N   ARG A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLY A 428 " --> pdb=" O   TRP A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 472
    Processing helix  chain 'A' and resid 480 through 485
      removed outlier: 4.052A  pdb=" N   ASN A 483 " --> pdb=" O   THR A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 517
      removed outlier: 3.723A  pdb=" N   GLN A 517 " --> pdb=" O   TRP A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 535
    Processing helix  chain 'A' and resid 581 through 593
    Processing helix  chain 'E' and resid 12 through 19
    Processing helix  chain 'E' and resid 33 through 50
      removed outlier: 3.570A  pdb=" N   LYS E  37 " --> pdb=" O   CYS E  33 " (cutoff:3.500A)
      Proline residue:  E  41  - end of helix
    Processing helix  chain 'E' and resid 66 through 71
      removed outlier: 3.808A  pdb=" N   LYS E  70 " --> pdb=" O   GLY E  66 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   TYR E  71 " --> pdb=" O   THR E  67 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 66 through 71'
    Processing helix  chain 'E' and resid 96 through 108
    Processing sheet with id=AA1, first strand: chain 'A' and resid 257 through 260
      removed outlier: 6.607A  pdb=" N   VAL A 318 " --> pdb=" O   ARG A 302 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   TYR A 304 " --> pdb=" O   ASN A 316 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ASN A 316 " --> pdb=" O   TYR A 304 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   LEU A 306 " --> pdb=" O   TYR A 314 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   TYR A 314 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   GLN A 308 " --> pdb=" O   GLY A 312 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   GLY A 312 " --> pdb=" O   GLN A 308 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   TYR A 313 " --> pdb=" O   ILE A   8 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   THR A 284 " --> pdb=" O   LYS A   9 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 128
    Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 131
    Processing sheet with id=AA4, first strand: chain 'A' and resid 135 through 148
      removed outlier: 7.781A  pdb=" N   ASN A 141 " --> pdb=" O   VAL A 155 " (cutoff:3.500A)
      removed outlier: 9.586A  pdb=" N   VAL A 155 " --> pdb=" O   ASN A 141 " (cutoff:3.500A)
      removed outlier: 8.476A  pdb=" N   ASN A 143 " --> pdb=" O   ILE A 153 " (cutoff:3.500A)
      removed outlier: 9.331A  pdb=" N   ILE A 153 " --> pdb=" O   ASN A 143 " (cutoff:3.500A)
      removed outlier: 8.650A  pdb=" N   GLY A 151 " --> pdb=" O   PRO A 145 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 393
      removed outlier: 3.957A  pdb=" N   VAL A 385 " --> pdb=" O   PHE A 393 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ILE A 475 " --> pdb=" O   HIS A 539 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 564 through 565
    Processing sheet with id=AA7, first strand: chain 'E' and resid 6 through 7
      removed outlier: 6.626A  pdb=" N   ILE E   6 " --> pdb=" O   LYS E  58 " (cutoff:3.500A)
      removed outlier: 8.131A  pdb=" N   ASN E  60 " --> pdb=" O   ILE E   6 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   ALA E  23 " --> pdb=" O   THR E  55 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   ALA E  57 " --> pdb=" O   ALA E  23 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   LEU E  25 " --> pdb=" O   ALA E  57 " (cutoff:3.500A)
      removed outlier: 7.620A  pdb=" N   LEU E  59 " --> pdb=" O   LEU E  25 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   ASP E  27 " --> pdb=" O   LEU E  59 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   THR E  78 " --> pdb=" O   PHE E  28 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   LEU E  79 " --> pdb=" O   THR E  90 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   THR E  90 " --> pdb=" O   LEU E  79 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   LEU E  81 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLU E  86 " --> pdb=" O   LYS E  83 " (cutoff:3.500A)

    272 hydrogen bonds defined for protein.
    765 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      170 hydrogen bonds
      332 hydrogen bond angles
      0 basepair planarities
      68 basepair parallelities
      98 stacking parallelities
  Total time for adding SS restraints: 1.98

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2299
        1.33 -     1.46: 2996
        1.46 -     1.58: 4078
        1.58 -     1.70: 342
        1.70 -     1.82: 22
  Bond restraints: 9737
  Sorted by residual:
  bond pdb=" N   LYS E   4 "
       pdb=" CA  LYS E   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.02e+00
  bond pdb=" N   MET A   1 "
       pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.79e+00
  bond pdb=" C   VAL A 375 "
       pdb=" N   GLY A 376 "
    ideal  model  delta    sigma   weight residual
    1.330  1.344 -0.014 8.50e-03 1.38e+04 2.68e+00
  bond pdb=" C1'  DC D   5 "
       pdb=" N1   DC D   5 "
    ideal  model  delta    sigma   weight residual
    1.490  1.444  0.046 3.00e-02 1.11e+03 2.36e+00
  bond pdb=" CG  GLU E 102 "
       pdb=" CD  GLU E 102 "
    ideal  model  delta    sigma   weight residual
    1.516  1.553 -0.037 2.50e-02 1.60e+03 2.22e+00
  ... (remaining 9732 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 12901
        1.04 -     2.09: 869
        2.09 -     3.13: 156
        3.13 -     4.17: 42
        4.17 -     5.22: 4
  Bond angle restraints: 13972
  Sorted by residual:
  angle pdb=" N   GLU A 596 "
        pdb=" CA  GLU A 596 "
        pdb=" CB  GLU A 596 "
      ideal   model   delta    sigma   weight residual
     112.78  108.83    3.95 1.53e+00 4.27e-01 6.66e+00
  angle pdb=" C2'   G B 175 "
        pdb=" C1'   G B 175 "
        pdb=" N9    G B 175 "
      ideal   model   delta    sigma   weight residual
     112.00  115.87   -3.87 1.50e+00 4.44e-01 6.65e+00
  angle pdb=" N   GLU E 102 "
        pdb=" CA  GLU E 102 "
        pdb=" CB  GLU E 102 "
      ideal   model   delta    sigma   weight residual
     110.28  114.16   -3.88 1.55e+00 4.16e-01 6.28e+00
  angle pdb=" C2'   A B 102 "
