Starting phenix.real_space_refine
on Fri Jun 20 15:55:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pwx_20514/06_2025/6pwx_20514.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pwx_20514/06_2025/6pwx_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_20514/06_2025/6pwx_20514.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pwx_20514/06_2025/6pwx_20514.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pwx_20514/06_2025/6pwx_20514.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pwx_20514/06_2025/6pwx_20514.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.44, per 1000 atoms: 0.59
  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: 3.88
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 6.28
  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: 5.52

  Time building geometry restraints manager: 4.52 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=" CB  GLU L  52 "
       pdb=" CG  GLU L  52 "
    ideal  model  delta    sigma   weight residual
    1.520  1.568 -0.048 3.00e-02 1.11e+03 2.60e+00
  bond pdb=" CB  GLU H  52 "
       pdb=" CG  GLU H  52 "
    ideal  model  delta    sigma   weight residual
    1.520  1.568 -0.048 3.00e-02 1.11e+03 2.56e+00
  bond pdb=" C3'  DC P 126 "
       pdb=" O3'  DC P 126 "
    ideal  model  delta    sigma   weight residual
    1.422  1.466 -0.044 3.00e-02 1.11e+03 2.12e+00
  bond pdb=" CG  GLU H  52 "
       pdb=" CD  GLU H  52 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 2.50e-02 1.60e+03 1.43e+00
  bond pdb=" CG  ASP K 106 "
       pdb=" OD1 ASP K 106 "
    ideal  model  delta    sigma   weight residual
    1.249  1.226  0.023 1.90e-02 2.77e+03 1.41e+00
  ... (remaining 15266 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 21339
        1.65 -     3.29: 541
        3.29 -     4.94: 24
        4.94 -     6.58: 7
        6.58 -     8.23: 4
  Bond angle restraints: 21915
  Sorted by residual:
  angle pdb=" CA  GLU L  52 "
        pdb=" CB  GLU L  52 "
        pdb=" CG  GLU L  52 "
      ideal   model   delta    sigma   weight residual
     114.10  122.33   -8.23 2.00e+00 2.50e-01 1.69e+01
  angle pdb=" CA  GLU H  52 "
        pdb=" CB  GLU H  52 "
        pdb=" CG  GLU H  52 "
      ideal   model   delta    sigma   weight residual
     114.10  122.29   -8.19 2.00e+00 2.50e-01 1.68e+01
  angle pdb=" CB  GLU H  52 "
        pdb=" CG  GLU H  52 "
        pdb=" CD  GLU H  52 "
      ideal   model   delta    sigma   weight residual
     112.60  118.82   -6.22 1.70e+00 3.46e-01 1.34e+01
  angle pdb=" CB  GLU L  52 "
        pdb=" CG  GLU L  52 "
        pdb=" CD  GLU L  52 "
      ideal   model   delta    sigma   weight residual
     112.60  118.76   -6.16 1.70e+00 3.46e-01 1.32e+01
  angle pdb=" N   ASP G 106 "
        pdb=" CA  ASP G 106 "
        pdb=" CB  ASP G 106 "
      ideal   model   delta    sigma   weight residual
     110.28  115.41   -5.13 1.55e+00 4.16e-01 1.10e+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 -    0.028: 1634
       0.028 -    0.057: 609
       0.057 -    0.085: 165
       0.085 -    0.113: 84
       0.113 -    0.141: 17
  Chirality restraints: 2509
  Sorted by residual:
  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
  chirality pdb=" CA  VAL A 125 "
            pdb=" N   VAL A 125 "
            pdb=" C   VAL A 125 "
            pdb=" CB  VAL A 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.74e-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:             4.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.150
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     38.920
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
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      :  0.003   0.048  15271  Z= 0.159
