Starting phenix.real_space_refine
on Sun Sep 13 14:11:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pwx_20514/09_2026/6pwx_20514.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pwx_20514/09_2026/6pwx_20514.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6pwx_20514/09_2026/6pwx_20514.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pwx_20514/09_2026/6pwx_20514.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pwx_20514/09_2026/6pwx_20514.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pwx_20514/09_2026/6pwx_20514.cif"
  }
  resolution = 4.2
  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=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 11964 atoms to isotropic.
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     292      5.49       5
     S      27      5.16       5
     C    8152      2.51       5
     N    2673      2.21       5
     O    3267      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14411
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 2447
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2447
          Classifications: {'peptide': 314}
          Link IDs: {'PTRANS': 12, 'TRANS': 301}
    Chain: "G"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 801
          Classifications: {'peptide': 98}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "H"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "I"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 811
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
    Chain: "J"
      Number of atoms: 718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 718
          Classifications: {'peptide': 93}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "K"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 801
          Classifications: {'peptide': 98}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "M"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 815
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "N"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "O"
      Number of atoms: 2975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 2975
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "P"
      Number of atoms: 3011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3011
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "L"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 3.08, per 1000 atoms: 0.21
  Number of scatterers: 14411
  At special positions: 0
  Unit cell: (102.01, 129.28, 123.22, 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      27     16.00
     P     292     15.00
     O    3267      8.00
     N    2673      7.00
     C    8152      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.29
  Conformation dependent library (CDL) restraints added in 515.9 milliseconds
  

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2012

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 15 sheets defined
      51.7% alpha, 12.1% beta
      147 base pairs and 241 stacking pairs defined.
    Time for finding SS restraints: 2.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 227 through 234
    Processing helix  chain 'G' and resid 44 through 57
    Processing helix  chain 'G' and resid 63 through 76
    Processing helix  chain 'G' and resid 85 through 114
    Processing helix  chain 'G' and resid 120 through 132
    Processing helix  chain 'H' and resid 24 through 29
      removed outlier: 4.311A  pdb=" N   GLN H  27 " --> pdb=" O   ASP H  24 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 30 through 41
    Processing helix  chain 'H' and resid 49 through 77
      removed outlier: 3.951A  pdb=" N   GLU H  53 " --> pdb=" O   LEU H  49 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   ARG H  67 " --> pdb=" O   GLU H  63 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 82 through 93
      removed outlier: 3.534A  pdb=" N   VAL H  86 " --> pdb=" O   THR H  82 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 16 through 22
    Processing helix  chain 'I' and resid 26 through 36
    Processing helix  chain 'I' and resid 45 through 73
      removed outlier: 4.339A  pdb=" N   VAL I  49 " --> pdb=" O   ALA I  45 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LEU I  65 " --> pdb=" O   GLU I  61 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 79 through 90
    Processing helix  chain 'I' and resid 90 through 97
      removed outlier: 3.562A  pdb=" N   ASN I  94 " --> pdb=" O   ASP I  90 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 34 through 46
    Processing helix  chain 'J' and resid 52 through 81
    Processing helix  chain 'J' and resid 87 through 99
    Processing helix  chain 'J' and resid 100 through 120
      removed outlier: 3.685A  pdb=" N   ALA J 104 " --> pdb=" O   PRO J 100 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 44 through 57
    Processing helix  chain 'K' and resid 63 through 76
    Processing helix  chain 'K' and resid 85 through 114
    Processing helix  chain 'K' and resid 120 through 132
    Processing helix  chain 'M' and resid 16 through 21
    Processing helix  chain 'M' and resid 26 through 37
    Processing helix  chain 'M' and resid 45 through 73
      removed outlier: 4.484A  pdb=" N   VAL M  49 " --> pdb=" O   ALA M  45 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 79 through 89
    Processing helix  chain 'M' and resid 90 through 97
    Processing helix  chain 'N' and resid 34 through 46
    Processing helix  chain 'N' and resid 52 through 81
    Processing helix  chain 'N' and resid 87 through 99
    Processing helix  chain 'N' and resid 101 through 121
      removed outlier: 3.863A  pdb=" N   ALA N 121 " --> pdb=" O   LYS N 117 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 24 through 29
      removed outlier: 4.310A  pdb=" N   GLN L  27 " --> pdb=" O   ASP L  24 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 30 through 41
    Processing helix  chain 'L' and resid 49 through 77
      removed outlier: 3.951A  pdb=" N   GLU L  53 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   ARG L  67 " --> pdb=" O   GLU L  63 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 82 through 93
      removed outlier: 3.533A  pdb=" N   VAL L  86 " --> pdb=" O   THR L  82 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21
      removed outlier: 4.394A  pdb=" N   VAL A 318 " --> pdb=" O   LEU A  21 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   ILE A 309 " --> pdb=" O   TRP A 303 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   TRP A 303 " --> pdb=" O   ILE A 309 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   ALA A 311 " --> pdb=" O   VAL A 301 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   VAL A 301 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ILE A 313 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32
      removed outlier: 6.652A  pdb=" N   ILE A  48 " --> pdb=" O   ILE A  61 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   ILE A  61 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ILE A  50 " --> pdb=" O   ALA A  59 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 74
      removed outlier: 7.102A  pdb=" N   ALA A  84 " --> pdb=" O   CYS A  70 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   LEU A  72 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   VAL A  82 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
      removed outlier: 5.091A  pdb=" N   TRP A  74 " --> pdb=" O   LYS A  80 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   LYS A  80 " --> pdb=" O   TRP A  74 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ILE A  89 " --> pdb=" O   SER A  85 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   ASP A  94 " --> pdb=" O   CYS A 100 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   CYS A 100 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 115
      removed outlier: 4.062A  pdb=" N   LYS A 112 " --> pdb=" O   CYS A 126 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 159
      removed outlier: 6.976A  pdb=" N   LYS A 179 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
      removed outlier: 7.403A  pdb=" N   LEU A 185 " --> pdb=" O   LYS A 179 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 206
    Processing sheet with id=AA7, first strand: chain 'A' and resid 258 through 259
      removed outlier: 6.142A  pdb=" N   GLU A 280 " --> pdb=" O   LEU A 286 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LEU A 286 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 83 through 84
      removed outlier: 7.050A  pdb=" N   ARG G  83 " --> pdb=" O   VAL H  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 118 through 119
    Processing sheet with id=AB1, first strand: chain 'I' and resid 42 through 43
      removed outlier: 7.169A  pdb=" N   ARG I  42 " --> pdb=" O   ILE J  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'I' and resid 77 through 78
    Processing sheet with id=AB3, first strand: chain 'K' and resid 83 through 84
      removed outlier: 7.382A  pdb=" N   ARG K  83 " --> pdb=" O   VAL L  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'K' and resid 118 through 119
    Processing sheet with id=AB5, first strand: chain 'M' and resid 42 through 43
      removed outlier: 7.055A  pdb=" N   ARG M  42 " --> pdb=" O   ILE N  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'M' and resid 77 through 78

    479 hydrogen bonds defined for protein.
    1398 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      377 hydrogen bonds
      750 hydrogen bond angles
      0 basepair planarities
      147 basepair parallelities
      241 stacking parallelities
  Total time for adding SS restraints: 3.02

  Time building geometry restraints manager: 1.73 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: 3042
        1.33 -     1.45: 4521
        1.45 -     1.57: 7085
        1.57 -     1.69: 582
        1.69 -     1.81: 41
  Bond restraints: 15271
  Sorted by residual:
  bond pdb=" C3'  DA P  44 "
       pdb=" C2'  DA P  44 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.22e+01
  bond pdb=" C3'  DC O  56 "
       pdb=" C2'  DC O  56 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.19e+01
  bond pdb=" C3'  DG O  73 "
       pdb=" C2'  DG O  73 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.13e+01