        pdb=" C1'   A B 102 "
        pdb=" N9    A B 102 "
      ideal   model   delta    sigma   weight residual
     112.00  115.65   -3.65 1.50e+00 4.44e-01 5.93e+00
  angle pdb=" C4'   A B 105 "
        pdb=" C3'   A B 105 "
        pdb=" O3'   A B 105 "
      ideal   model   delta    sigma   weight residual
     109.40  112.92   -3.52 1.50e+00 4.44e-01 5.50e+00
  ... (remaining 13967 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.89: 5384
       30.89 -    61.78: 452
       61.78 -    92.67: 116
       92.67 -   123.57: 1
      123.57 -   154.46: 2
  Dihedral angle restraints: 5955
    sinusoidal: 3970
      harmonic: 1985
  Sorted by residual:
  dihedral pdb=" CA  PHE E  28 "
           pdb=" C   PHE E  28 "
           pdb=" N   TRP E  29 "
           pdb=" CA  TRP E  29 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.78  -24.22     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" CA  LEU A  65 "
           pdb=" C   LEU A  65 "
           pdb=" N   LYS A  66 "
           pdb=" CA  LYS A  66 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.31  -19.69     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" O4'   U B 174 "
           pdb=" C1'   U B 174 "
           pdb=" N1    U B 174 "
           pdb=" C2    U B 174 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -71.35  -56.65     1      1.70e+01 3.46e-03 1.50e+01
  ... (remaining 5952 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1146
       0.037 -    0.074: 399
       0.074 -    0.112: 88
       0.112 -    0.149: 28
       0.149 -    0.186: 6
  Chirality restraints: 1667
  Sorted by residual:
  chirality pdb=" CG  LEU A 449 "
            pdb=" CB  LEU A 449 "
            pdb=" CD1 LEU A 449 "
            pdb=" CD2 LEU A 449 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.63e-01
  chirality pdb=" C1'   G B 175 "
            pdb=" O4'   G B 175 "
            pdb=" C2'   G B 175 "
            pdb=" N9    G B 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.29    0.17 2.00e-01 2.50e+01 6.95e-01
  chirality pdb=" C3'  DA C  15 "
            pdb=" C4'  DA C  15 "
            pdb=" O3'  DA C  15 "
            pdb=" C2'  DA C  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.50   -0.16 2.00e-01 2.50e+01 6.65e-01
  ... (remaining 1664 not shown)

  Planarity restraints: 1142
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B 175 "   -0.031 2.00e-02 2.50e+03   1.38e-02 5.75e+00
        pdb=" N9    G B 175 "    0.034 2.00e-02 2.50e+03
        pdb=" C8    G B 175 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    G B 175 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    G B 175 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    G B 175 "   -0.001 2.00e-02 2.50e+03
        pdb=" O6    G B 175 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1    G B 175 "    0.000 2.00e-02 2.50e+03
        pdb=" C2    G B 175 "    0.000 2.00e-02 2.50e+03
        pdb=" N2    G B 175 "    0.000 2.00e-02 2.50e+03
        pdb=" N3    G B 175 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    G B 175 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B 102 "   -0.031 2.00e-02 2.50e+03   1.43e-02 5.59e+00
        pdb=" N9    A B 102 "    0.034 2.00e-02 2.50e+03
        pdb=" C8    A B 102 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    A B 102 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    A B 102 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A B 102 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6    A B 102 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1    A B 102 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    A B 102 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A B 102 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A B 102 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU E 102 "    0.011 2.00e-02 2.50e+03   2.32e-02 5.39e+00
        pdb=" CD  GLU E 102 "   -0.040 2.00e-02 2.50e+03
        pdb=" OE1 GLU E 102 "    0.015 2.00e-02 2.50e+03
        pdb=" OE2 GLU E 102 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1139 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 127
        2.60 -     3.18: 7835
        3.18 -     3.75: 15938
        3.75 -     4.33: 21472
        4.33 -     4.90: 31108
  Nonbonded interactions: 76480
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 414 "
            pdb=" O2'   U B 185 "
     model   vdw
     2.026 3.040
  nonbonded pdb=" OD1 ASN A 198 "
            pdb=" N   ASN A 200 "
     model   vdw
     2.102 3.120
  nonbonded pdb=" OH  TYR A  45 "
            pdb=" O   VAL A 113 "
     model   vdw
     2.124 3.040
  nonbonded pdb=" OG1 THR A  11 "
            pdb=" OD1 ASP A  13 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" OD1 ASP A 421 "
            pdb=" NH1 ARG A 433 "
     model   vdw
     2.192 3.120
  ... (remaining 76475 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.150
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9739  Z= 0.245
  Angle     :  0.616   5.216  13976  Z= 0.348
  Chirality :  0.041   0.186   1667
  Planarity :  0.005   0.047   1142
  Dihedral  : 20.304 154.457   4663
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.34), residues: 678
  helix:  2.13 (0.31), residues: 300
  sheet:  0.41 (0.63), residues: 70
  loop : -0.65 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 587 
 TYR   0.018   0.002   TYR A 472 
 PHE   0.020   0.002   PHE E  28 
 TRP   0.020   0.002   TRP A 290 
 HIS   0.010   0.002   HIS A 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 9737)
  covalent geometry    : angle       0.61557 (13972)
  SS BOND              : bond        0.00402 (    2)
  SS BOND              : angle       1.10143 (    4)
  hydrogen bonds       : bond        0.11649 (  442)
  hydrogen bonds       : angle       4.80976 ( 1097)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 CYS cc_start: 0.8169 (t) cc_final: 0.7934 (t)
REVERT: A  101 ARG cc_start: 0.6721 (mtp180) cc_final: 0.6398 (ttm110)
REVERT: A  175 HIS cc_start: 0.7681 (t70) cc_final: 0.7330 (t70)
REVERT: A  215 GLN cc_start: 0.8452 (mt0) cc_final: 0.8191 (mt0)
REVERT: A  243 SER cc_start: 0.8510 (m) cc_final: 0.8307 (p)
REVERT: A  252 SER cc_start: 0.9020 (p) cc_final: 0.8739 (p)