  Angle     :  0.591   8.229  21915  Z= 0.368
  Chirality :  0.036   0.141   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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (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
 TRP   0.016   0.001   TRP A 279 
 HIS   0.003   0.001   HIS H  75 
 PHE   0.006   0.001   PHE H 100 
 TYR   0.008   0.001   TYR I  57 
 ARG   0.002   0.000   ARG H  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11259 (  856)
  hydrogen bonds       : angle       5.12876 ( 2148)
  covalent geometry    : bond        0.00324 (15271)
  covalent geometry    : angle       0.59145 (21915)

*********************** 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  : 1.055 
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   53 PHE cc_start: 0.8503 (m-80) cc_final: 0.8185 (m-80)
REVERT: A   81 LEU cc_start: 0.8838 (mt) cc_final: 0.8470 (pp)
REVERT: A  134 MET cc_start: 0.8204 (ttp) cc_final: 0.6763 (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: 0.7142 (tp30)
REVERT: A  265 TYR cc_start: 0.7885 (m-10) cc_final: 0.7662 (m-10)
REVERT: G   41 TYR cc_start: 0.8597 (m-80) cc_final: 0.8208 (m-80)
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: 0.8739 (tt0)
REVERT: G  106 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8764 (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: 0.6797 (t70)
REVERT: G  124 ILE cc_start: 0.9596 (mt) cc_final: 0.9288 (tp)
REVERT: G  125 GLN cc_start: 0.9126 (mt0) cc_final: 0.8763 (mt0)
REVERT: H   22 LEU cc_start: 0.7817 (mm) cc_final: 0.7131 (mm)
REVERT: H   39 ARG cc_start: 0.9191 (mmt-90) cc_final: 0.8838 (tpp-160)
REVERT: H   43 VAL cc_start: 0.8535 (t) cc_final: 0.7835 (t)
REVERT: H   51 TYR cc_start: 0.8158 (m-80) cc_final: 0.6959 (m-10)
REVERT: H   55 ARG cc_start: 0.9131 (mtt90) cc_final: 0.8756 (mtm-85)
REVERT: H   64 ASN cc_start: 0.9109 (m-40) cc_final: 0.8686 (m-40)
REVERT: H   75 HIS cc_start: 0.8678 (t70) cc_final: 0.8356 (t-90)
REVERT: H   77 LYS cc_start: 0.9483 (mttt) cc_final: 0.9192 (mmtm)
REVERT: I   42 ARG cc_start: 0.9350 (mtm180) cc_final: 0.8922 (ttm110)
REVERT: I   61 GLU cc_start: 0.9363 (mm-30) cc_final: 0.8814 (tp30)
REVERT: I   75 LYS cc_start: 0.9360 (mmtm) cc_final: 0.8983 (mmtp)
REVERT: I   76 THR cc_start: 0.9233 (m) cc_final: 0.8920 (p)
REVERT: I   84 GLN cc_start: 0.9603 (tp40) cc_final: 0.9402 (tp40)
REVERT: I   94 ASN cc_start: 0.9066 (t0) cc_final: 0.8524 (t0)
REVERT: I   95 LYS cc_start: 0.9580 (tptt) cc_final: 0.9298 (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: 0.8318 (pp20)
REVERT: J   40 LYS cc_start: 0.9651 (mttt) cc_final: 0.9331 (mtpt)
REVERT: J   62 PHE cc_start: 0.9567 (t80) cc_final: 0.9154 (t80)
REVERT: J   65 ASP cc_start: 0.8605 (t70) cc_final: 0.7657 (t0)
REVERT: J   68 GLU cc_start: 0.9083 (tp30) cc_final: 0.8737 (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: 0.8398 (m-40)
REVERT: J   85 THR cc_start: 0.8640 (p) cc_final: 0.8385 (p)
REVERT: J   90 GLU cc_start: 0.9256 (mp0) cc_final: 0.9041 (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: 0.8568 (tm-30)
REVERT: J  103 LEU cc_start: 0.9338 (mt) cc_final: 0.9102 (mt)
REVERT: J  110 GLU cc_start: 0.9231 (mm-30) cc_final: 0.9001 (mm-30)
REVERT: K   48 LEU cc_start: 0.9613 (mp) cc_final: 0.9275 (mp)
REVERT: K   50 GLU cc_start: 0.8350 (tp30) cc_final: 0.7679 (tp30)
REVERT: K   52 ARG cc_start: 0.9252 (mtt90) cc_final: 0.8808 (mtm-85)
REVERT: K   54 TYR cc_start: 0.8942 (m-10) cc_final: 0.8680 (m-10)
REVERT: K   60 LEU cc_start: 0.9241 (mt) cc_final: 0.8956 (mt)
REVERT: K   65 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9257 (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: 0.9000 (tt0)