  bond pdb=" C3'  DG P   5 "
       pdb=" C2'  DG P   5 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.08e+01
  bond pdb=" C3'  DG P  95 "
       pdb=" C2'  DG P  95 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.05e+01
  ... (remaining 15266 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 20747
        1.65 -     3.29: 1121
        3.29 -     4.94: 35
        4.94 -     6.58: 8
        6.58 -     8.23: 4
  Bond angle restraints: 21915
  Sorted by residual:
  angle pdb=" O4'  DA P  14 "
        pdb=" C4'  DA P  14 "
        pdb=" C3'  DA P  14 "
      ideal   model   delta    sigma   weight residual
     106.00  103.12    2.88 6.00e-01 2.78e+00 2.31e+01
  angle pdb=" O4'  DC P  93 "
        pdb=" C4'  DC P  93 "
        pdb=" C3'  DC P  93 "
      ideal   model   delta    sigma   weight residual
     106.00  103.15    2.85 6.00e-01 2.78e+00 2.26e+01
  angle pdb=" N3   DT P 105 "
        pdb=" C4   DT P 105 "
        pdb=" O4   DT P 105 "
      ideal   model   delta    sigma   weight residual
     119.90  122.58   -2.68 6.00e-01 2.78e+00 1.99e+01
  angle pdb=" N3   DT O   9 "
        pdb=" C4   DT O   9 "
        pdb=" O4   DT O   9 "
      ideal   model   delta    sigma   weight residual
     119.90  122.57   -2.67 6.00e-01 2.78e+00 1.98e+01
  angle pdb=" N3   DT O  57 "
        pdb=" C4   DT O  57 "
        pdb=" O4   DT O  57 "
      ideal   model   delta    sigma   weight residual
     119.90  122.52   -2.62 6.00e-01 2.78e+00 1.91e+01
  ... (remaining 21910 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.55: 6405
       26.55 -    53.09: 1583
       53.09 -    79.64: 404
       79.64 -   106.18: 13
      106.18 -   132.73: 3
  Dihedral angle restraints: 8408
    sinusoidal: 5295
      harmonic: 3113
  Sorted by residual:
  dihedral pdb=" CA  ILE L  50 "
           pdb=" C   ILE L  50 "
           pdb=" N   TYR L  51 "
           pdb=" CA  TYR L  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.36  -19.64     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  ILE H  50 "
           pdb=" C   ILE H  50 "
           pdb=" N   TYR H  51 "
           pdb=" CA  TYR H  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.39  -19.61     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" C4'  DG P  94 "
           pdb=" C3'  DG P  94 "
           pdb=" O3'  DG P  94 "
           pdb=" P    DG P  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   -7.27 -132.73     1      3.50e+01 8.16e-04 1.32e+01
  ... (remaining 8405 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1532
       0.035 -    0.069: 666
       0.069 -    0.104: 253
       0.104 -    0.138: 55
       0.138 -    0.173: 3
  Chirality restraints: 2509
  Sorted by residual:
  chirality pdb=" C3'  DC P 126 "
            pdb=" C4'  DC P 126 "
            pdb=" O3'  DC P 126 "
            pdb=" C2'  DC P 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.56   -0.17 2.00e-01 2.50e+01 7.48e-01
  chirality pdb=" CB  ILE A 221 "
            pdb=" CA  ILE A 221 "
            pdb=" CG1 ILE A 221 "
            pdb=" CG2 ILE A 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 4.99e-01
  chirality pdb=" CA  ILE A 289 "
            pdb=" N   ILE A 289 "
            pdb=" C   ILE A 289 "
            pdb=" CB  ILE A 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.81e-01
  ... (remaining 2506 not shown)

  Planarity restraints: 1765
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN L  64 "    0.010 2.00e-02 2.50e+03   2.05e-02 4.22e+00
        pdb=" C   ASN L  64 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   ASN L  64 "    0.013 2.00e-02 2.50e+03
        pdb=" N   VAL L  65 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN H  64 "   -0.010 2.00e-02 2.50e+03   2.03e-02 4.13e+00
        pdb=" C   ASN H  64 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ASN H  64 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   VAL H  65 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC O  80 "   -0.007 2.00e-02 2.50e+03   1.33e-02 4.00e+00
        pdb=" N1   DC O  80 "    0.013 2.00e-02 2.50e+03
        pdb=" C2   DC O  80 "    0.031 2.00e-02 2.50e+03
        pdb=" O2   DC O  80 "   -0.018 2.00e-02 2.50e+03
        pdb=" N3   DC O  80 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4   DC O  80 "   -0.003 2.00e-02 2.50e+03
        pdb=" N4   DC O  80 "    0.000 2.00e-02 2.50e+03
        pdb=" C5   DC O  80 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DC O  80 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1762 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 419
        2.66 -     3.22: 13370
        3.22 -     3.78: 29040
        3.78 -     4.34: 34913
        4.34 -     4.90: 49905
  Nonbonded interactions: 127647
  Sorted by model distance:
  nonbonded pdb=" N2   DG O  83 "
            pdb=" O2   DC P  65 "
     model   vdw
     2.098 2.496
  nonbonded pdb=" OG1 THR A 217 "
            pdb=" OD1 ASP A 219 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OE1 GLU L  52 "
            pdb=" N   GLU L  53 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" OE1 GLU H  52 "
            pdb=" N   GLU H  53 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" OP1  DA P 102 "
            pdb=" N   LYS L  79 "
     model   vdw
     2.236 3.120
  ... (remaining 127642 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
Found NCS groups:
ncs_group {
  reference = chain 'G'
  selection = chain 'K'
}
ncs_group {
  reference = chain 'H'
  selection = chain 'L'
}
ncs_group {
  reference = (chain 'I' and (resid 12 through 73 or (resid 74 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 75 through 118))
  selection = (chain 'M' and ((resid 12 through 14 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 37 through 118))
}
ncs_group {
  reference = chain 'J'
  selection = (chain 'N' and (resid 29 through 30 or (resid 31 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 56 through 121))
}

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 group one per residue
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:             4.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.010
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
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   0.048  15271  Z= 0.468
  Angle     :  0.741   8.229  21915  Z= 0.648
  Chirality :  0.043   0.173   2509
  Planarity :  0.003   0.038   1765
  Dihedral  : 27.209 132.729   6396
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  :  3.80 %
    Favored  : 92.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.76 (0.24), residues: 1056
  helix: -0.03 (0.20), residues: 546
  sheet: -2.08 (0.44), residues: 134
  loop : -2.45 (0.28), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  36 
 TYR   0.008   0.001   TYR I  57 
 PHE   0.006   0.001   PHE H 100 
 TRP   0.016   0.001   TRP A 279 
 HIS   0.003   0.001   HIS H  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00507 /  0.47 (15271)
  covalent geometry    : angle       0.74124 /  0.65 (21915)
  hydrogen bonds       : bond        0.11259 /  7.52 (  856)
  hydrogen bonds       : angle       5.12876 /  3.50 ( 2148)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  459 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 427
  time to evaluate  : 0.403 
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: A   53 PHE cc_start: 0.8503 (m-80) cc_final: 0.8183 (m-80)
REVERT: A   81 LEU cc_start: 0.8838 (mt) cc_final: 0.8473 (pp)
REVERT: A  134 MET cc_start: 0.8204 (ttp) cc_final: 0.6761 (mpp)
REVERT: A  251 ARG cc_start: 0.8917 (mmt90) cc_final: 0.8545 (mmt180)
REVERT: A  264 GLU cc_start: 0.7380 (tp30) cc_final: 0.7124 (tp30)
REVERT: A  265 TYR cc_start: 0.7885 (m-10) cc_final: 0.7666 (m-10)
REVERT: G   77 ASP cc_start: 0.9475 (OUTLIER) cc_final: 0.8920 (t70)
REVERT: G   93 GLN cc_start: 0.9191 (tt0) cc_final: 0.8740 (tt0)
REVERT: G  106 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8761 (p0)
REVERT: G  107 THR cc_start: 0.9431 (p) cc_final: 0.8885 (p)
REVERT: G  123 ASP cc_start: 0.8536 (t70) cc_final: 0.6799 (t70)
REVERT: G  124 ILE cc_start: 0.9596 (mt) cc_final: 0.9290 (tp)
REVERT: G  125 GLN cc_start: 0.9126 (mt0) cc_final: 0.8768 (mt0)
REVERT: H   22 LEU cc_start: 0.7817 (mm) cc_final: 0.7130 (mm)
REVERT: H   39 ARG cc_start: 0.9191 (mmt-90) cc_final: 0.8733 (mmt-90)
REVERT: H   43 VAL cc_start: 0.8535 (t) cc_final: 0.7810 (t)
REVERT: H   44 LYS cc_start: 0.7748 (tttt) cc_final: 0.7454 (ttmt)
REVERT: H   46 ILE cc_start: 0.9004 (mp) cc_final: 0.8768 (mp)
REVERT: H   51 TYR cc_start: 0.8158 (m-80) cc_final: 0.6966 (m-10)
REVERT: H   55 ARG cc_start: 0.9131 (mtt90) cc_final: 0.8755 (mtm-85)
REVERT: H   64 ASN cc_start: 0.9109 (m-40) cc_final: 0.8692 (m-40)
REVERT: H   75 HIS cc_start: 0.8678 (t70) cc_final: 0.8354 (t-90)
REVERT: H   77 LYS cc_start: 0.9483 (mttt) cc_final: 0.9186 (mmtm)
REVERT: I   42 ARG cc_start: 0.9350 (mtm180) cc_final: 0.8710 (mtm-85)
REVERT: I   61 GLU cc_start: 0.9363 (mm-30) cc_final: 0.8817 (tp30)
REVERT: I   75 LYS cc_start: 0.9360 (mmtm) cc_final: 0.8986 (mmtp)
REVERT: I   94 ASN cc_start: 0.9066 (t0) cc_final: 0.8529 (t0)
REVERT: I   95 LYS cc_start: 0.9580 (tptt) cc_final: 0.9299 (tppt)
REVERT: I  104 GLN cc_start: 0.9291 (mm-40) cc_final: 0.8584 (mp10)
REVERT: J   32 GLU cc_start: 0.9040 (pp20) cc_final: 0.8320 (pp20)
REVERT: J   39 TYR cc_start: 0.8517 (t80) cc_final: 0.8161 (t80)
REVERT: J   40 LYS cc_start: 0.9651 (mttt) cc_final: 0.9330 (mtpt)
REVERT: J   62 PHE cc_start: 0.9567 (t80) cc_final: 0.9157 (t80)
REVERT: J   65 ASP cc_start: 0.8605 (t70) cc_final: 0.7656 (t0)
REVERT: J   68 GLU cc_start: 0.9083 (tp30) cc_final: 0.8730 (tp30)
REVERT: J   76 ARG cc_start: 0.9236 (ttm110) cc_final: 0.8763 (ttm110)
REVERT: J   81 ASN cc_start: 0.9278 (m-40) cc_final: 0.8400 (m-40)
REVERT: J   85 THR cc_start: 0.8640 (p) cc_final: 0.7364 (p)
REVERT: J   90 GLU cc_start: 0.9256 (mp0) cc_final: 0.9042 (mp0)
REVERT: J   93 THR cc_start: 0.9750 (m) cc_final: 0.9500 (p)
REVERT: J  102 GLU cc_start: 0.8794 (tp30) cc_final: 0.8573 (tm-30)
REVERT: J  103 LEU cc_start: 0.9338 (mt) cc_final: 0.9033 (mt)
REVERT: J  110 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8999 (mm-30)
REVERT: K   48 LEU cc_start: 0.9613 (mp) cc_final: 0.9273 (mp)
REVERT: K   50 GLU cc_start: 0.8350 (tp30) cc_final: 0.7681 (tp30)