REVERT: A  269 ASP cc_start: 0.7104 (t70) cc_final: 0.6664 (t70)
REVERT: A  323 LEU cc_start: 0.9053 (mp) cc_final: 0.8720 (mt)
REVERT: A  326 GLU cc_start: 0.7657 (mp0) cc_final: 0.7372 (mp0)
REVERT: A  333 LYS cc_start: 0.8677 (mttm) cc_final: 0.8243 (mttm)
REVERT: A  347 GLU cc_start: 0.7416 (mp0) cc_final: 0.7197 (mm-30)
REVERT: A  378 ASP cc_start: 0.8278 (t0) cc_final: 0.7955 (t0)
REVERT: A  386 SER cc_start: 0.8781 (t) cc_final: 0.8270 (p)
REVERT: A  387 THR cc_start: 0.9000 (m) cc_final: 0.8668 (p)
REVERT: A  407 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7530 (mt-10)
REVERT: A  424 TRP cc_start: 0.8293 (t-100) cc_final: 0.7954 (t-100)
REVERT: A  433 ARG cc_start: 0.7267 (ttp-170) cc_final: 0.6448 (ttp-170)
REVERT: A  444 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7645 (mt-10)
REVERT: A  469 SER cc_start: 0.9076 (m) cc_final: 0.8023 (t)
REVERT: A  537 ASN cc_start: 0.7790 (m110) cc_final: 0.7508 (m110)
REVERT: A  590 LYS cc_start: 0.8647 (tttt) cc_final: 0.8275 (ttmt)
REVERT: E   91 LYS cc_start: 0.8113 (tppt) cc_final: 0.7582 (tptp)
REVERT: E   97 LYS cc_start: 0.7237 (tttt) cc_final: 0.6996 (tttt)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.1278
  time to fit residues: 34.2501
Evaluate side-chains
  173 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0010
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.8788

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  90 GLN
A 219 HIS
** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 443 GLN
** A 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 107 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.114955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.090339 restraints weight = 21641.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.80
r_work: 0.3193 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9739  Z= 0.189
  Angle     :  0.577   6.962  13976  Z= 0.312
  Chirality :  0.038   0.217   1667
  Planarity :  0.004   0.047   1142
  Dihedral  : 22.012 167.175   3255
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 10.87 %
    Favored  : 86.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.34), residues: 678
  helix:  2.49 (0.31), residues: 302
  sheet:  0.15 (0.59), residues: 70
  loop : -0.31 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 188 
 TYR   0.012   0.001   TYR A 348 
 PHE   0.019   0.002   PHE E 103 
 TRP   0.012   0.002   TRP A 167 
 HIS   0.006   0.001   HIS A 589 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 9737)
  covalent geometry    : angle       0.57705 (13972)
  SS BOND              : bond        0.00304 (    2)
  SS BOND              : angle       0.79406 (    4)
  hydrogen bonds       : bond        0.04512 (  442)
  hydrogen bonds       : angle       3.64797 ( 1097)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 185
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 CYS cc_start: 0.8487 (t) cc_final: 0.8209 (t)
REVERT: A   47 TRP cc_start: 0.8893 (t60) cc_final: 0.8349 (t60)
REVERT: A   61 LYS cc_start: 0.8815 (mmmt) cc_final: 0.8389 (tttm)
REVERT: A   78 ARG cc_start: 0.7308 (tpt90) cc_final: 0.6597 (tpt90)
REVERT: A  101 ARG cc_start: 0.7507 (mtp180) cc_final: 0.6994 (ttm110)
REVERT: A  122 TYR cc_start: 0.8381 (m-10) cc_final: 0.8135 (m-10)
REVERT: A  175 HIS cc_start: 0.8066 (t70) cc_final: 0.7658 (t70)
REVERT: A  184 LYS cc_start: 0.8504 (tmtt) cc_final: 0.8198 (tmtt)
REVERT: A  243 SER cc_start: 0.8753 (m) cc_final: 0.8435 (p)
REVERT: A  252 SER cc_start: 0.9361 (p) cc_final: 0.9149 (p)
REVERT: A  267 ARG cc_start: 0.8369 (ttm-80) cc_final: 0.7832 (mtp-110)
REVERT: A  269 ASP cc_start: 0.7694 (t70) cc_final: 0.7112 (t70)
REVERT: A  314 TYR cc_start: 0.8718 (m-80) cc_final: 0.8510 (m-10)
REVERT: A  326 GLU cc_start: 0.8183 (mp0) cc_final: 0.7620 (mp0)
REVERT: A  333 LYS cc_start: 0.8869 (mttm) cc_final: 0.8454 (mttm)
REVERT: A  407 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7892 (mt-10)
REVERT: A  418 LEU cc_start: 0.9081 (tp) cc_final: 0.8839 (tt)
REVERT: A  424 TRP cc_start: 0.8805 (t-100) cc_final: 0.8523 (t-100)
REVERT: A  444 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8180 (mt-10)
REVERT: A  472 TYR cc_start: 0.8896 (m-80) cc_final: 0.8544 (m-10)
REVERT: A  478 GLU cc_start: 0.6621 (tp30) cc_final: 0.5886 (tp30)
REVERT: A  515 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7452 (mmt)
REVERT: A  537 ASN cc_start: 0.8291 (m110) cc_final: 0.7985 (m110)
REVERT: A  589 HIS cc_start: 0.8581 (m170) cc_final: 0.8345 (m-70)
REVERT: E   45 GLU cc_start: 0.8805 (tp30) cc_final: 0.7993 (tp30)
REVERT: E   71 TYR cc_start: 0.7831 (m-80) cc_final: 0.7535 (m-80)
REVERT: E   91 LYS cc_start: 0.8305 (tppt) cc_final: 0.7693 (tptp)
REVERT: E   97 LYS cc_start: 0.7789 (tttt) cc_final: 0.7446 (tttt)
  outliers start: 15
  outliers final: 8
  residues processed: 189
  average time/residue: 0.1283
  time to fit residues: 31.6686
Evaluate side-chains
  166 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 157
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  426 SER
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  515 MET
Chi-restraints excluded: chain E residue   26 VAL
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  102 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0020
   chunk 6 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0870
   chunk 72 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 19 optimal weight:    0.4980
   chunk 52 optimal weight:    2.9990
   chunk 78 optimal weight:    0.2980
   overall best weight:    0.3766

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 389 HIS
A 420 ASN
A 584 ASN
** A 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  84 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.117091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.092289 restraints weight = 21612.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 2.82
r_work: 0.3228 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9739  Z= 0.121
  Angle     :  0.513   6.884  13976  Z= 0.279
  Chirality :  0.035   0.206   1667
  Planarity :  0.004   0.054   1142
  Dihedral  : 21.953 166.368   3255