REVERT: K   86 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8303 (t)
REVERT: K   93 GLN cc_start: 0.9622 (tt0) cc_final: 0.9393 (tm-30)
REVERT: K   94 GLU cc_start: 0.9367 (tt0) cc_final: 0.9164 (tm-30)
REVERT: K  123 ASP cc_start: 0.7897 (t70) cc_final: 0.6271 (t70)
REVERT: M   36 LYS cc_start: 0.9139 (mttm) cc_final: 0.8822 (tttt)
REVERT: M   42 ARG cc_start: 0.9210 (ptm160) cc_final: 0.8747 (ptm160)
REVERT: M   64 GLU cc_start: 0.9463 (tt0) cc_final: 0.8913 (tm-30)
REVERT: M   68 ASN cc_start: 0.9462 (m-40) cc_final: 0.8186 (m-40)
REVERT: M   78 ILE cc_start: 0.9640 (mt) cc_final: 0.9403 (mm)
REVERT: M  112 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8623 (mp10)
REVERT: N   65 ASP cc_start: 0.9313 (t0) cc_final: 0.8889 (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   97 LEU cc_start: 0.9438 (mt) cc_final: 0.9097 (mt)
REVERT: N  105 LYS cc_start: 0.9155 (mttt) cc_final: 0.8455 (mtpp)
REVERT: N  110 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8409 (mt-10)
REVERT: L   25 ASN cc_start: 0.8035 (t0) cc_final: 0.6719 (t0)
REVERT: L   51 TYR cc_start: 0.8022 (m-80) cc_final: 0.7624 (m-80)
REVERT: L   79 LYS cc_start: 0.8682 (mmtt) cc_final: 0.7922 (mmmt)
REVERT: L   82 THR cc_start: 0.9304 (p) cc_final: 0.9058 (p)
REVERT: L   98 TYR cc_start: 0.8930 (m-10) cc_final: 0.8041 (m-80)
  outliers start: 32
  outliers final: 11
  residues processed: 436
  average time/residue: 0.3226
  time to fit residues: 191.8567
Evaluate side-chains
  350 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 335
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 99 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 33 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 76 optimal weight:   10.0000
   chunk 118 optimal weight:    3.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A  79 HIS
A 197 ASN
** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  39 HIS
G  68 GLN
H  25 ASN
** H  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  39 HIS
K  68 GLN
K  76 GLN
K 108 ASN
N  46 HIS
L  25 ASN
L  64 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.056480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.041517 restraints weight = 77748.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.043028 restraints weight = 36052.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.043976 restraints weight = 22141.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  15271  Z= 0.221
  Angle     :  0.633   8.212  21915  Z= 0.364
  Chirality :  0.038   0.174   2509
  Planarity :  0.005   0.075   1765
  Dihedral  : 30.369 132.028   4372
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.25), residues: 1056
  helix:  1.03 (0.21), residues: 554
  sheet: -1.97 (0.44), residues: 139
  loop : -1.80 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A  35 
 HIS   0.007   0.001   HIS H  75 
 PHE   0.029   0.002   PHE G  67 
 TYR   0.026   0.002   TYR H  88 
 ARG   0.006   0.001   ARG M  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06033 (  856)
  hydrogen bonds       : angle       4.01411 ( 2148)
  covalent geometry    : bond        0.00484 (15271)
  covalent geometry    : angle       0.63286 (21915)

*********************** 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
  366 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 366
  time to evaluate  : 1.064 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8873 (mt) cc_final: 0.8523 (pp)
REVERT: A  134 MET cc_start: 0.7980 (ttp) cc_final: 0.6639 (mpp)
REVERT: A  225 TYR cc_start: 0.7172 (m-80) cc_final: 0.6896 (m-80)
REVERT: A  251 ARG cc_start: 0.9032 (mmt90) cc_final: 0.8588 (mmt180)
REVERT: A  265 TYR cc_start: 0.7759 (m-10) cc_final: 0.7544 (m-10)