REVERT: K   52 ARG cc_start: 0.9252 (mtt90) cc_final: 0.8809 (mtm-85)
REVERT: K   54 TYR cc_start: 0.8942 (m-10) cc_final: 0.8683 (m-10)
REVERT: K   60 LEU cc_start: 0.9241 (mt) cc_final: 0.8954 (mt)
REVERT: K   65 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9258 (tp)
REVERT: K   67 PHE cc_start: 0.9575 (t80) cc_final: 0.9359 (t80)
REVERT: K   68 GLN cc_start: 0.9305 (tt0) cc_final: 0.9005 (tt0)
REVERT: K   86 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8301 (t)
REVERT: K   93 GLN cc_start: 0.9622 (tt0) cc_final: 0.9395 (tm-30)
REVERT: K   94 GLU cc_start: 0.9367 (tt0) cc_final: 0.9160 (tm-30)
REVERT: K  110 CYS cc_start: 0.9470 (m) cc_final: 0.9266 (p)
REVERT: K  121 PRO cc_start: 0.9110 (Cg_exo) cc_final: 0.8733 (Cg_endo)
REVERT: K  123 ASP cc_start: 0.7897 (t70) cc_final: 0.6294 (t70)
REVERT: K  124 ILE cc_start: 0.9656 (mt) cc_final: 0.9345 (mm)
REVERT: M   35 ARG cc_start: 0.8849 (mtm-85) cc_final: 0.8142 (mtm-85)
REVERT: M   36 LYS cc_start: 0.9139 (mttm) cc_final: 0.8797 (tttt)
REVERT: M   64 GLU cc_start: 0.9463 (tt0) cc_final: 0.8914 (tm-30)
REVERT: M   68 ASN cc_start: 0.9462 (m-40) cc_final: 0.8189 (m-40)
REVERT: M   78 ILE cc_start: 0.9640 (mt) cc_final: 0.9400 (mm)
REVERT: M  112 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8629 (mp10)
REVERT: N   65 ASP cc_start: 0.9313 (t0) cc_final: 0.8888 (t0)
REVERT: N   91 ILE cc_start: 0.9716 (mm) cc_final: 0.9316 (tt)
REVERT: N   96 ARG cc_start: 0.9129 (mtp180) cc_final: 0.8600 (ttm110)
REVERT: N  105 LYS cc_start: 0.9155 (mttt) cc_final: 0.8456 (mtpp)
REVERT: N  110 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8408 (mt-10)
REVERT: L   25 ASN cc_start: 0.8035 (t0) cc_final: 0.6532 (t0)
REVERT: L   51 TYR cc_start: 0.8022 (m-80) cc_final: 0.7630 (m-80)
REVERT: L   68 ASP cc_start: 0.9510 (m-30) cc_final: 0.9185 (m-30)
REVERT: L   79 LYS cc_start: 0.8682 (mmtt) cc_final: 0.7923 (mmmt)
REVERT: L   82 THR cc_start: 0.9304 (p) cc_final: 0.9059 (p)
REVERT: L   98 TYR cc_start: 0.8930 (m-10) cc_final: 0.8031 (m-80)
  outliers start: 32
  outliers final: 11
  residues processed: 436
  average time/residue: 0.1487
  time to fit residues: 89.7338
Evaluate side-chains
  357 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 342
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  79 HIS
A 197 ASN
A 274 HIS
G  39 HIS
G  68 GLN
** H  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  39 HIS
K  76 GLN
** M  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  46 HIS
L  64 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.056603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.041519 restraints weight = 78485.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.043029 restraints weight = 36809.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.044013 restraints weight = 22718.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.044643 restraints weight = 16530.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.044997 restraints weight = 13616.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  15271  Z= 0.206
  Angle     :  0.713  10.492  21915  Z= 0.409
  Chirality :  0.047   0.311   2509
  Planarity :  0.005   0.056   1765
  Dihedral  : 30.705 135.978   4372
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.81 %
    Favored  : 95.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.25), residues: 1056
  helix:  0.85 (0.21), residues: 552
  sheet: -2.08 (0.43), residues: 139
  loop : -2.03 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG K  42 
 TYR   0.019   0.002   TYR H  88 
 PHE   0.031   0.002   PHE G  67 
 TRP   0.030   0.002   TRP A  35 
 HIS   0.009   0.001   HIS A 274 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00377 /  0.21 (15271)
  covalent geometry    : angle       0.71320 /  0.41 (21915)
  hydrogen bonds       : bond        0.06974 /  4.83 (  856)
  hydrogen bonds       : angle       4.24060 /  2.94 ( 2148)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  376 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 375
  time to evaluate  : 0.428 
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: A   51 TRP cc_start: 0.7485 (t60) cc_final: 0.7282 (t60)
REVERT: A   81 LEU cc_start: 0.8899 (mt) cc_final: 0.8548 (pp)
REVERT: A  134 MET cc_start: 0.7904 (ttp) cc_final: 0.6636 (mpp)
REVERT: A  225 TYR cc_start: 0.7165 (m-80) cc_final: 0.6948 (m-80)
REVERT: A  251 ARG cc_start: 0.9056 (mmt90) cc_final: 0.8662 (mmt180)
REVERT: A  259 PHE cc_start: 0.7022 (m-80) cc_final: 0.6205 (m-80)
REVERT: A  265 TYR cc_start: 0.7839 (m-10) cc_final: 0.7603 (m-10)
REVERT: A  280 GLU cc_start: 0.8402 (tt0) cc_final: 0.8115 (tt0)
REVERT: G   50 GLU cc_start: 0.8475 (tp30) cc_final: 0.8235 (tp30)
REVERT: G   55 GLN cc_start: 0.9427 (mt0) cc_final: 0.9199 (mt0)
REVERT: G   60 LEU cc_start: 0.9256 (mp) cc_final: 0.8905 (mp)
REVERT: G   73 GLU cc_start: 0.8724 (tt0) cc_final: 0.8405 (tt0)
REVERT: G   77 ASP cc_start: 0.8963 (t70) cc_final: 0.8534 (t70)
REVERT: G   93 GLN cc_start: 0.9404 (tt0) cc_final: 0.9134 (tm-30)
REVERT: G  125 GLN cc_start: 0.9137 (mt0) cc_final: 0.8783 (mt0)
REVERT: H   25 ASN cc_start: 0.8295 (t0) cc_final: 0.7381 (t0)
REVERT: H   59 LYS cc_start: 0.9355 (ttpp) cc_final: 0.9099 (ttmm)
REVERT: H   64 ASN cc_start: 0.9365 (m-40) cc_final: 0.9030 (m-40)
REVERT: H   68 ASP cc_start: 0.9368 (m-30) cc_final: 0.8948 (m-30)
REVERT: I   38 ASN cc_start: 0.8737 (m-40) cc_final: 0.8495 (m110)
REVERT: I   42 ARG cc_start: 0.9310 (mtm180) cc_final: 0.8567 (mtp85)
REVERT: I   61 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8944 (mm-30)
REVERT: I   68 ASN cc_start: 0.9380 (m-40) cc_final: 0.9159 (m110)
REVERT: I   75 LYS cc_start: 0.9511 (mmtm) cc_final: 0.9032 (mmtp)
REVERT: I   87 VAL cc_start: 0.9696 (m) cc_final: 0.9480 (m)
REVERT: I   94 ASN cc_start: 0.9154 (t0) cc_final: 0.8648 (t0)
REVERT: I   95 LYS cc_start: 0.9581 (tptt) cc_final: 0.9336 (tppt)
REVERT: J   32 GLU cc_start: 0.9190 (pp20) cc_final: 0.8525 (pp20)
REVERT: J   39 TYR cc_start: 0.8714 (t80) cc_final: 0.8281 (t80)
REVERT: J   44 GLN cc_start: 0.9100 (tm-30) cc_final: 0.8663 (tm-30)
REVERT: J   65 ASP cc_start: 0.8534 (t70) cc_final: 0.7771 (t0)
REVERT: J   68 GLU cc_start: 0.8903 (tp30) cc_final: 0.8651 (tp30)
REVERT: J   76 ARG cc_start: 0.9202 (ttm110) cc_final: 0.8749 (ttm110)
REVERT: J   81 ASN cc_start: 0.9268 (m-40) cc_final: 0.8140 (p0)
REVERT: J   93 THR cc_start: 0.9768 (m) cc_final: 0.9545 (p)
REVERT: J   98 LEU cc_start: 0.9046 (tt) cc_final: 0.8696 (tt)
REVERT: J  103 LEU cc_start: 0.9398 (mt) cc_final: 0.9073 (mt)
REVERT: K   42 ARG cc_start: 0.7939 (mmp80) cc_final: 0.7700 (mmp80)
REVERT: K   48 LEU cc_start: 0.9684 (mp) cc_final: 0.9363 (mp)
REVERT: K   50 GLU cc_start: 0.8404 (tp30) cc_final: 0.7679 (tp30)
REVERT: K   52 ARG cc_start: 0.9225 (mtt90) cc_final: 0.8789 (mtm-85)
REVERT: K   54 TYR cc_start: 0.8808 (m-10) cc_final: 0.8540 (m-10)
REVERT: K   65 LEU cc_start: 0.9588 (mm) cc_final: 0.9376 (tp)
REVERT: K   82 LEU cc_start: 0.8971 (mt) cc_final: 0.8674 (mt)
REVERT: K   85 GLN cc_start: 0.9496 (mm-40) cc_final: 0.9249 (mm110)
REVERT: K  124 ILE cc_start: 0.9678 (mt) cc_final: 0.9349 (tp)
REVERT: K  125 GLN cc_start: 0.9077 (mp-120) cc_final: 0.8694 (mm-40)
REVERT: M   56 GLU cc_start: 0.9431 (tt0) cc_final: 0.9190 (mt-10)
REVERT: M   64 GLU cc_start: 0.9470 (tt0) cc_final: 0.9005 (tm-30)
REVERT: M   68 ASN cc_start: 0.9582 (m-40) cc_final: 0.8181 (m-40)
REVERT: M  112 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8737 (mp10)
REVERT: N   44 GLN cc_start: 0.9322 (tm-30) cc_final: 0.9040 (tm-30)
REVERT: N   65 ASP cc_start: 0.9229 (t0) cc_final: 0.8851 (t0)
REVERT: N   96 ARG cc_start: 0.9006 (mtp180) cc_final: 0.8570 (ttm110)
REVERT: N  110 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8495 (mt-10)
REVERT: L   25 ASN cc_start: 0.7400 (t0) cc_final: 0.6995 (t0)
REVERT: L   43 VAL cc_start: 0.9773 (t) cc_final: 0.9515 (m)
REVERT: L   44 LYS cc_start: 0.9236 (mtpt) cc_final: 0.9010 (mtpt)
REVERT: L   45 ARG cc_start: 0.9149 (mtp180) cc_final: 0.8896 (mtm-85)
REVERT: L   51 TYR cc_start: 0.8469 (m-80) cc_final: 0.8267 (m-80)
REVERT: L   54 THR cc_start: 0.9632 (m) cc_final: 0.9386 (m)
REVERT: L   63 GLU cc_start: 0.8790 (tp30) cc_final: 0.8558 (tp30)
REVERT: L   75 HIS cc_start: 0.8874 (t-90) cc_final: 0.8387 (t-90)
REVERT: L   79 LYS cc_start: 0.8705 (mmtt) cc_final: 0.8115 (mmmt)
REVERT: L   98 TYR cc_start: 0.8829 (m-10) cc_final: 0.8412 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 376
  average time/residue: 0.1306
  time to fit residues: 70.4292
Evaluate side-chains
  324 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 324
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 126 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 6 optimal weight:   10.0000
   chunk 89 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 118 optimal weight:   10.0000
   chunk 94 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 102 optimal weight:    9.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 274 HIS
G  68 GLN
K  39 HIS
K  68 GLN
** K  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 108 ASN
** M  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  25 ASN
** L  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.057158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.042161 restraints weight = 78757.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.043700 restraints weight = 36417.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.044714 restraints weight = 22177.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.045285 restraints weight = 16044.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.045681 restraints weight = 13223.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15271  Z= 0.171
  Angle     :  0.674   7.532  21915  Z= 0.390
  Chirality :  0.046   0.317   2509
  Planarity :  0.005   0.053   1765
  Dihedral  : 30.683 136.140   4372
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.25), residues: 1056
  helix:  1.11 (0.21), residues: 552
  sheet: -1.81 (0.43), residues: 139
  loop : -1.90 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG I  20 
 TYR   0.037   0.003   TYR H  88 
 PHE   0.038   0.002   PHE K  67 
 TRP   0.019   0.002   TRP A 279 
 HIS   0.007   0.001   HIS I  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.17 (15271)