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 13.18 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.34), residues: 678
  helix:  2.65 (0.31), residues: 304
  sheet:  0.41 (0.55), residues: 82
  loop : -0.15 (0.38), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 178 
 TYR   0.017   0.001   TYR A 472 
 PHE   0.014   0.001   PHE E 103 
 TRP   0.010   0.001   TRP E  29 
 HIS   0.005   0.001   HIS A 589 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9737)
  covalent geometry    : angle       0.51268 (13972)
  SS BOND              : bond        0.00328 (    2)
  SS BOND              : angle       0.68297 (    4)
  hydrogen bonds       : bond        0.03782 (  442)
  hydrogen bonds       : angle       3.26078 ( 1097)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 165
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 CYS cc_start: 0.8366 (t) cc_final: 0.8136 (t)
REVERT: A   47 TRP cc_start: 0.8883 (t60) cc_final: 0.8520 (t60)
REVERT: A   61 LYS cc_start: 0.8881 (mmmt) cc_final: 0.8509 (tttm)
REVERT: A   78 ARG cc_start: 0.7226 (tpt90) cc_final: 0.6364 (tpt90)
REVERT: A  101 ARG cc_start: 0.7513 (mtp180) cc_final: 0.6998 (ttm110)
REVERT: A  175 HIS cc_start: 0.7975 (t70) cc_final: 0.7629 (t70)
REVERT: A  243 SER cc_start: 0.8766 (m) cc_final: 0.8504 (p)
REVERT: A  267 ARG cc_start: 0.8430 (ttm-80) cc_final: 0.8052 (mtp-110)
REVERT: A  269 ASP cc_start: 0.7684 (t70) cc_final: 0.7078 (t70)
REVERT: A  272 LYS cc_start: 0.8923 (mmtm) cc_final: 0.8709 (mmtm)
REVERT: A  314 TYR cc_start: 0.8666 (m-80) cc_final: 0.8449 (m-10)
REVERT: A  323 LEU cc_start: 0.8989 (mp) cc_final: 0.8475 (mt)
REVERT: A  326 GLU cc_start: 0.8255 (mp0) cc_final: 0.7714 (mp0)
REVERT: A  333 LYS cc_start: 0.8837 (mttm) cc_final: 0.8444 (mttm)
REVERT: A  352 LYS cc_start: 0.9049 (mmtp) cc_final: 0.8798 (mtpp)
REVERT: A  354 LYS cc_start: 0.8850 (mmmm) cc_final: 0.8280 (mmmm)
REVERT: A  356 LYS cc_start: 0.8967 (mmtm) cc_final: 0.8440 (mmtm)
REVERT: A  360 GLN cc_start: 0.8787 (mm110) cc_final: 0.8306 (mt0)
REVERT: A  407 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7812 (mt-10)
REVERT: A  418 LEU cc_start: 0.8977 (tp) cc_final: 0.8767 (tt)
REVERT: A  424 TRP cc_start: 0.8847 (t-100) cc_final: 0.8583 (t60)
REVERT: A  451 GLU cc_start: 0.7899 (tt0) cc_final: 0.7523 (tp30)
REVERT: A  537 ASN cc_start: 0.8222 (m110) cc_final: 0.7871 (m110)
REVERT: A  579 GLN cc_start: 0.6624 (pp30) cc_final: 0.6390 (pp30)
REVERT: E   45 GLU cc_start: 0.8805 (tp30) cc_final: 0.7914 (tp30)
REVERT: E   71 TYR cc_start: 0.7674 (m-80) cc_final: 0.7403 (m-80)
REVERT: E   97 LYS cc_start: 0.7669 (tttt) cc_final: 0.7330 (tttt)
  outliers start: 14
  outliers final: 11
  residues processed: 171
  average time/residue: 0.1226
  time to fit residues: 27.3367
Evaluate side-chains
  164 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 153
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  382 GLN
Chi-restraints excluded: chain A residue  426 SER
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  584 ASN
Chi-restraints excluded: chain E residue   26 VAL
Chi-restraints excluded: chain E residue   74 ARG
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  102 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  69 GLN
** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.114199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.089641 restraints weight = 21851.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 2.80
r_work: 0.3196 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9739  Z= 0.166
  Angle     :  0.538   6.593  13976  Z= 0.291
  Chirality :  0.037   0.220   1667
  Planarity :  0.004   0.049   1142
  Dihedral  : 22.079 169.516   3255
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.65 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.66 (0.34), residues: 678
  helix:  2.54 (0.30), residues: 304
  sheet:  0.45 (0.63), residues: 70
  loop : -0.22 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 433 
 TYR   0.029   0.002   TYR A 472 
 PHE   0.012   0.002   PHE A 595 
 TRP   0.018   0.001   TRP E  29 
 HIS   0.004   0.001   HIS A 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 9737)
  covalent geometry    : angle       0.53838 (13972)
  SS BOND              : bond        0.00359 (    2)
  SS BOND              : angle       0.76121 (    4)
  hydrogen bonds       : bond        0.04185 (  442)
  hydrogen bonds       : angle       3.34501 ( 1097)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 160
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 CYS cc_start: 0.8488 (t) cc_final: 0.8262 (t)
REVERT: A   78 ARG cc_start: 0.7105 (tpt90) cc_final: 0.6584 (tpt170)
REVERT: A  101 ARG cc_start: 0.7502 (mtp180) cc_final: 0.6999 (ttm110)
REVERT: A  175 HIS cc_start: 0.7852 (t70) cc_final: 0.7487 (t70)
REVERT: A  243 SER cc_start: 0.8737 (m) cc_final: 0.8462 (p)
REVERT: A  267 ARG cc_start: 0.8488 (ttm-80) cc_final: 0.8109 (mtp-110)
REVERT: A  269 ASP cc_start: 0.7829 (t70) cc_final: 0.7044 (t70)
REVERT: A  272 LYS cc_start: 0.8975 (mmtm) cc_final: 0.8697 (mmtm)
REVERT: A  326 GLU cc_start: 0.8285 (mp0) cc_final: 0.7738 (mp0)
REVERT: A  328 ILE cc_start: 0.8980 (tp) cc_final: 0.8595 (tp)
REVERT: A  332 LYS cc_start: 0.9202 (mmmt) cc_final: 0.8953 (mmmt)
REVERT: A  333 LYS cc_start: 0.8875 (mttm) cc_final: 0.8516 (mttm)
REVERT: A  360 GLN cc_start: 0.8744 (mm110) cc_final: 0.8346 (tm-30)
REVERT: A  407 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7859 (mt-10)
REVERT: A  418 LEU cc_start: 0.8962 (tp) cc_final: 0.8717 (tt)
REVERT: A  451 GLU cc_start: 0.7931 (tt0) cc_final: 0.7650 (tp30)
REVERT: A  478 GLU cc_start: 0.6108 (tp30) cc_final: 0.5468 (tp30)
REVERT: A  534 ARG cc_start: 0.8449 (ttm170) cc_final: 0.8171 (ttm110)
REVERT: A  537 ASN cc_start: 0.8229 (m110) cc_final: 0.7877 (m110)
REVERT: A  579 GLN cc_start: 0.6680 (pp30) cc_final: 0.6463 (pp30)
REVERT: A  589 HIS cc_start: 0.8594 (m-70) cc_final: 0.8393 (m-70)
REVERT: E   45 GLU cc_start: 0.8757 (tp30) cc_final: 0.8258 (tp30)
REVERT: E   71 TYR cc_start: 0.7745 (m-80) cc_final: 0.7484 (m-80)
REVERT: E   97 LYS cc_start: 0.7698 (tttt) cc_final: 0.7381 (tttt)
  outliers start: 14
  outliers final: 13
  residues processed: 167
  average time/residue: 0.1407