REVERT: A  280 GLU cc_start: 0.8463 (tt0) cc_final: 0.8191 (tt0)
REVERT: G   41 TYR cc_start: 0.8772 (m-80) cc_final: 0.8283 (m-80)
REVERT: G   50 GLU cc_start: 0.8450 (tp30) cc_final: 0.8235 (tp30)
REVERT: G   51 ILE cc_start: 0.9521 (mt) cc_final: 0.9269 (mm)
REVERT: G   55 GLN cc_start: 0.9425 (mt0) cc_final: 0.9216 (mt0)
REVERT: G   60 LEU cc_start: 0.9253 (mp) cc_final: 0.8778 (mp)
REVERT: G   77 ASP cc_start: 0.9005 (t70) cc_final: 0.8684 (t70)
REVERT: G   93 GLN cc_start: 0.9493 (tt0) cc_final: 0.9158 (tm-30)
REVERT: G  122 LYS cc_start: 0.8865 (ptmt) cc_final: 0.8499 (ptpt)
REVERT: G  125 GLN cc_start: 0.9113 (mt0) cc_final: 0.8688 (mt0)
REVERT: H   22 LEU cc_start: 0.7828 (mm) cc_final: 0.7179 (mm)
REVERT: H   25 ASN cc_start: 0.8446 (t0) cc_final: 0.7790 (t0)
REVERT: H   30 THR cc_start: 0.9321 (p) cc_final: 0.8875 (t)
REVERT: H   51 TYR cc_start: 0.8256 (m-80) cc_final: 0.7990 (m-80)
REVERT: I   42 ARG cc_start: 0.9267 (mtm180) cc_final: 0.8944 (ttm110)
REVERT: I   61 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8959 (mm-30)
REVERT: I   68 ASN cc_start: 0.9401 (m-40) cc_final: 0.9189 (m110)
REVERT: I   75 LYS cc_start: 0.9511 (mmtm) cc_final: 0.9070 (mmtp)
REVERT: I   76 THR cc_start: 0.9213 (m) cc_final: 0.8916 (p)
REVERT: I   84 GLN cc_start: 0.9636 (tp40) cc_final: 0.9410 (tp40)
REVERT: I   94 ASN cc_start: 0.9132 (t0) cc_final: 0.8646 (t0)
REVERT: I   95 LYS cc_start: 0.9600 (tptt) cc_final: 0.9358 (tppt)
REVERT: J   32 GLU cc_start: 0.9247 (pp20) cc_final: 0.8539 (pp20)
REVERT: J   44 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8696 (tm-30)
REVERT: J   65 ASP cc_start: 0.8540 (t70) cc_final: 0.8132 (t0)
REVERT: J   73 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8682 (mm-30)
REVERT: J   76 ARG cc_start: 0.9222 (ttm110) cc_final: 0.8764 (ttm110)
REVERT: J   81 ASN cc_start: 0.9233 (m-40) cc_final: 0.8185 (p0)
REVERT: J   85 THR cc_start: 0.8752 (p) cc_final: 0.8322 (p)
REVERT: J   93 THR cc_start: 0.9748 (m) cc_final: 0.9522 (p)
REVERT: J   98 LEU cc_start: 0.9148 (tt) cc_final: 0.8772 (tt)
REVERT: K   50 GLU cc_start: 0.8243 (tp30) cc_final: 0.7640 (tp30)
REVERT: K   85 GLN cc_start: 0.9461 (mm110) cc_final: 0.9223 (mm110)
REVERT: K   90 MET cc_start: 0.8842 (ptp) cc_final: 0.8635 (ptp)
REVERT: K  120 MET cc_start: 0.9005 (mmp) cc_final: 0.8767 (mmm)
REVERT: K  123 ASP cc_start: 0.6945 (t70) cc_final: 0.6727 (t70)
REVERT: M   36 LYS cc_start: 0.9158 (mttm) cc_final: 0.8919 (pttt)
REVERT: M   56 GLU cc_start: 0.9429 (tt0) cc_final: 0.9139 (mt-10)
REVERT: M   57 TYR cc_start: 0.9316 (t80) cc_final: 0.9071 (t80)
REVERT: M   64 GLU cc_start: 0.9477 (tt0) cc_final: 0.8988 (tm-30)
REVERT: M   68 ASN cc_start: 0.9560 (m-40) cc_final: 0.8175 (m-40)
REVERT: M   93 LEU cc_start: 0.9726 (tp) cc_final: 0.9479 (tt)
REVERT: M  112 GLN cc_start: 0.9037 (mm-40) cc_final: 0.8815 (mp10)
REVERT: N   44 GLN cc_start: 0.9365 (tm-30) cc_final: 0.9007 (tm-30)
REVERT: N   56 MET cc_start: 0.9160 (tpt) cc_final: 0.8922 (tpp)
REVERT: N   65 ASP cc_start: 0.9249 (t0) cc_final: 0.8856 (t0)
REVERT: N   86 ILE cc_start: 0.9380 (mt) cc_final: 0.8896 (mt)
REVERT: N   90 GLU cc_start: 0.9051 (mp0) cc_final: 0.8821 (mp0)
REVERT: N   96 ARG cc_start: 0.8824 (mtp180) cc_final: 0.8374 (ttm110)
REVERT: N  110 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8618 (mt-10)
REVERT: L   43 VAL cc_start: 0.9760 (t) cc_final: 0.9508 (m)
REVERT: L   51 TYR cc_start: 0.8691 (m-80) cc_final: 0.8338 (m-80)
REVERT: L   63 GLU cc_start: 0.8817 (tp30) cc_final: 0.8608 (tp30)
REVERT: L   88 TYR cc_start: 0.9371 (m-10) cc_final: 0.8780 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 366
  average time/residue: 0.2793
  time to fit residues: 148.6666