  covalent geometry    : angle       0.67449 /  0.39 (21915)
  hydrogen bonds       : bond        0.06467 /  4.48 (  856)
  hydrogen bonds       : angle       4.05350 /  2.83 ( 2148)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  373 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 373
  time to evaluate  : 0.418 
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   81 LEU cc_start: 0.8901 (mt) cc_final: 0.8536 (pp)
REVERT: A  134 MET cc_start: 0.7844 (ttp) cc_final: 0.6543 (mpp)
REVERT: A  251 ARG cc_start: 0.9077 (mmt90) cc_final: 0.8661 (mmt180)
REVERT: A  259 PHE cc_start: 0.6901 (m-80) cc_final: 0.6028 (m-80)
REVERT: A  265 TYR cc_start: 0.7802 (m-10) cc_final: 0.7523 (m-10)
REVERT: A  280 GLU cc_start: 0.8604 (tt0) cc_final: 0.8257 (tt0)
REVERT: G   50 GLU cc_start: 0.8421 (tp30) cc_final: 0.8163 (tp30)
REVERT: G   55 GLN cc_start: 0.9427 (mt0) cc_final: 0.9193 (mt0)
REVERT: G   60 LEU cc_start: 0.9250 (mp) cc_final: 0.8887 (mp)
REVERT: G   73 GLU cc_start: 0.8746 (tt0) cc_final: 0.8085 (tt0)
REVERT: G   77 ASP cc_start: 0.8918 (t70) cc_final: 0.8512 (t70)
REVERT: G   93 GLN cc_start: 0.9425 (tt0) cc_final: 0.9182 (tm-30)
REVERT: G  105 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8791 (tm-30)
REVERT: G  122 LYS cc_start: 0.8799 (ptmt) cc_final: 0.8572 (ptmt)
REVERT: G  125 GLN cc_start: 0.9035 (mt0) cc_final: 0.8587 (mt0)
REVERT: H   51 TYR cc_start: 0.8332 (m-10) cc_final: 0.7975 (m-10)
REVERT: H   64 ASN cc_start: 0.9281 (m-40) cc_final: 0.8616 (m-40)
REVERT: H   68 ASP cc_start: 0.9028 (m-30) cc_final: 0.8778 (m-30)
REVERT: I   61 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8963 (mm-30)
REVERT: I   68 ASN cc_start: 0.9366 (m-40) cc_final: 0.9150 (m110)
REVERT: I   73 ASN cc_start: 0.9218 (t0) cc_final: 0.8918 (t0)
REVERT: I   75 LYS cc_start: 0.9527 (mmtm) cc_final: 0.8897 (mmtp)
REVERT: I   87 VAL cc_start: 0.9684 (m) cc_final: 0.9475 (m)
REVERT: I   94 ASN cc_start: 0.9066 (t0) cc_final: 0.8615 (t0)
REVERT: I   95 LYS cc_start: 0.9578 (tptt) cc_final: 0.9323 (tppt)
REVERT: J   32 GLU cc_start: 0.9183 (pp20) cc_final: 0.8528 (pp20)
REVERT: J   39 TYR cc_start: 0.8699 (t80) cc_final: 0.8396 (t80)
REVERT: J   40 LYS cc_start: 0.9618 (ttmm) cc_final: 0.9369 (mtpt)
REVERT: J   44 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8658 (tm-30)
REVERT: J   65 ASP cc_start: 0.8492 (t70) cc_final: 0.7745 (t0)
REVERT: J   76 ARG cc_start: 0.9197 (ttm110) cc_final: 0.8801 (ttm110)
REVERT: J   77 LEU cc_start: 0.9672 (tp) cc_final: 0.9353 (tp)
REVERT: J   81 ASN cc_start: 0.9198 (m-40) cc_final: 0.8092 (p0)
REVERT: J   87 THR cc_start: 0.9071 (p) cc_final: 0.8542 (p)
REVERT: J   93 THR cc_start: 0.9776 (m) cc_final: 0.9557 (p)
REVERT: J   98 LEU cc_start: 0.9062 (tt) cc_final: 0.8852 (tt)
REVERT: J   99 LEU cc_start: 0.9397 (mt) cc_final: 0.9116 (mp)
REVERT: K   48 LEU cc_start: 0.9664 (mp) cc_final: 0.9236 (mp)
REVERT: K   50 GLU cc_start: 0.8366 (tp30) cc_final: 0.7649 (tp30)
REVERT: K   52 ARG cc_start: 0.9230 (mtt90) cc_final: 0.8859 (mtm-85)
REVERT: K   54 TYR cc_start: 0.8724 (m-10) cc_final: 0.8460 (m-10)
REVERT: K   64 LYS cc_start: 0.9174 (mtmt) cc_final: 0.8854 (mtmm)
REVERT: K   85 GLN cc_start: 0.9491 (mm-40) cc_final: 0.9174 (mm110)
REVERT: K  120 MET cc_start: 0.9073 (mmp) cc_final: 0.8807 (mmm)
REVERT: K  123 ASP cc_start: 0.8169 (t0) cc_final: 0.6673 (t0)
REVERT: M   56 GLU cc_start: 0.9430 (tt0) cc_final: 0.9108 (mt-10)
REVERT: M   64 GLU cc_start: 0.9453 (tt0) cc_final: 0.9010 (tm-30)
REVERT: M   68 ASN cc_start: 0.9559 (m-40) cc_final: 0.8147 (m-40)
REVERT: N   42 LEU cc_start: 0.9605 (tp) cc_final: 0.9380 (tp)
REVERT: N   43 LYS cc_start: 0.9592 (tppp) cc_final: 0.9375 (tppp)
REVERT: N   44 GLN cc_start: 0.9334 (tm-30) cc_final: 0.9035 (tm-30)
REVERT: N   65 ASP cc_start: 0.9226 (t0) cc_final: 0.8805 (t0)
REVERT: N   86 ILE cc_start: 0.9344 (mt) cc_final: 0.8800 (mt)
REVERT: N   96 ARG cc_start: 0.8974 (mtp180) cc_final: 0.8519 (ttm110)
REVERT: N  105 LYS cc_start: 0.9313 (mttt) cc_final: 0.8861 (mtpt)
REVERT: N  110 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8510 (mt-10)
REVERT: L   39 ARG cc_start: 0.8959 (mmt-90) cc_final: 0.8276 (tpp-160)
REVERT: L   43 VAL cc_start: 0.9715 (t) cc_final: 0.9474 (m)
REVERT: L   44 LYS cc_start: 0.9166 (mtpt) cc_final: 0.8884 (mtpt)
REVERT: L   98 TYR cc_start: 0.8856 (m-10) cc_final: 0.8532 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 373
  average time/residue: 0.1418
  time to fit residues: 74.4366
Evaluate side-chains
  320 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 320
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 34 optimal weight:    0.2980
   chunk 101 optimal weight:   10.0000
   chunk 42 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 110 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 85 optimal weight:    0.8980
   chunk 109 optimal weight:   10.0000
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 274 HIS
G  68 GLN
G  76 GLN
G 108 ASN
K  39 HIS
K  68 GLN
** K  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  81 ASN
** L  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  93 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.057275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.042311 restraints weight = 78447.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.043808 restraints weight = 36414.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.044803 restraints weight = 22456.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.045401 restraints weight = 16356.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.045764 restraints weight = 13434.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.093  15271  Z= 0.172
  Angle     :  0.677   7.218  21915  Z= 0.392
  Chirality :  0.046   0.316   2509
  Planarity :  0.005   0.054   1765
  Dihedral  : 30.665 136.613   4372
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.68 %
    Favored  : 97.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.25), residues: 1056
  helix:  1.09 (0.21), residues: 552
  sheet: -1.79 (0.43), residues: 139
  loop : -1.79 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L  45 
 TYR   0.043   0.003   TYR H  88 
 PHE   0.022   0.002   PHE A 206 
 TRP   0.021   0.002   TRP A 279 
 HIS   0.010   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.17 (15271)
  covalent geometry    : angle       0.67711 /  0.39 (21915)
  hydrogen bonds       : bond        0.06385 /  4.44 (  856)
  hydrogen bonds       : angle       4.04605 /  2.83 ( 2148)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  359 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 358
  time to evaluate  : 0.406 
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   81 LEU cc_start: 0.8903 (mt) cc_final: 0.8565 (pp)
REVERT: A  134 MET cc_start: 0.7865 (ttp) cc_final: 0.6604 (mpp)
REVERT: A  259 PHE cc_start: 0.6801 (m-80) cc_final: 0.5854 (m-80)
REVERT: A  265 TYR cc_start: 0.7709 (m-80) cc_final: 0.7418 (m-10)
REVERT: A  280 GLU cc_start: 0.8551 (tt0) cc_final: 0.8225 (tt0)
REVERT: G   50 GLU cc_start: 0.8379 (tp30) cc_final: 0.8116 (tp30)
REVERT: G   55 GLN cc_start: 0.9438 (mt0) cc_final: 0.9203 (mt0)
REVERT: G   60 LEU cc_start: 0.9320 (mp) cc_final: 0.8856 (mp)
REVERT: G   77 ASP cc_start: 0.9030 (t70) cc_final: 0.8584 (t70)
REVERT: G   93 GLN cc_start: 0.9365 (tt0) cc_final: 0.9142 (tm-30)
REVERT: G  122 LYS cc_start: 0.8745 (ptmt) cc_final: 0.8528 (ptmt)
REVERT: G  125 GLN cc_start: 0.9073 (mt0) cc_final: 0.8600 (mt0)
REVERT: H   31 LYS cc_start: 0.8982 (tptp) cc_final: 0.8311 (tptp)
REVERT: H   43 VAL cc_start: 0.9075 (t) cc_final: 0.8649 (t)
REVERT: H   51 TYR cc_start: 0.8203 (m-10) cc_final: 0.7822 (m-10)
REVERT: H   64 ASN cc_start: 0.9273 (m-40) cc_final: 0.8543 (m-40)
REVERT: I   61 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8926 (mm-30)
REVERT: I   68 ASN cc_start: 0.9394 (m-40) cc_final: 0.9185 (m110)
REVERT: I   73 ASN cc_start: 0.9236 (t0) cc_final: 0.8905 (t0)
REVERT: I   75 LYS cc_start: 0.9528 (mmtm) cc_final: 0.8924 (mmtp)
REVERT: I   87 VAL cc_start: 0.9670 (m) cc_final: 0.9445 (m)
REVERT: I   94 ASN cc_start: 0.9111 (t0) cc_final: 0.8624 (t0)
REVERT: I   95 LYS cc_start: 0.9593 (tptt) cc_final: 0.9310 (tppt)
REVERT: J   32 GLU cc_start: 0.9175 (pp20) cc_final: 0.8541 (pp20)
REVERT: J   44 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8689 (tm-30)
REVERT: J   65 ASP cc_start: 0.8514 (t70) cc_final: 0.7895 (t0)
REVERT: J   76 ARG cc_start: 0.9189 (ttm110) cc_final: 0.8741 (ttm110)
REVERT: J   81 ASN cc_start: 0.9249 (m-40) cc_final: 0.8080 (p0)
REVERT: J   98 LEU cc_start: 0.9060 (tt) cc_final: 0.8845 (tt)
REVERT: J   99 LEU cc_start: 0.9340 (mt) cc_final: 0.9027 (mp)
REVERT: K   48 LEU cc_start: 0.9677 (mp) cc_final: 0.9230 (mp)
REVERT: K   50 GLU cc_start: 0.8768 (tp30) cc_final: 0.7807 (tp30)
REVERT: K   52 ARG cc_start: 0.9219 (mtt90) cc_final: 0.8805 (mtm-85)
REVERT: K   64 LYS cc_start: 0.9251 (mtmt) cc_final: 0.8966 (mttp)
REVERT: K   65 LEU cc_start: 0.9680 (tp) cc_final: 0.9388 (tp)
REVERT: K   70 LEU cc_start: 0.9762 (tt) cc_final: 0.9505 (tt)
REVERT: K   85 GLN cc_start: 0.9534 (mm-40) cc_final: 0.9220 (mm110)
REVERT: K  124 ILE cc_start: 0.9472 (tp) cc_final: 0.9234 (tp)
REVERT: M   64 GLU cc_start: 0.9434 (tt0) cc_final: 0.8994 (tm-30)
REVERT: M   68 ASN cc_start: 0.9562 (m-40) cc_final: 0.8143 (m-40)
REVERT: N   42 LEU cc_start: 0.9478 (tp) cc_final: 0.9234 (tp)
REVERT: N   43 LYS cc_start: 0.9576 (tppp) cc_final: 0.9343 (tppp)
REVERT: N   44 GLN cc_start: 0.9348 (tm-30) cc_final: 0.9013 (tm-30)
REVERT: N   65 ASP cc_start: 0.9255 (t0) cc_final: 0.8869 (t0)
REVERT: N   76 ARG cc_start: 0.9378 (ttm-80) cc_final: 0.8832 (ttm-80)
REVERT: N   80 TYR cc_start: 0.8585 (m-80) cc_final: 0.7724 (m-10)
REVERT: N   96 ARG cc_start: 0.8948 (mtp180) cc_final: 0.8485 (ttm110)
REVERT: N  105 LYS cc_start: 0.9295 (mttt) cc_final: 0.9033 (mtmm)
REVERT: N  110 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8586 (mt-10)
REVERT: L   25 ASN cc_start: 0.7369 (t0) cc_final: 0.6924 (t0)
REVERT: L   39 ARG cc_start: 0.8884 (mmt-90) cc_final: 0.8316 (tpp-160)
REVERT: L   44 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8712 (mtpt)
REVERT: L   54 THR cc_start: 0.9723 (m) cc_final: 0.9383 (m)
REVERT: L   75 HIS cc_start: 0.9036 (t-170) cc_final: 0.8728 (t-170)