  time to fit residues: 30.1484
Evaluate side-chains
  166 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 153
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   69 GLN
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  426 SER
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  584 ASN
Chi-restraints excluded: chain E residue    5 ILE
Chi-restraints excluded: chain E residue   26 VAL
Chi-restraints excluded: chain E residue   74 ARG
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  102 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 76 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 389 HIS
** A 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 569 ASN
** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 589 HIS
E 107 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.114336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.089809 restraints weight = 21602.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.78
r_work: 0.3191 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9739  Z= 0.167
  Angle     :  0.553   5.906  13976  Z= 0.296
  Chirality :  0.037   0.218   1667
  Planarity :  0.004   0.048   1142
  Dihedral  : 22.099 169.470   3255
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 18.12 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.33), residues: 678
  helix:  2.52 (0.30), residues: 303
  sheet:  0.55 (0.64), residues: 67
  loop : -0.31 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 433 
 TYR   0.018   0.002   TYR A 348 
 PHE   0.015   0.001   PHE A 357 
 TRP   0.023   0.002   TRP A 424 
 HIS   0.003   0.001   HIS A 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 9737)
  covalent geometry    : angle       0.55276 (13972)
  SS BOND              : bond        0.00326 (    2)
  SS BOND              : angle       0.63834 (    4)
  hydrogen bonds       : bond        0.04090 (  442)
  hydrogen bonds       : angle       3.37061 ( 1097)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 151
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 CYS cc_start: 0.8521 (t) cc_final: 0.8279 (t)
REVERT: A   47 TRP cc_start: 0.8803 (t60) cc_final: 0.8469 (t60)
REVERT: A   78 ARG cc_start: 0.7073 (tpt90) cc_final: 0.6382 (tpt90)
REVERT: A  184 LYS cc_start: 0.8894 (ptmm) cc_final: 0.8547 (ptmm)
REVERT: A  230 GLU cc_start: 0.8124 (tp30) cc_final: 0.7903 (mm-30)
REVERT: A  243 SER cc_start: 0.8760 (m) cc_final: 0.8423 (p)
REVERT: A  267 ARG cc_start: 0.8503 (ttm-80) cc_final: 0.8120 (mtp-110)
REVERT: A  269 ASP cc_start: 0.7828 (t70) cc_final: 0.6892 (t70)
REVERT: A  272 LYS cc_start: 0.8962 (mmtm) cc_final: 0.8610 (mmtm)
REVERT: A  326 GLU cc_start: 0.8317 (mp0) cc_final: 0.7762 (mp0)
REVERT: A  332 LYS cc_start: 0.9221 (mmmt) cc_final: 0.8967 (mmmt)
REVERT: A  333 LYS cc_start: 0.8941 (mttm) cc_final: 0.8577 (mttm)
REVERT: A  356 LYS cc_start: 0.8918 (pptt) cc_final: 0.8392 (mmtm)
REVERT: A  360 GLN cc_start: 0.8759 (mm110) cc_final: 0.8359 (mt0)
REVERT: A  407 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7877 (mt-10)
REVERT: A  418 LEU cc_start: 0.8958 (tp) cc_final: 0.8711 (tt)
REVERT: A  478 GLU cc_start: 0.6102 (tp30) cc_final: 0.5425 (tp30)
REVERT: A  537 ASN cc_start: 0.8258 (m110) cc_final: 0.7913 (m110)
REVERT: A  579 GLN cc_start: 0.6803 (pp30) cc_final: 0.6537 (pp30)
REVERT: E   45 GLU cc_start: 0.8744 (tp30) cc_final: 0.8053 (tp30)
REVERT: E   71 TYR cc_start: 0.7777 (m-80) cc_final: 0.7515 (m-80)
REVERT: E   97 LYS cc_start: 0.7672 (tttt) cc_final: 0.7337 (tttt)
  outliers start: 19
  outliers final: 15
  residues processed: 157
  average time/residue: 0.1308
  time to fit residues: 26.5684
Evaluate side-chains
  164 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 149
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  426 SER
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain E residue    5 ILE
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   26 VAL
Chi-restraints excluded: chain E residue   29 TRP
Chi-restraints excluded: chain E residue   74 ARG
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  102 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   chunk 0 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0040
   chunk 60 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0070
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.9414

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

Flipped N/Q/H residues before XYZ refinement:
A  69 GLN
A 589 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.112999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.088282 restraints weight = 21716.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.77
r_work: 0.3169 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.3768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9739  Z= 0.191
  Angle     :  0.573   6.798  13976  Z= 0.307
  Chirality :  0.037   0.224   1667
  Planarity :  0.004   0.049   1142
  Dihedral  : 22.233 170.478   3255
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 16.14 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.33), residues: 678
  helix:  2.41 (0.29), residues: 303
  sheet:  0.36 (0.65), residues: 67
  loop : -0.42 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 534 
 TYR   0.034   0.002   TYR A 472 
 PHE   0.013   0.002   PHE A 357 
 TRP   0.043   0.002   TRP A 424 
 HIS   0.004   0.001   HIS A 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 9737)
  covalent geometry    : angle       0.57285 (13972)
  SS BOND              : bond        0.00354 (    2)
  SS BOND              : angle       0.70808 (    4)
  hydrogen bonds       : bond        0.04321 (  442)
  hydrogen bonds       : angle       3.46770 ( 1097)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 155
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 CYS cc_start: 0.8596 (t) cc_final: 0.8327 (t)
REVERT: A  116 ARG cc_start: 0.8569 (ttm110) cc_final: 0.8047 (ttm110)
REVERT: A  184 LYS cc_start: 0.8861 (ptmm) cc_final: 0.8473 (ptmm)
REVERT: A  230 GLU cc_start: 0.8082 (tp30) cc_final: 0.7875 (mm-30)
REVERT: A  243 SER cc_start: 0.8735 (m) cc_final: 0.8388 (p)
REVERT: A  267 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.8132 (mtp-110)