REVERT: L   88 TYR cc_start: 0.9020 (m-10) cc_final: 0.8358 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 358
  average time/residue: 0.1253
  time to fit residues: 65.2125
Evaluate side-chains
  311 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 311
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 98 optimal weight:    9.9990
   chunk 36 optimal weight:    4.9990
   chunk 34 optimal weight:    0.5980
   chunk 90 optimal weight:    0.9990
   chunk 76 optimal weight:    6.9990
   chunk 108 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 48 optimal weight:    0.4980
   chunk 17 optimal weight:    0.3980
   overall best weight:    0.6782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 274 HIS
G  68 GLN
G  76 GLN
G 113 HIS
** J  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  39 HIS
K 108 ASN
** L  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.057795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.042909 restraints weight = 77848.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.044406 restraints weight = 36016.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.045398 restraints weight = 22091.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.046059 restraints weight = 16058.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.046408 restraints weight = 13139.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  15271  Z= 0.158
  Angle     :  0.675  14.346  21915  Z= 0.387
  Chirality :  0.046   0.419   2509
  Planarity :  0.004   0.054   1765
  Dihedral  : 30.623 137.061   4372
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.68 %
    Favored  : 97.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.25), residues: 1056
  helix:  1.28 (0.21), residues: 540
  sheet: -1.74 (0.44), residues: 139
  loop : -1.76 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG H  92 
 TYR   0.054   0.003   TYR H  88 
 PHE   0.026   0.002   PHE K  67 
 TRP   0.043   0.003   TRP A  35 
 HIS   0.007   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.16 (15271)
  covalent geometry    : angle       0.67450 /  0.39 (21915)
  hydrogen bonds       : bond        0.06190 /  4.33 (  856)
  hydrogen bonds       : angle       3.93136 /  2.75 ( 2148)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 354
  time to evaluate  : 0.316 
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: symmetry clash
REVERT: A   81 LEU cc_start: 0.8790 (mt) cc_final: 0.8552 (pp)
REVERT: A  134 MET cc_start: 0.7728 (ttp) cc_final: 0.6665 (mpp)
REVERT: A  167 TYR cc_start: 0.7302 (m-80) cc_final: 0.7026 (m-80)
REVERT: A  242 MET cc_start: 0.8016 (ptt) cc_final: 0.7600 (ppp)
REVERT: A  259 PHE cc_start: 0.6787 (m-80) cc_final: 0.5993 (m-80)
REVERT: A  265 TYR cc_start: 0.7637 (m-80) cc_final: 0.7359 (m-10)
REVERT: A  280 GLU cc_start: 0.8574 (tt0) cc_final: 0.8208 (tt0)
REVERT: G   55 GLN cc_start: 0.9452 (mt0) cc_final: 0.9193 (mt0)
REVERT: G   60 LEU cc_start: 0.9344 (mp) cc_final: 0.8808 (mp)
REVERT: G   77 ASP cc_start: 0.9014 (t70) cc_final: 0.8683 (t70)
REVERT: G   93 GLN cc_start: 0.9319 (tt0) cc_final: 0.9106 (tm-30)
REVERT: G  105 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8785 (tm-30)
REVERT: G  122 LYS cc_start: 0.8693 (ptmt) cc_final: 0.8411 (ptmt)
REVERT: G  125 GLN cc_start: 0.9040 (mt0) cc_final: 0.8532 (mt0)
REVERT: H   31 LYS cc_start: 0.8953 (tptp) cc_final: 0.8247 (tptp)
REVERT: H   51 TYR cc_start: 0.8275 (m-80) cc_final: 0.7817 (m-10)
REVERT: I   61 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8923 (mm-30)
REVERT: I   68 ASN cc_start: 0.9394 (m-40) cc_final: 0.9185 (m110)
REVERT: I   73 ASN cc_start: 0.9214 (t0) cc_final: 0.8733 (t0)
REVERT: I   75 LYS cc_start: 0.9534 (mmtm) cc_final: 0.8860 (mmtm)
REVERT: I   87 VAL cc_start: 0.9654 (m) cc_final: 0.9440 (m)
REVERT: I   92 GLU cc_start: 0.8498 (mt-10) cc_final: 0.7959 (mt-10)
REVERT: I   94 ASN cc_start: 0.9098 (t0) cc_final: 0.8623 (t0)
REVERT: I   95 LYS cc_start: 0.9585 (tptt) cc_final: 0.9321 (tppt)
REVERT: I  104 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8615 (mp10)
REVERT: J   32 GLU cc_start: 0.9165 (pp20) cc_final: 0.8938 (pp20)
REVERT: J   44 GLN cc_start: 0.9147 (tm-30) cc_final: 0.8672 (tm-30)
REVERT: J   65 ASP cc_start: 0.8524 (t70) cc_final: 0.8272 (t0)
REVERT: J   68 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8801 (tp30)
REVERT: J   76 ARG cc_start: 0.9193 (ttm110) cc_final: 0.8856 (ttm110)
REVERT: J   81 ASN cc_start: 0.9143 (m-40) cc_final: 0.7919 (p0)
REVERT: J   98 LEU cc_start: 0.9203 (tt) cc_final: 0.8942 (tt)
REVERT: J   99 LEU cc_start: 0.9342 (mt) cc_final: 0.9059 (mp)
REVERT: K   48 LEU cc_start: 0.9699 (mp) cc_final: 0.9278 (mp)
REVERT: K   50 GLU cc_start: 0.8876 (tp30) cc_final: 0.7958 (tp30)
REVERT: K   52 ARG cc_start: 0.9210 (mtt90) cc_final: 0.8836 (mtm-85)
REVERT: K   64 LYS cc_start: 0.9250 (mtmt) cc_final: 0.8598 (pttm)
REVERT: K   85 GLN cc_start: 0.9455 (mm-40) cc_final: 0.9146 (mm110)
REVERT: K   86 SER cc_start: 0.9103 (p) cc_final: 0.7430 (t)
REVERT: K   90 MET cc_start: 0.9116 (mtm) cc_final: 0.8524 (mtt)
REVERT: K  120 MET cc_start: 0.9258 (mmp) cc_final: 0.8658 (mmm)
REVERT: K  125 GLN cc_start: 0.9003 (mp-120) cc_final: 0.8593 (mm-40)
REVERT: M   64 GLU cc_start: 0.9426 (tt0) cc_final: 0.8996 (tm-30)
REVERT: M   68 ASN cc_start: 0.9564 (m-40) cc_final: 0.8146 (m-40)
REVERT: N   44 GLN cc_start: 0.9335 (tm-30) cc_final: 0.9032 (tm-30)
REVERT: N   65 ASP cc_start: 0.9294 (t0) cc_final: 0.8890 (t0)
REVERT: N   80 TYR cc_start: 0.8595 (m-80) cc_final: 0.7939 (m-10)
REVERT: N   96 ARG cc_start: 0.8845 (mtp180) cc_final: 0.8362 (ttm110)
REVERT: N  105 LYS cc_start: 0.9305 (mttt) cc_final: 0.8891 (mtmm)
REVERT: N  110 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8583 (mt-10)
REVERT: L   25 ASN cc_start: 0.8084 (t0) cc_final: 0.7020 (t0)
REVERT: L   29 ILE cc_start: 0.9753 (tp) cc_final: 0.9540 (mm)
REVERT: L   39 ARG cc_start: 0.8961 (mmt-90) cc_final: 0.8549 (tpp-160)
REVERT: L   92 ARG cc_start: 0.8560 (tmm-80) cc_final: 0.7745 (ttp-170)
  outliers start: 1
  outliers final: 0
  residues processed: 354
  average time/residue: 0.1268
  time to fit residues: 65.2501
Evaluate side-chains
  305 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 305
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 11 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 125 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 75 optimal weight:    0.7980
   chunk 112 optimal weight:   10.0000
   chunk 102 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   overall best weight:    3.2786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 GLN
G  76 GLN
G 108 ASN
H  27 GLN
I  89 ASN
** J  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  39 HIS
K 108 ASN
K 125 GLN
** N  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.054625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.039951 restraints weight = 80599.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.041428 restraints weight = 37805.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.042323 restraints weight = 23201.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.042998 restraints weight = 16988.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.043333 restraints weight = 13854.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8645
moved from start:          0.2961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.084  15271  Z= 0.304
  Angle     :  0.785  13.147  21915  Z= 0.439
  Chirality :  0.047   0.281   2509
  Planarity :  0.006   0.078   1765
  Dihedral  : 30.662 137.099   4372
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 19.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  2.13 %
    Favored  : 97.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.62 (0.25), residues: 1056
  helix:  0.93 (0.21), residues: 542
  sheet: -1.90 (0.42), residues: 139
  loop : -1.76 (0.29), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  45 
 TYR   0.060   0.003   TYR H  88 
 PHE   0.034   0.003   PHE A  53 
 TRP   0.041   0.003   TRP A  51 
 HIS   0.015   0.002   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00599 /  0.30 (15271)
  covalent geometry    : angle       0.78464 /  0.44 (21915)
  hydrogen bonds       : bond        0.07890 /  5.35 (  856)
  hydrogen bonds       : angle       4.40608 /  3.10 ( 2148)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 336
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 PHE cc_start: 0.8495 (m-80) cc_final: 0.8096 (m-80)
REVERT: A   81 LEU cc_start: 0.8920 (mt) cc_final: 0.8543 (pp)
REVERT: A  134 MET cc_start: 0.7737 (ttp) cc_final: 0.6455 (mpp)
REVERT: A  167 TYR cc_start: 0.7332 (m-80) cc_final: 0.6923 (m-80)
REVERT: A  251 ARG cc_start: 0.8920 (mmt180) cc_final: 0.8575 (mpt90)
REVERT: A  259 PHE cc_start: 0.6977 (m-80) cc_final: 0.5970 (m-80)
REVERT: A  265 TYR cc_start: 0.7697 (m-80) cc_final: 0.7413 (m-10)
REVERT: A  280 GLU cc_start: 0.8662 (tt0) cc_final: 0.8286 (tt0)
REVERT: G   55 GLN cc_start: 0.9374 (mt0) cc_final: 0.9143 (mt0)
REVERT: G   60 LEU cc_start: 0.9497 (mp) cc_final: 0.8645 (mp)
REVERT: G   77 ASP cc_start: 0.9155 (t70) cc_final: 0.8855 (t70)
REVERT: G   85 GLN cc_start: 0.9099 (mt0) cc_final: 0.8890 (mt0)
REVERT: G   93 GLN cc_start: 0.9462 (tt0) cc_final: 0.9181 (tm-30)
REVERT: G  122 LYS cc_start: 0.8769 (ptmt) cc_final: 0.8545 (ptmt)
REVERT: G  125 GLN cc_start: 0.9098 (mt0) cc_final: 0.8656 (mt0)
REVERT: H   43 VAL cc_start: 0.9413 (t) cc_final: 0.9108 (t)
REVERT: H   51 TYR cc_start: 0.8488 (m-80) cc_final: 0.8287 (m-80)
REVERT: H   74 GLU cc_start: 0.9319 (mt-10) cc_final: 0.8826 (tm-30)
REVERT: I   61 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8941 (mm-30)
REVERT: I   68 ASN cc_start: 0.9436 (m-40) cc_final: 0.9231 (m110)
REVERT: I   73 ASN cc_start: 0.9333 (t0) cc_final: 0.8822 (t0)
REVERT: I   75 LYS cc_start: 0.9588 (mmtm) cc_final: 0.8906 (mmtm)
REVERT: I   87 VAL cc_start: 0.9710 (m) cc_final: 0.9454 (m)
REVERT: I   94 ASN cc_start: 0.9175 (t0) cc_final: 0.8580 (t0)
REVERT: I   95 LYS cc_start: 0.9617 (tptt) cc_final: 0.9356 (tppt)
REVERT: I  104 GLN cc_start: 0.9244 (mm-40) cc_final: 0.8829 (mp10)
REVERT: J   32 GLU cc_start: 0.9239 (pp20) cc_final: 0.8566 (pp20)
REVERT: J   44 GLN cc_start: 0.9220 (tm-30) cc_final: 0.8776 (tm-30)
REVERT: J   65 ASP cc_start: 0.8574 (t70) cc_final: 0.8192 (t0)
REVERT: J   81 ASN cc_start: 0.9192 (m-40) cc_final: 0.8057 (p0)
REVERT: J   87 THR cc_start: 0.9109 (p) cc_final: 0.8588 (p)
REVERT: J   98 LEU cc_start: 0.9125 (tt) cc_final: 0.8745 (tt)
REVERT: K   50 GLU cc_start: 0.8861 (tp30) cc_final: 0.8130 (tp30)
REVERT: K   85 GLN cc_start: 0.9491 (mm-40) cc_final: 0.9175 (mm110)
REVERT: K   90 MET cc_start: 0.9151 (mtm) cc_final: 0.8702 (mtt)
REVERT: K  120 MET cc_start: 0.9275 (mmp) cc_final: 0.8601 (mmm)
REVERT: K  123 ASP cc_start: 0.9119 (m-30) cc_final: 0.8773 (m-30)
REVERT: M   39 TYR cc_start: 0.9168 (m-10) cc_final: 0.8901 (m-80)
REVERT: M   62 ILE cc_start: 0.9672 (mm) cc_final: 0.9426 (tt)
REVERT: M   64 GLU cc_start: 0.9448 (tt0) cc_final: 0.8994 (tm-30)
REVERT: M   68 ASN cc_start: 0.9483 (m-40) cc_final: 0.8115 (m-40)
REVERT: N   65 ASP cc_start: 0.9333 (t0) cc_final: 0.8987 (t0)
REVERT: N   83 ARG cc_start: 0.8849 (mmt90) cc_final: 0.8495 (mmm-85)
REVERT: N   96 ARG cc_start: 0.9030 (mtp180) cc_final: 0.8598 (ttm110)
REVERT: N  102 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8317 (mm-30)
REVERT: N  105 LYS cc_start: 0.9345 (mttt) cc_final: 0.8762 (mtmm)
REVERT: N  110 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8604 (mt-10)
REVERT: L   25 ASN cc_start: 0.7611 (t0) cc_final: 0.6995 (t0)
REVERT: L   39 ARG cc_start: 0.9191 (mmt-90) cc_final: 0.8698 (tpp-160)
REVERT: L   74 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8733 (tm-30)
REVERT: L   79 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8173 (mmtm)
  outliers start: 2
  outliers final: 0
  residues processed: 337
  average time/residue: 0.1277
  time to fit residues: 62.5910
Evaluate side-chains
  294 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 294
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 123 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   chunk 114 optimal weight:   10.0000
   chunk 107 optimal weight:   10.0000
   chunk 66 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 120 optimal weight:   10.0000
   chunk 22 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 129 optimal weight:    3.9990
   overall best weight:    1.6584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 274 HIS
A 291 HIS
G  68 GLN
G  76 GLN
** J  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  39 HIS
K 108 ASN
** N  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  25 ASN
** L  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.055817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.041100 restraints weight = 79189.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.042598 restraints weight = 36670.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.043590 restraints weight = 22409.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.044152 restraints weight = 16257.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.044551 restraints weight = 13415.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.3041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.095  15271  Z= 0.202
  Angle     :  0.701  10.106  21915  Z= 0.403
  Chirality :  0.046   0.315   2509
  Planarity :  0.005   0.065   1765
  Dihedral  : 30.639 137.539   4372
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 15.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.01 %
    Favored  : 98.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.25), residues: 1056
  helix:  1.13 (0.21), residues: 542
  sheet: -1.95 (0.42), residues: 145
  loop : -1.84 (0.29), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K  42 
 TYR   0.077   0.003   TYR H  88 
 PHE   0.025   0.002   PHE A 206 
 TRP   0.018   0.002   TRP A 279 
 HIS   0.009   0.001   HIS H  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00403 /  0.20 (15271)
  covalent geometry    : angle       0.70142 /  0.40 (21915)
  hydrogen bonds       : bond        0.06587 /  4.54 (  856)
  hydrogen bonds       : angle       4.14942 /  2.93 ( 2148)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 349
  time to evaluate  : 0.407 
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: A   51 TRP cc_start: 0.8101 (t60) cc_final: 0.7753 (t60)
REVERT: A   81 LEU cc_start: 0.8895 (mt) cc_final: 0.8536 (pp)
REVERT: A  134 MET cc_start: 0.7712 (ttp) cc_final: 0.6477 (mpp)
REVERT: A  167 TYR cc_start: 0.7255 (m-80) cc_final: 0.6838 (m-80)
REVERT: A  259 PHE cc_start: 0.6969 (m-80) cc_final: 0.6481 (m-80)
REVERT: A  265 TYR cc_start: 0.7646 (m-80) cc_final: 0.7346 (m-10)
REVERT: A  280 GLU cc_start: 0.8657 (tt0) cc_final: 0.8284 (tt0)
REVERT: G   55 GLN cc_start: 0.9356 (mt0) cc_final: 0.9080 (mt0)
REVERT: G   77 ASP cc_start: 0.9098 (t70) cc_final: 0.8833 (t70)
REVERT: G   93 GLN cc_start: 0.9423 (tt0) cc_final: 0.9138 (tm-30)
REVERT: G  122 LYS cc_start: 0.8869 (ptmt) cc_final: 0.8433 (ptmt)
REVERT: G  125 GLN cc_start: 0.9102 (mt0) cc_final: 0.8637 (mp10)
REVERT: H   31 LYS cc_start: 0.9023 (tptp) cc_final: 0.8650 (tptp)
REVERT: H   74 GLU cc_start: 0.9315 (mt-10) cc_final: 0.8796 (tm-30)
REVERT: H   75 HIS cc_start: 0.8823 (t-90) cc_final: 0.8561 (t-90)
REVERT: H   85 ASP cc_start: 0.9181 (m-30) cc_final: 0.8969 (m-30)
REVERT: I   61 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8922 (mm-30)
REVERT: I   68 ASN cc_start: 0.9422 (m-40) cc_final: 0.9207 (m110)
REVERT: I   73 ASN cc_start: 0.9272 (t0) cc_final: 0.8987 (t0)
REVERT: I   75 LYS cc_start: 0.9572 (mmtm) cc_final: 0.8980 (mmtp)
REVERT: I   87 VAL cc_start: 0.9685 (m) cc_final: 0.9427 (m)
REVERT: I   94 ASN cc_start: 0.9098 (t0) cc_final: 0.8520 (m-40)
REVERT: I   95 LYS cc_start: 0.9578 (tptt) cc_final: 0.9307 (tppt)
REVERT: I  104 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8776 (mp10)
REVERT: J   32 GLU cc_start: 0.9223 (pp20) cc_final: 0.8976 (pp20)
REVERT: J   44 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8699 (tm-30)
REVERT: J   65 ASP cc_start: 0.8540 (t70) cc_final: 0.8061 (t70)
REVERT: J   73 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8879 (mm-30)
REVERT: J   76 ARG cc_start: 0.9346 (ttm110) cc_final: 0.8853 (ttm110)
REVERT: J   81 ASN cc_start: 0.9073 (m-40) cc_final: 0.7884 (p0)
REVERT: J   98 LEU cc_start: 0.9199 (tt) cc_final: 0.8811 (tt)
REVERT: K   50 GLU cc_start: 0.8896 (tp30) cc_final: 0.8375 (tp30)
REVERT: K   52 ARG cc_start: 0.9251 (mtt90) cc_final: 0.8909 (mtm-85)
REVERT: K   64 LYS cc_start: 0.9195 (mtmt) cc_final: 0.8765 (pttt)
REVERT: K   70 LEU cc_start: 0.9801 (tt) cc_final: 0.9510 (tt)
REVERT: K   85 GLN cc_start: 0.9450 (mm-40) cc_final: 0.9157 (mm110)
REVERT: K   90 MET cc_start: 0.9063 (mtm) cc_final: 0.8671 (mtt)
REVERT: K  120 MET cc_start: 0.9238 (mmp) cc_final: 0.8576 (mmm)
REVERT: K  123 ASP cc_start: 0.9150 (m-30) cc_final: 0.8822 (m-30)
REVERT: M   39 TYR cc_start: 0.9131 (m-10) cc_final: 0.8861 (m-80)
REVERT: M   62 ILE cc_start: 0.9685 (mm) cc_final: 0.9384 (tt)
REVERT: M   64 GLU cc_start: 0.9423 (tt0) cc_final: 0.8972 (tm-30)
REVERT: M   68 ASN cc_start: 0.9487 (m-40) cc_final: 0.8154 (m-40)
REVERT: N   44 GLN cc_start: 0.9362 (tm-30) cc_final: 0.8976 (tm-30)
REVERT: N   65 ASP cc_start: 0.9291 (t0) cc_final: 0.8857 (t0)
REVERT: N   80 TYR cc_start: 0.8325 (m-80) cc_final: 0.7845 (m-10)
REVERT: N   83 ARG cc_start: 0.8808 (mmt90) cc_final: 0.8422 (mmm-85)
REVERT: N   96 ARG cc_start: 0.8918 (mtp180) cc_final: 0.8504 (ttm110)
REVERT: N  105 LYS cc_start: 0.9335 (mttt) cc_final: 0.8999 (mtpt)
REVERT: N  110 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8349 (tp30)
REVERT: N  113 LYS cc_start: 0.9493 (tmmt) cc_final: 0.9117 (ttpp)
REVERT: L   25 ASN cc_start: 0.7590 (t0) cc_final: 0.7072 (t0)
REVERT: L   39 ARG cc_start: 0.9092 (mmt-90) cc_final: 0.8767 (tpp-160)
REVERT: L   63 GLU cc_start: 0.8822 (tp30) cc_final: 0.8529 (tp30)
REVERT: L   68 ASP cc_start: 0.9211 (m-30) cc_final: 0.8910 (m-30)
REVERT: L   79 LYS cc_start: 0.8582 (mmtt) cc_final: 0.8225 (mmtm)
REVERT: L   92 ARG cc_start: 0.8591 (tmm-80) cc_final: 0.7853 (ttp-170)
  outliers start: 1
  outliers final: 0
  residues processed: 350
  average time/residue: 0.1291
  time to fit residues: 65.1323
Evaluate side-chains
  295 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 295
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 64 optimal weight:    0.0870
   chunk 109 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 8 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 87 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.7360

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 274 HIS
G  68 GLN
G  76 GLN
** J  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 108 ASN
** N  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.057045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.042108 restraints weight = 78023.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.043616 restraints weight = 36224.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.044522 restraints weight = 22197.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.045206 restraints weight = 16392.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.045557 restraints weight = 13453.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  15271  Z= 0.159
  Angle     :  0.681   8.306  21915  Z= 0.392
  Chirality :  0.046   0.326   2509
  Planarity :  0.005   0.055   1765
  Dihedral  : 30.590 136.906   4372
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.23 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.41 (0.25), residues: 1056
  helix:  1.21 (0.21), residues: 540
  sheet: -1.83 (0.41), residues: 156
  loop : -1.81 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  67 
 TYR   0.085   0.003   TYR H  88 
 PHE   0.036   0.002   PHE K  67 
 TRP   0.022   0.002   TRP A 279 
 HIS   0.007   0.001   HIS H  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.16 (15271)
  covalent geometry    : angle       0.68061 /  0.39 (21915)
  hydrogen bonds       : bond        0.06143 /  4.30 (  856)
  hydrogen bonds       : angle       4.00152 /  2.82 ( 2148)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  357 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 356
  time to evaluate  : 0.341 
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: A   51 TRP cc_start: 0.8030 (t60) cc_final: 0.7739 (t60)
REVERT: A   81 LEU cc_start: 0.8850 (mt) cc_final: 0.8564 (pp)
REVERT: A  134 MET cc_start: 0.7705 (ttp) cc_final: 0.6573 (mpp)