REVERT: A  272 LYS cc_start: 0.9020 (mmtm) cc_final: 0.8762 (mmtm)
REVERT: A  323 LEU cc_start: 0.9057 (mp) cc_final: 0.8612 (mt)
REVERT: A  326 GLU cc_start: 0.8345 (mp0) cc_final: 0.7734 (mp0)
REVERT: A  328 ILE cc_start: 0.8932 (tp) cc_final: 0.8591 (tp)
REVERT: A  332 LYS cc_start: 0.9169 (mmmt) cc_final: 0.8969 (mmmt)
REVERT: A  354 LYS cc_start: 0.8931 (tppt) cc_final: 0.8471 (tppt)
REVERT: A  360 GLN cc_start: 0.8780 (mm110) cc_final: 0.8295 (mt0)
REVERT: A  387 THR cc_start: 0.8941 (m) cc_final: 0.8461 (p)
REVERT: A  407 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7879 (mt-10)
REVERT: A  418 LEU cc_start: 0.8967 (tp) cc_final: 0.8727 (tt)
REVERT: A  478 GLU cc_start: 0.6237 (tp30) cc_final: 0.5369 (tp30)
REVERT: A  522 ASP cc_start: 0.8240 (t0) cc_final: 0.8025 (t0)
REVERT: A  537 ASN cc_start: 0.8303 (m110) cc_final: 0.7970 (m110)
REVERT: A  579 GLN cc_start: 0.6857 (pp30) cc_final: 0.6591 (pp30)
REVERT: E   45 GLU cc_start: 0.8744 (tp30) cc_final: 0.8410 (tp30)
REVERT: E   71 TYR cc_start: 0.7844 (m-80) cc_final: 0.7562 (m-80)
REVERT: E   97 LYS cc_start: 0.7819 (tttt) cc_final: 0.7508 (tttt)
  outliers start: 27
  outliers final: 20
  residues processed: 166
  average time/residue: 0.1304
  time to fit residues: 27.9303
Evaluate side-chains
  175 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   41 CYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   69 GLN
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  426 SER
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  584 ASN
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain E residue    5 ILE
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   26 VAL
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain E residue   74 ARG
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  102 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 74 optimal weight:    6.9990
   chunk 37 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  69 GLN
A 589 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.113743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.090045 restraints weight = 21670.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 2.70
r_work: 0.3197 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.3989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9739  Z= 0.160
  Angle     :  0.562   6.897  13976  Z= 0.302
  Chirality :  0.036   0.217   1667
  Planarity :  0.004   0.047   1142
  Dihedral  : 22.198 169.736   3255
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 17.63 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.33), residues: 678
  helix:  2.47 (0.30), residues: 303
  sheet:  0.20 (0.65), residues: 67
  loop : -0.37 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 534 
 TYR   0.027   0.002   TYR A 472 
 PHE   0.012   0.001   PHE A 357 
 TRP   0.055   0.002   TRP A 424 
 HIS   0.003   0.001   HIS A 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 9737)
  covalent geometry    : angle       0.56167 (13972)
  SS BOND              : bond        0.00321 (    2)
  SS BOND              : angle       0.61251 (    4)
  hydrogen bonds       : bond        0.04147 (  442)
  hydrogen bonds       : angle       3.43025 ( 1097)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 CYS cc_start: 0.8547 (t) cc_final: 0.8301 (t)
REVERT: A   78 ARG cc_start: 0.7042 (tpt170) cc_final: 0.6687 (tpt170)
REVERT: A  108 ASP cc_start: 0.8432 (m-30) cc_final: 0.7985 (t0)
REVERT: A  184 LYS cc_start: 0.8818 (ptmm) cc_final: 0.8411 (ptmm)
REVERT: A  230 GLU cc_start: 0.8064 (tp30) cc_final: 0.7859 (mm-30)
REVERT: A  243 SER cc_start: 0.8727 (m) cc_final: 0.8362 (p)
REVERT: A  267 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.8127 (mtp-110)
REVERT: A  272 LYS cc_start: 0.8982 (mmtm) cc_final: 0.8712 (mmtm)
REVERT: A  326 GLU cc_start: 0.8323 (mp0) cc_final: 0.7724 (mp0)
REVERT: A  328 ILE cc_start: 0.8941 (tp) cc_final: 0.8573 (tp)
REVERT: A  332 LYS cc_start: 0.9137 (mmmt) cc_final: 0.8911 (mmmt)
REVERT: A  354 LYS cc_start: 0.8929 (tppt) cc_final: 0.8548 (tppt)
REVERT: A  360 GLN cc_start: 0.8743 (mm110) cc_final: 0.8384 (tm-30)
REVERT: A  378 ASP cc_start: 0.8833 (t0) cc_final: 0.8557 (t0)
REVERT: A  387 THR cc_start: 0.8895 (m) cc_final: 0.8425 (p)
REVERT: A  407 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7834 (mt-10)
REVERT: A  418 LEU cc_start: 0.8946 (tp) cc_final: 0.8693 (tt)
REVERT: A  451 GLU cc_start: 0.7940 (tt0) cc_final: 0.7557 (tp30)
REVERT: A  522 ASP cc_start: 0.8226 (t0) cc_final: 0.8005 (t0)
REVERT: A  537 ASN cc_start: 0.8290 (m110) cc_final: 0.7945 (m110)
REVERT: E   37 LYS cc_start: 0.8604 (ttmt) cc_final: 0.7933 (ptmm)
REVERT: E   45 GLU cc_start: 0.8775 (tp30) cc_final: 0.8298 (tp30)
REVERT: E   71 TYR cc_start: 0.7801 (m-80) cc_final: 0.7552 (m-80)
REVERT: E   86 GLU cc_start: 0.7863 (pm20) cc_final: 0.7388 (pm20)
REVERT: E   97 LYS cc_start: 0.7756 (tttt) cc_final: 0.7455 (tttt)
  outliers start: 24
  outliers final: 20
  residues processed: 172
  average time/residue: 0.1326
  time to fit residues: 29.3717
Evaluate side-chains
  174 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 154
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   41 CYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   69 GLN
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  426 SER
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  584 ASN
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain E residue    5 ILE
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   26 VAL
Chi-restraints excluded: chain E residue   74 ARG
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  102 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 36 optimal weight:    0.3980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  69 GLN
A 579 GLN
A 589 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.114035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.090402 restraints weight = 21547.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 2.67
r_work: 0.3204 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.4155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9739  Z= 0.156
  Angle     :  0.567   6.904  13976  Z= 0.305