REVERT: A  167 TYR cc_start: 0.7242 (m-80) cc_final: 0.6859 (m-80)
REVERT: A  242 MET cc_start: 0.8100 (ptt) cc_final: 0.7762 (ppp)
REVERT: A  259 PHE cc_start: 0.6688 (m-80) cc_final: 0.6178 (m-80)
REVERT: A  265 TYR cc_start: 0.7557 (m-80) cc_final: 0.7275 (m-80)
REVERT: A  280 GLU cc_start: 0.8640 (tt0) cc_final: 0.8147 (tt0)
REVERT: G   55 GLN cc_start: 0.9359 (mt0) cc_final: 0.9128 (mt0)
REVERT: G   63 ARG cc_start: 0.8279 (mmt-90) cc_final: 0.7871 (mmm-85)
REVERT: G   67 PHE cc_start: 0.9713 (t80) cc_final: 0.9462 (t80)
REVERT: G   77 ASP cc_start: 0.9113 (t70) cc_final: 0.8834 (t70)
REVERT: G  105 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8694 (tm-30)
REVERT: G  122 LYS cc_start: 0.8777 (ptmt) cc_final: 0.8314 (ptmt)
REVERT: G  125 GLN cc_start: 0.9119 (mt0) cc_final: 0.8650 (mp10)
REVERT: H   31 LYS cc_start: 0.9087 (tptp) cc_final: 0.8621 (tptp)
REVERT: H   43 VAL cc_start: 0.9468 (t) cc_final: 0.9090 (p)
REVERT: H   51 TYR cc_start: 0.8538 (m-10) cc_final: 0.8078 (m-10)
REVERT: H   74 GLU cc_start: 0.9328 (mt-10) cc_final: 0.8767 (tm-30)
REVERT: H   75 HIS cc_start: 0.8782 (t-90) cc_final: 0.8446 (t-90)
REVERT: I   61 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8934 (mm-30)
REVERT: I   68 ASN cc_start: 0.9427 (m-40) cc_final: 0.9225 (m110)
REVERT: I   73 ASN cc_start: 0.9246 (t0) cc_final: 0.8957 (t0)
REVERT: I   75 LYS cc_start: 0.9582 (mmtm) cc_final: 0.9022 (mmtp)
REVERT: I   87 VAL cc_start: 0.9676 (m) cc_final: 0.9402 (m)
REVERT: I   94 ASN cc_start: 0.9064 (t0) cc_final: 0.8493 (t0)
REVERT: I   95 LYS cc_start: 0.9561 (tptt) cc_final: 0.9281 (tppt)
REVERT: I  104 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8690 (mp10)
REVERT: J   32 GLU cc_start: 0.9190 (pp20) cc_final: 0.8943 (pp20)
REVERT: J   39 TYR cc_start: 0.8741 (t80) cc_final: 0.8532 (t80)
REVERT: J   44 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8681 (tm-30)
REVERT: J   65 ASP cc_start: 0.8525 (t70) cc_final: 0.7787 (t70)
REVERT: J   73 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8888 (mm-30)
REVERT: J   76 ARG cc_start: 0.9288 (ttm110) cc_final: 0.8927 (ttm110)
REVERT: J   81 ASN cc_start: 0.8996 (m-40) cc_final: 0.7800 (p0)
REVERT: J   98 LEU cc_start: 0.9172 (tt) cc_final: 0.8793 (tt)
REVERT: J  103 LEU cc_start: 0.9292 (mm) cc_final: 0.9030 (mm)
REVERT: K   50 GLU cc_start: 0.8895 (tp30) cc_final: 0.8293 (tp30)
REVERT: K   52 ARG cc_start: 0.9226 (mtt90) cc_final: 0.8760 (mtm-85)
REVERT: K   64 LYS cc_start: 0.9176 (mtmt) cc_final: 0.8729 (pttt)
REVERT: K   73 GLU cc_start: 0.8169 (pt0) cc_final: 0.7003 (mt-10)
REVERT: K   84 PHE cc_start: 0.8839 (m-80) cc_final: 0.8626 (m-10)
REVERT: K   85 GLN cc_start: 0.9437 (mm-40) cc_final: 0.9176 (mm110)
REVERT: K  105 GLU cc_start: 0.9492 (mm-30) cc_final: 0.9247 (mm-30)
REVERT: K  120 MET cc_start: 0.9258 (mmp) cc_final: 0.8613 (mmm)
REVERT: K  123 ASP cc_start: 0.9132 (m-30) cc_final: 0.8798 (m-30)
REVERT: M   39 TYR cc_start: 0.9071 (m-10) cc_final: 0.8856 (m-80)
REVERT: M   56 GLU cc_start: 0.9414 (tt0) cc_final: 0.9135 (mt-10)
REVERT: M   62 ILE cc_start: 0.9680 (mm) cc_final: 0.9346 (tt)
REVERT: M   64 GLU cc_start: 0.9425 (tt0) cc_final: 0.8939 (tm-30)
REVERT: M   68 ASN cc_start: 0.9509 (m-40) cc_final: 0.8268 (m-40)
REVERT: N   44 GLN cc_start: 0.9379 (tm-30) cc_final: 0.8983 (tm-30)
REVERT: N   65 ASP cc_start: 0.9276 (t0) cc_final: 0.8863 (t0)
REVERT: N   80 TYR cc_start: 0.8315 (m-80) cc_final: 0.7801 (m-10)
REVERT: N   83 ARG cc_start: 0.8759 (mmt90) cc_final: 0.8471 (mtp85)
REVERT: N   85 THR cc_start: 0.8501 (p) cc_final: 0.7668 (p)
REVERT: N   96 ARG cc_start: 0.8914 (mtp180) cc_final: 0.8668 (ttm110)
REVERT: N  102 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8385 (mm-30)
REVERT: N  105 LYS cc_start: 0.9317 (mttt) cc_final: 0.8639 (mtmm)
REVERT: N  110 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8333 (tp30)
REVERT: N  113 LYS cc_start: 0.9504 (tmmt) cc_final: 0.9214 (ttpp)
REVERT: L   25 ASN cc_start: 0.8014 (t0) cc_final: 0.7526 (p0)
REVERT: L   39 ARG cc_start: 0.9044 (mmt-90) cc_final: 0.8732 (tpp-160)
REVERT: L   44 LYS cc_start: 0.9037 (mttt) cc_final: 0.8630 (mttp)
REVERT: L   63 GLU cc_start: 0.8894 (tp30) cc_final: 0.8599 (tp30)
REVERT: L   68 ASP cc_start: 0.9185 (m-30) cc_final: 0.8932 (m-30)
REVERT: L   77 LYS cc_start: 0.9451 (mmtp) cc_final: 0.9230 (mmtm)
REVERT: L   79 LYS cc_start: 0.8570 (mmtt) cc_final: 0.8061 (mmtm)
REVERT: L   91 LYS cc_start: 0.9433 (tttt) cc_final: 0.9144 (tttt)
REVERT: L   92 ARG cc_start: 0.8688 (tmm-80) cc_final: 0.7908 (ttp-170)
  outliers start: 1
  outliers final: 0
  residues processed: 357
  average time/residue: 0.1243
  time to fit residues: 64.0209
Evaluate side-chains
  303 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 303
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 127 optimal weight:    0.8980
   chunk 27 optimal weight:    6.9990
   chunk 41 optimal weight:    0.5980
   chunk 88 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 17 optimal weight:   10.0000
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 274 HIS
G  68 GLN
** J  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.057362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.042426 restraints weight = 78400.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.043944 restraints weight = 36274.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.044925 restraints weight = 22157.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.045560 restraints weight = 16154.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.045894 restraints weight = 13277.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.3252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  15271  Z= 0.160
  Angle     :  0.678   7.594  21915  Z= 0.391
  Chirality :  0.045   0.321   2509
  Planarity :  0.005   0.056   1765
  Dihedral  : 30.541 137.997   4372
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.25), residues: 1056
  helix:  1.11 (0.21), residues: 546
  sheet: -1.87 (0.43), residues: 153
  loop : -1.63 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  67 
 TYR   0.027   0.002   TYR H  88 
 PHE   0.040   0.002   PHE K  67 
 TRP   0.045   0.004   TRP A  35 
 HIS   0.010   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.16 (15271)
  covalent geometry    : angle       0.67827 /  0.39 (21915)
  hydrogen bonds       : bond        0.06118 /  4.28 (  856)
  hydrogen bonds       : angle       3.96595 /  2.80 ( 2148)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 350
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TRP cc_start: 0.7861 (t60) cc_final: 0.7660 (t60)
REVERT: A   81 LEU cc_start: 0.8786 (mt) cc_final: 0.8557 (pp)
REVERT: A  134 MET cc_start: 0.7662 (ttp) cc_final: 0.6617 (mpp)
REVERT: A  167 TYR cc_start: 0.7299 (m-80) cc_final: 0.6875 (m-80)
REVERT: A  206 PHE cc_start: 0.5741 (m-80) cc_final: 0.5489 (m-80)
REVERT: A  242 MET cc_start: 0.8125 (ptt) cc_final: 0.7853 (ppp)
REVERT: A  259 PHE cc_start: 0.6722 (m-80) cc_final: 0.5891 (m-80)
REVERT: A  265 TYR cc_start: 0.7578 (m-80) cc_final: 0.7265 (m-80)
REVERT: A  280 GLU cc_start: 0.8623 (tt0) cc_final: 0.8005 (tt0)
REVERT: G   55 GLN cc_start: 0.9340 (mt0) cc_final: 0.9131 (mt0)
REVERT: G   67 PHE cc_start: 0.9724 (t80) cc_final: 0.9457 (t80)
REVERT: G   73 GLU cc_start: 0.9259 (tt0) cc_final: 0.8849 (tt0)
REVERT: G   77 ASP cc_start: 0.9110 (t70) cc_final: 0.8909 (t70)
REVERT: G  105 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8690 (tm-30)
REVERT: G  109 LEU cc_start: 0.9617 (mm) cc_final: 0.9308 (mp)
REVERT: G  122 LYS cc_start: 0.8819 (ptmt) cc_final: 0.8411 (ptmt)
REVERT: G  125 GLN cc_start: 0.9108 (mt0) cc_final: 0.8631 (mp10)
REVERT: H   31 LYS cc_start: 0.9067 (tptp) cc_final: 0.8601 (tptp)
REVERT: H   51 TYR cc_start: 0.8402 (m-10) cc_final: 0.7960 (m-10)
REVERT: H   74 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8771 (tm-30)
REVERT: H   75 HIS cc_start: 0.8809 (t-90) cc_final: 0.8416 (t-90)
REVERT: I   61 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8940 (mm-30)
REVERT: I   73 ASN cc_start: 0.9231 (t0) cc_final: 0.8966 (t0)
REVERT: I   75 LYS cc_start: 0.9588 (mmtm) cc_final: 0.9021 (mmtp)
REVERT: I   87 VAL cc_start: 0.9652 (m) cc_final: 0.9395 (m)
REVERT: I   90 ASP cc_start: 0.9098 (t0) cc_final: 0.8845 (t0)
REVERT: I   94 ASN cc_start: 0.9047 (t0) cc_final: 0.8567 (t0)
REVERT: I   95 LYS cc_start: 0.9567 (tptt) cc_final: 0.9290 (tppt)
REVERT: I  104 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8651 (mp10)
REVERT: J   32 GLU cc_start: 0.9223 (pp20) cc_final: 0.8964 (pp20)
REVERT: J   39 TYR cc_start: 0.8739 (t80) cc_final: 0.8495 (t80)
REVERT: J   44 GLN cc_start: 0.9192 (tm-30) cc_final: 0.8721 (tm-30)
REVERT: J   65 ASP cc_start: 0.8560 (t70) cc_final: 0.7819 (t70)
REVERT: J   73 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8801 (mm-30)
REVERT: J   76 ARG cc_start: 0.9160 (ttm110) cc_final: 0.8809 (ttm110)
REVERT: J   81 ASN cc_start: 0.8970 (m-40) cc_final: 0.7829 (p0)
REVERT: J   98 LEU cc_start: 0.9101 (tt) cc_final: 0.8702 (tt)
REVERT: K   50 GLU cc_start: 0.8890 (tp30) cc_final: 0.8283 (tp30)
REVERT: K   52 ARG cc_start: 0.9235 (mtt90) cc_final: 0.8776 (mtm-85)
REVERT: K   64 LYS cc_start: 0.9173 (mtmt) cc_final: 0.8706 (pttm)
REVERT: K   85 GLN cc_start: 0.9436 (mm-40) cc_final: 0.9181 (mm110)
REVERT: K   90 MET cc_start: 0.9046 (mtm) cc_final: 0.8443 (mtt)
REVERT: K   93 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8540 (tm-30)
REVERT: K   99 TYR cc_start: 0.9598 (t80) cc_final: 0.9285 (t80)
REVERT: K  105 GLU cc_start: 0.9547 (mm-30) cc_final: 0.9279 (mm-30)
REVERT: K  120 MET cc_start: 0.9290 (mmp) cc_final: 0.8697 (mmm)
REVERT: K  123 ASP cc_start: 0.9134 (m-30) cc_final: 0.8834 (m-30)
REVERT: M   39 TYR cc_start: 0.9059 (m-10) cc_final: 0.8851 (m-80)
REVERT: M   56 GLU cc_start: 0.9432 (tt0) cc_final: 0.9154 (mt-10)
REVERT: M   62 ILE cc_start: 0.9702 (mm) cc_final: 0.9296 (tt)
REVERT: M   64 GLU cc_start: 0.9435 (tt0) cc_final: 0.8947 (tm-30)
REVERT: M   68 ASN cc_start: 0.9519 (m-40) cc_final: 0.8292 (m-40)
REVERT: M   99 ARG cc_start: 0.7799 (tpt170) cc_final: 0.7482 (tpt170)
REVERT: N   44 GLN cc_start: 0.9386 (tm-30) cc_final: 0.8956 (tm-30)
REVERT: N   65 ASP cc_start: 0.9284 (t0) cc_final: 0.8882 (t0)
REVERT: N   80 TYR cc_start: 0.8252 (m-80) cc_final: 0.7829 (m-10)
REVERT: N   83 ARG cc_start: 0.8633 (mmt90) cc_final: 0.8266 (mmm-85)
REVERT: N   96 ARG cc_start: 0.8906 (mtp180) cc_final: 0.8678 (ttm110)
REVERT: N  102 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8583 (mm-30)
REVERT: N  105 LYS cc_start: 0.9309 (mttt) cc_final: 0.8860 (mtpt)
REVERT: N  110 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8335 (tp30)
REVERT: N  113 LYS cc_start: 0.9515 (tmmt) cc_final: 0.9225 (ttpp)
REVERT: L   25 ASN cc_start: 0.8069 (t0) cc_final: 0.6985 (t0)
REVERT: L   39 ARG cc_start: 0.8989 (mmt-90) cc_final: 0.8724 (tpp-160)
REVERT: L   44 LYS cc_start: 0.9024 (mttt) cc_final: 0.8710 (mttp)
REVERT: L   63 GLU cc_start: 0.8884 (tp30) cc_final: 0.8571 (tp30)
REVERT: L   68 ASP cc_start: 0.9154 (m-30) cc_final: 0.8885 (m-30)
REVERT: L   77 LYS cc_start: 0.9446 (mmtp) cc_final: 0.9236 (mmtp)
REVERT: L   79 LYS cc_start: 0.8524 (mmtt) cc_final: 0.7974 (mmtm)
REVERT: L   91 LYS cc_start: 0.9451 (tttt) cc_final: 0.9156 (tttt)
REVERT: L   92 ARG cc_start: 0.8667 (tmm-80) cc_final: 0.7868 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 350
  average time/residue: 0.1219
  time to fit residues: 61.8907
Evaluate side-chains
  303 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 303
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 29 optimal weight:   20.0000
   chunk 82 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 100 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 120 optimal weight:    9.9990
   chunk 69 optimal weight:    2.9990
   chunk 127 optimal weight:    0.9990
   chunk 103 optimal weight:   10.0000
   overall best weight:    1.5986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 274 HIS
G  68 GLN
G  76 GLN
G 108 ASN
** J  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  39 HIS
K 108 ASN
** L  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.056768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.041965 restraints weight = 78053.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.043442 restraints weight = 36188.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.044349 restraints weight = 22160.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.044989 restraints weight = 16315.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.045348 restraints weight = 13347.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.3315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  15271  Z= 0.192
  Angle     :  0.699   9.722  21915  Z= 0.401
  Chirality :  0.046   0.309   2509
  Planarity :  0.005   0.057   1765
  Dihedral  : 30.517 137.762   4372
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 16.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.11 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.25), residues: 1056
  helix:  1.14 (0.21), residues: 540
  sheet: -1.86 (0.41), residues: 161
  loop : -1.71 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  67 
 TYR   0.050   0.002   TYR H  88 
 PHE   0.022   0.002   PHE A 206 
 TRP   0.030   0.002   TRP A  35 
 HIS   0.007   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00378 /  0.19 (15271)
  covalent geometry    : angle       0.69898 /  0.40 (21915)
  hydrogen bonds       : bond        0.06363 /  4.43 (  856)
  hydrogen bonds       : angle       4.03825 /  2.86 ( 2148)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 343
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TRP cc_start: 0.7897 (t60) cc_final: 0.7681 (t60)
REVERT: A   81 LEU cc_start: 0.8826 (mt) cc_final: 0.8568 (pp)
REVERT: A  134 MET cc_start: 0.7620 (ttp) cc_final: 0.6563 (mpp)
REVERT: A  167 TYR cc_start: 0.7323 (m-80) cc_final: 0.6849 (m-80)
REVERT: A  206 PHE cc_start: 0.5722 (m-80) cc_final: 0.5223 (m-80)
REVERT: A  242 MET cc_start: 0.7981 (ptt) cc_final: 0.7755 (ppp)
REVERT: A  259 PHE cc_start: 0.6857 (m-80) cc_final: 0.6133 (m-80)
REVERT: A  265 TYR cc_start: 0.7450 (m-80) cc_final: 0.7130 (m-80)
REVERT: A  280 GLU cc_start: 0.8653 (tt0) cc_final: 0.8100 (tt0)
REVERT: G   55 GLN cc_start: 0.9359 (mt0) cc_final: 0.9137 (mt0)
REVERT: G   60 LEU cc_start: 0.9232 (mp) cc_final: 0.8904 (tp)
REVERT: G   63 ARG cc_start: 0.8228 (mmt-90) cc_final: 0.7678 (mmp80)
REVERT: G   73 GLU cc_start: 0.9159 (tt0) cc_final: 0.8728 (tt0)
REVERT: G   77 ASP cc_start: 0.9151 (t70) cc_final: 0.8913 (t70)
REVERT: G   90 MET cc_start: 0.9079 (mmm) cc_final: 0.7933 (mmp)
REVERT: G   97 GLU cc_start: 0.9137 (tt0) cc_final: 0.8681 (tt0)
REVERT: G   99 TYR cc_start: 0.9390 (t80) cc_final: 0.9077 (t80)
REVERT: G  122 LYS cc_start: 0.8826 (ptmt) cc_final: 0.8408 (ptmt)
REVERT: G  125 GLN cc_start: 0.9095 (mt0) cc_final: 0.8632 (mp10)
REVERT: H   31 LYS cc_start: 0.9092 (tptp) cc_final: 0.8604 (tptp)
REVERT: H   51 TYR cc_start: 0.8421 (m-10) cc_final: 0.7969 (m-10)
REVERT: H   74 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8784 (tm-30)
REVERT: H   75 HIS cc_start: 0.8885 (t-90) cc_final: 0.8492 (t-90)
REVERT: H   81 VAL cc_start: 0.9345 (t) cc_final: 0.8917 (t)
REVERT: I   61 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8923 (mm-30)
REVERT: I   75 LYS cc_start: 0.9606 (mmtm) cc_final: 0.9155 (mmtp)
REVERT: I   87 VAL cc_start: 0.9646 (m) cc_final: 0.9399 (m)
REVERT: I   94 ASN cc_start: 0.9079 (t0) cc_final: 0.8579 (t0)
REVERT: I   95 LYS cc_start: 0.9575 (tptt) cc_final: 0.9276 (tppt)
REVERT: I  104 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8696 (mp10)
REVERT: J   32 GLU cc_start: 0.9229 (pp20) cc_final: 0.8974 (pp20)
REVERT: J   39 TYR cc_start: 0.8768 (t80) cc_final: 0.8518 (t80)
REVERT: J   44 GLN cc_start: 0.9144 (tm-30) cc_final: 0.8703 (tm-30)
REVERT: J   65 ASP cc_start: 0.8585 (t70) cc_final: 0.7866 (t70)
REVERT: J   81 ASN cc_start: 0.8987 (m-40) cc_final: 0.7845 (p0)
REVERT: J   98 LEU cc_start: 0.9143 (tt) cc_final: 0.8742 (tt)
REVERT: K   48 LEU cc_start: 0.9662 (mp) cc_final: 0.9447 (mp)
REVERT: K   50 GLU cc_start: 0.8877 (tp30) cc_final: 0.8316 (tp30)
REVERT: K   52 ARG cc_start: 0.9219 (mtt90) cc_final: 0.8906 (mtm-85)
REVERT: K   73 GLU cc_start: 0.8201 (pt0) cc_final: 0.7230 (mt-10)
REVERT: K   84 PHE cc_start: 0.8910 (m-80) cc_final: 0.8704 (m-10)
REVERT: K   85 GLN cc_start: 0.9419 (mm-40) cc_final: 0.9185 (mm110)
REVERT: K   90 MET cc_start: 0.9039 (mtm) cc_final: 0.8460 (mtt)
REVERT: K   99 TYR cc_start: 0.9580 (t80) cc_final: 0.9287 (t80)
REVERT: K  105 GLU cc_start: 0.9548 (mm-30) cc_final: 0.9308 (mm-30)
REVERT: K  120 MET cc_start: 0.9298 (mmp) cc_final: 0.8690 (mmm)
REVERT: K  123 ASP cc_start: 0.9167 (m-30) cc_final: 0.8887 (m-30)
REVERT: M   39 TYR cc_start: 0.9073 (m-10) cc_final: 0.8855 (m-80)
REVERT: M   56 GLU cc_start: 0.9427 (tt0) cc_final: 0.9171 (mt-10)
REVERT: M   64 GLU cc_start: 0.9415 (tt0) cc_final: 0.8961 (tm-30)
REVERT: M   68 ASN cc_start: 0.9514 (m-40) cc_final: 0.8278 (m-40)
REVERT: M   99 ARG cc_start: 0.7771 (tpt170) cc_final: 0.7498 (tpt170)
REVERT: N   44 GLN cc_start: 0.9407 (tm-30) cc_final: 0.9067 (tm-30)
REVERT: N   65 ASP cc_start: 0.9278 (t0) cc_final: 0.8872 (t0)
REVERT: N   80 TYR cc_start: 0.8274 (m-80) cc_final: 0.7795 (m-10)
REVERT: N   83 ARG cc_start: 0.8695 (mmt90) cc_final: 0.8368 (mmm-85)
REVERT: N   96 ARG cc_start: 0.8933 (mtp180) cc_final: 0.8688 (ttm110)
REVERT: N  110 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8346 (tp30)
REVERT: N  113 LYS cc_start: 0.9517 (tmmt) cc_final: 0.9232 (ttpp)
REVERT: L   39 ARG cc_start: 0.9039 (mmt-90) cc_final: 0.8807 (tpp-160)
REVERT: L   44 LYS cc_start: 0.9046 (mttt) cc_final: 0.8711 (mttp)
REVERT: L   53 GLU cc_start: 0.8492 (pp20) cc_final: 0.8188 (tm-30)
REVERT: L   63 GLU cc_start: 0.8866 (tp30) cc_final: 0.8553 (tp30)
REVERT: L   68 ASP cc_start: 0.9145 (m-30) cc_final: 0.8905 (m-30)
REVERT: L   77 LYS cc_start: 0.9453 (mmtp) cc_final: 0.9221 (mmtm)
REVERT: L   79 LYS cc_start: 0.8531 (mmtt) cc_final: 0.7969 (mmtm)
REVERT: L   91 LYS cc_start: 0.9479 (tttt) cc_final: 0.9137 (tttt)
REVERT: L   92 ARG cc_start: 0.8689 (tmm-80) cc_final: 0.7967 (ttp-170)
  outliers start: 2
  outliers final: 0
  residues processed: 343
  average time/residue: 0.1241
  time to fit residues: 61.9726
Evaluate side-chains
  297 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 297
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 71 optimal weight:    0.0980
   chunk 89 optimal weight:    0.8980
   chunk 10 optimal weight:    8.9990
   chunk 95 optimal weight:   20.0000
   chunk 87 optimal weight:    0.6980
   chunk 106 optimal weight:   10.0000
   chunk 99 optimal weight:    9.9990
   chunk 62 optimal weight:    0.8980
   chunk 116 optimal weight:   10.0000
   chunk 29 optimal weight:   20.0000
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 274 HIS
G  68 GLN
** J  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 108 ASN
N 106 HIS
** L  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.057849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.042871 restraints weight = 77859.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.044391 restraints weight = 36179.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.045401 restraints weight = 22221.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.046013 restraints weight = 16128.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.046396 restraints weight = 13202.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.3412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  15271  Z= 0.155
  Angle     :  0.672   8.481  21915  Z= 0.389
  Chirality :  0.045   0.324   2509
  Planarity :  0.005   0.055   1765
  Dihedral  : 30.476 136.946   4372
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.11 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.25), residues: 1056
  helix:  1.18 (0.21), residues: 546
  sheet: -1.72 (0.44), residues: 149
  loop : -1.65 (0.30), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG K 129 
 TYR   0.049   0.003   TYR H  88 
 PHE   0.046   0.002   PHE K  67 
 TRP   0.025   0.002   TRP A  35 
 HIS   0.009   0.001   HIS N 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.16 (15271)
  covalent geometry    : angle       0.67205 /  0.39 (21915)
  hydrogen bonds       : bond        0.06067 /  4.26 (  856)
  hydrogen bonds       : angle       3.95301 /  2.80 ( 2148)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2624.99 seconds
wall clock time: 46 minutes 4.59 seconds (2764.59 seconds total)