  Chirality :  0.036   0.216   1667
  Planarity :  0.004   0.050   1142
  Dihedral  : 22.174 169.858   3255
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 18.45 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.33), residues: 678
  helix:  2.43 (0.30), residues: 303
  sheet:  0.06 (0.65), residues: 67
  loop : -0.43 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 534 
 TYR   0.042   0.002   TYR A 472 
 PHE   0.011   0.001   PHE A 357 
 TRP   0.050   0.002   TRP A 424 
 HIS   0.003   0.001   HIS A 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9737)
  covalent geometry    : angle       0.56705 (13972)
  SS BOND              : bond        0.00278 (    2)
  SS BOND              : angle       0.65734 (    4)
  hydrogen bonds       : bond        0.04145 (  442)
  hydrogen bonds       : angle       3.44526 ( 1097)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 159
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 CYS cc_start: 0.8504 (t) cc_final: 0.8265 (t)
REVERT: A   78 ARG cc_start: 0.7090 (tpt170) cc_final: 0.6641 (tpt170)
REVERT: A  184 LYS cc_start: 0.8817 (ptmm) cc_final: 0.8415 (ptmm)
REVERT: A  243 SER cc_start: 0.8724 (m) cc_final: 0.8337 (p)
REVERT: A  267 ARG cc_start: 0.8503 (ttm-80) cc_final: 0.8124 (mtp-110)
REVERT: A  272 LYS cc_start: 0.8955 (mmtm) cc_final: 0.8681 (mmtm)
REVERT: A  307 THR cc_start: 0.8703 (m) cc_final: 0.8483 (p)
REVERT: A  326 GLU cc_start: 0.8328 (mp0) cc_final: 0.7728 (mp0)
REVERT: A  328 ILE cc_start: 0.8940 (tp) cc_final: 0.8570 (tp)
REVERT: A  332 LYS cc_start: 0.9106 (mmmt) cc_final: 0.8791 (mmmt)
REVERT: A  336 LYS cc_start: 0.8594 (mmmt) cc_final: 0.8248 (mtmm)
REVERT: A  354 LYS cc_start: 0.8937 (tppt) cc_final: 0.8526 (tppt)
REVERT: A  360 GLN cc_start: 0.8730 (mm110) cc_final: 0.8331 (mt0)
REVERT: A  387 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8456 (p)
REVERT: A  407 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7809 (mt-10)
REVERT: A  418 LEU cc_start: 0.8920 (tp) cc_final: 0.8672 (tt)
REVERT: A  451 GLU cc_start: 0.7895 (tt0) cc_final: 0.7565 (tp30)
REVERT: A  537 ASN cc_start: 0.8293 (m110) cc_final: 0.7945 (m110)
REVERT: E   37 LYS cc_start: 0.8633 (ttmt) cc_final: 0.8308 (tttt)
REVERT: E   45 GLU cc_start: 0.8781 (tp30) cc_final: 0.8275 (tp30)
REVERT: E   71 TYR cc_start: 0.7788 (m-80) cc_final: 0.7555 (m-80)
REVERT: E   86 GLU cc_start: 0.7902 (pm20) cc_final: 0.7424 (pm20)
REVERT: E   97 LYS cc_start: 0.7682 (tttt) cc_final: 0.7350 (tttt)
  outliers start: 22
  outliers final: 19
  residues processed: 166
  average time/residue: 0.1332
  time to fit residues: 28.4977
Evaluate side-chains
  173 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   69 GLN
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  387 THR
Chi-restraints excluded: chain A residue  426 SER
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  584 ASN
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain E residue    5 ILE
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   26 VAL
Chi-restraints excluded: chain E residue   74 ARG
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  102 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 39 optimal weight:    0.0670
   chunk 66 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0170
   chunk 43 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.5556

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

Flipped N/Q/H residues before XYZ refinement:
A  69 GLN
** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 589 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.114563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.090342 restraints weight = 21833.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 2.78
r_work: 0.3210 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.4316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9739  Z= 0.145
  Angle     :  0.567   7.273  13976  Z= 0.307
  Chirality :  0.036   0.212   1667
  Planarity :  0.004   0.046   1142
  Dihedral  : 22.174 169.623   3255
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 19.28 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.33), residues: 678
  helix:  2.41 (0.29), residues: 303
  sheet: -0.08 (0.65), residues: 67
  loop : -0.42 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 534 
 TYR   0.031   0.002   TYR A 348 
 PHE   0.011   0.001   PHE A 595 
 TRP   0.028   0.002   TRP A 424 
 HIS   0.002   0.001   HIS A 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9737)
  covalent geometry    : angle       0.56657 (13972)
  SS BOND              : bond        0.00237 (    2)
  SS BOND              : angle       0.61872 (    4)
  hydrogen bonds       : bond        0.04096 (  442)
  hydrogen bonds       : angle       3.45749 ( 1097)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 160
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 CYS cc_start: 0.8489 (t) cc_final: 0.8265 (t)
REVERT: A   78 ARG cc_start: 0.7171 (tpt170) cc_final: 0.6810 (tpt170)
REVERT: A  102 TRP cc_start: 0.7406 (m-90) cc_final: 0.6159 (m-90)
REVERT: A  184 LYS cc_start: 0.8803 (ptmm) cc_final: 0.8390 (ptmm)
REVERT: A  243 SER cc_start: 0.8730 (m) cc_final: 0.8309 (p)
REVERT: A  267 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8109 (mtp-110)
REVERT: A  272 LYS cc_start: 0.8947 (mmtm) cc_final: 0.8714 (mmtm)
REVERT: A  326 GLU cc_start: 0.8340 (mp0) cc_final: 0.7733 (mp0)
REVERT: A  328 ILE cc_start: 0.8939 (tp) cc_final: 0.8462 (tp)
REVERT: A  332 LYS cc_start: 0.9099 (mmmt) cc_final: 0.8805 (mmmt)
REVERT: A  336 LYS cc_start: 0.8600 (mmmt) cc_final: 0.8240 (mtmm)
REVERT: A  354 LYS cc_start: 0.8941 (tppt) cc_final: 0.8526 (tppt)
REVERT: A  360 GLN cc_start: 0.8760 (mm110) cc_final: 0.8331 (mt0)
REVERT: A  386 SER cc_start: 0.9095 (t) cc_final: 0.8821 (m)
REVERT: A  418 LEU cc_start: 0.8923 (tp) cc_final: 0.8673 (tt)
REVERT: A  451 GLU cc_start: 0.7886 (tt0) cc_final: 0.7563 (tp30)
REVERT: A  537 ASN cc_start: 0.8306 (m110) cc_final: 0.7985 (m110)
REVERT: E   37 LYS cc_start: 0.8646 (ttmt) cc_final: 0.8349 (ttpt)
REVERT: E   45 GLU cc_start: 0.8813 (tp30) cc_final: 0.8320 (tp30)
REVERT: E   59 LEU cc_start: 0.8062 (tt) cc_final: 0.7838 (tt)
REVERT: E   71 TYR cc_start: 0.7787 (m-80) cc_final: 0.7559 (m-80)
REVERT: E   86 GLU cc_start: 0.7916 (pm20) cc_final: 0.7447 (pm20)
REVERT: E   97 LYS cc_start: 0.7654 (tttt) cc_final: 0.7285 (tttt)
  outliers start: 19
  outliers final: 17
  residues processed: 165
  average time/residue: 0.1368
  time to fit residues: 29.0237
Evaluate side-chains
  170 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 153
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   69 GLN
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  426 SER
Chi-restraints excluded: chain A residue  584 ASN
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain E residue    5 ILE
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   26 VAL
Chi-restraints excluded: chain E residue   74 ARG
Chi-restraints excluded: chain E residue  102 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 41 optimal weight:    0.6980
   chunk 32 optimal weight:    0.1980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 316 ASN
** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 589 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.115080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.090851 restraints weight = 21913.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 2.80
r_work: 0.3217 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.4460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9739  Z= 0.143
  Angle     :  0.576   9.070  13976  Z= 0.312
  Chirality :  0.036   0.270   1667
  Planarity :  0.004   0.045   1142
  Dihedral  : 22.190 169.803   3255
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 20.26 %
    Favored  : 76.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.33), residues: 678
  helix:  2.41 (0.30), residues: 303
  sheet:  0.21 (0.59), residues: 74
  loop : -0.48 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 518 
 TYR   0.041   0.002   TYR A 472 
 PHE   0.010   0.001   PHE A 595 
 TRP   0.022   0.002   TRP A 424 
 HIS   0.002   0.001   HIS A 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9737)
  covalent geometry    : angle       0.57560 (13972)
  SS BOND              : bond        0.00220 (    2)
  SS BOND              : angle       0.64608 (    4)
  hydrogen bonds       : bond        0.04051 (  442)
  hydrogen bonds       : angle       3.45796 ( 1097)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 156
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 CYS cc_start: 0.8440 (t) cc_final: 0.8231 (t)
REVERT: A   63 ASP cc_start: 0.8039 (p0) cc_final: 0.7751 (p0)
REVERT: A   78 ARG cc_start: 0.7141 (tpt170) cc_final: 0.6840 (tpt170)
REVERT: A  102 TRP cc_start: 0.7385 (m-90) cc_final: 0.6144 (m-90)
REVERT: A  184 LYS cc_start: 0.8767 (ptmm) cc_final: 0.8354 (ptmm)
REVERT: A  243 SER cc_start: 0.8727 (m) cc_final: 0.8319 (p)
REVERT: A  267 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.8104 (mtp-110)
REVERT: A  272 LYS cc_start: 0.8954 (mmtm) cc_final: 0.8745 (mmtm)
REVERT: A  326 GLU cc_start: 0.8325 (mp0) cc_final: 0.7720 (mp0)
REVERT: A  328 ILE cc_start: 0.8876 (tp) cc_final: 0.8448 (tp)
REVERT: A  332 LYS cc_start: 0.9089 (mmmt) cc_final: 0.8789 (mmmt)
REVERT: A  336 LYS cc_start: 0.8590 (mmmt) cc_final: 0.8228 (mtmm)
REVERT: A  354 LYS cc_start: 0.8953 (tppt) cc_final: 0.8527 (tppt)
REVERT: A  356 LYS cc_start: 0.8910 (pptt) cc_final: 0.8179 (pptt)
REVERT: A  360 GLN cc_start: 0.8737 (mm110) cc_final: 0.8398 (pt0)
REVERT: A  418 LEU cc_start: 0.8915 (tp) cc_final: 0.8711 (tt)
REVERT: A  422 LYS cc_start: 0.8938 (ttpp) cc_final: 0.8633 (ttpp)
REVERT: A  451 GLU cc_start: 0.7882 (tt0) cc_final: 0.7557 (tp30)
REVERT: A  537 ASN cc_start: 0.8298 (m110) cc_final: 0.7991 (m110)
REVERT: E   37 LYS cc_start: 0.8650 (ttmt) cc_final: 0.8338 (tttt)
REVERT: E   45 GLU cc_start: 0.8771 (tp30) cc_final: 0.8304 (tp30)
REVERT: E   59 LEU cc_start: 0.8070 (tt) cc_final: 0.7860 (tt)
REVERT: E   71 TYR cc_start: 0.7779 (m-80) cc_final: 0.7524 (m-80)
REVERT: E   86 GLU cc_start: 0.7942 (pm20) cc_final: 0.7483 (pm20)
REVERT: E   97 LYS cc_start: 0.7621 (tttt) cc_final: 0.7267 (tttt)
  outliers start: 17
  outliers final: 17
  residues processed: 161
  average time/residue: 0.1362
  time to fit residues: 28.3083
Evaluate side-chains
  170 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 153
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  426 SER
Chi-restraints excluded: chain A residue  584 ASN
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain E residue    5 ILE
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   26 VAL
Chi-restraints excluded: chain E residue   74 ARG
Chi-restraints excluded: chain E residue  102 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 2 optimal weight:    0.4980
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  40 HIS
A  69 GLN
** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 589 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.113034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.088854 restraints weight = 21640.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 2.74
r_work: 0.3179 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.4582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9739  Z= 0.188
  Angle     :  0.613   8.643  13976  Z= 0.330
  Chirality :  0.038   0.239   1667
  Planarity :  0.005   0.046   1142
  Dihedral  : 22.302 170.597   3255
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 19.93 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.33), residues: 678
  helix:  2.25 (0.29), residues: 304
  sheet:  0.12 (0.59), residues: 74
  loop : -0.56 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 518 
 TYR   0.042   0.002   TYR A 472 
 PHE   0.010   0.001   PHE A 595 
 TRP   0.015   0.002   TRP A 477 
 HIS   0.005   0.001   HIS A 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 9737)
  covalent geometry    : angle       0.61324 (13972)
  SS BOND              : bond        0.00284 (    2)
  SS BOND              : angle       0.83818 (    4)
  hydrogen bonds       : bond        0.04468 (  442)
  hydrogen bonds       : angle       3.59019 ( 1097)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2358.05 seconds
wall clock time: 41 minutes 20.44 seconds (2480.44 seconds total)