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  : 1.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 17 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 114 optimal weight:    3.9990
   chunk 69 optimal weight:    6.9990
   chunk 92 optimal weight:    0.9980
   chunk 8 optimal weight:    9.9990
   chunk 124 optimal weight:    0.7980
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 GLN
G  76 GLN
** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  25 ASN
** J  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  39 HIS
K  68 GLN
** N  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  93 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.055518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.040611 restraints weight = 79014.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.042054 restraints weight = 36815.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.043022 restraints weight = 22770.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  15271  Z= 0.247
  Angle     :  0.636   7.301  21915  Z= 0.369
  Chirality :  0.039   0.201   2509
  Planarity :  0.005   0.059   1765
  Dihedral  : 30.265 133.022   4372
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.13 %
    Favored  : 96.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.25), residues: 1056
  helix:  1.42 (0.21), residues: 536
  sheet: -1.76 (0.43), residues: 144
  loop : -1.71 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A  51 
 HIS   0.009   0.001   HIS H  75 
 PHE   0.030   0.002   PHE K  67 
 TYR   0.038   0.002   TYR H  88 
 ARG   0.007   0.001   ARG H  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06101 (  856)
  hydrogen bonds       : angle       4.00364 ( 2148)
  covalent geometry    : bond        0.00536 (15271)
  covalent geometry    : angle       0.63638 (21915)

*********************** 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
  366 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 365
  time to evaluate  : 1.216 
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   26 MET cc_start: 0.8420 (mtp) cc_final: 0.8022 (mtp)
REVERT: A   81 LEU cc_start: 0.8860 (mt) cc_final: 0.8554 (pp)
REVERT: A  134 MET cc_start: 0.7902 (ttp) cc_final: 0.6486 (mpp)
REVERT: A  251 ARG cc_start: 0.9044 (mmt90) cc_final: 0.8614 (mmt180)
REVERT: A  259 PHE cc_start: 0.6687 (m-80) cc_final: 0.5758 (m-80)
REVERT: A  265 TYR cc_start: 0.7707 (m-80) cc_final: 0.7415 (m-10)
REVERT: A  280 GLU cc_start: 0.8609 (tt0) cc_final: 0.8311 (tt0)
REVERT: G   50 GLU cc_start: 0.8366 (tp30) cc_final: 0.8160 (tp30)
REVERT: G   55 GLN cc_start: 0.9415 (mt0) cc_final: 0.9139 (mt0)
REVERT: G   60 LEU cc_start: 0.9355 (mp) cc_final: 0.8680 (mp)
REVERT: G   63 ARG cc_start: 0.8271 (mmt-90) cc_final: 0.7777 (mmm-85)
REVERT: G   73 GLU cc_start: 0.8906 (tt0) cc_final: 0.8282 (tt0)
REVERT: G   77 ASP cc_start: 0.9151 (t70) cc_final: 0.8807 (t70)
REVERT: G   93 GLN cc_start: 0.9522 (tt0) cc_final: 0.9172 (tm-30)
REVERT: G  113 HIS cc_start: 0.9030 (t-170) cc_final: 0.8807 (t-170)
REVERT: G  122 LYS cc_start: 0.8859 (ptmt) cc_final: 0.8524 (ptpt)
REVERT: G  125 GLN cc_start: 0.9140 (mt0) cc_final: 0.8755 (pt0)
REVERT: H   25 ASN cc_start: 0.8776 (t160) cc_final: 0.8219 (m-40)
REVERT: H   30 THR cc_start: 0.9453 (p) cc_final: 0.8972 (t)
REVERT: H   43 VAL cc_start: 0.9668 (t) cc_final: 0.9327 (p)
REVERT: H   64 ASN cc_start: 0.9354 (m-40) cc_final: 0.9137 (m110)
REVERT: H   68 ASP cc_start: 0.9172 (m-30) cc_final: 0.8834 (m-30)
REVERT: H   74 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8898 (tm-30)
REVERT: I   61 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8928 (mm-30)
REVERT: I   73 ASN cc_start: 0.9302 (t0) cc_final: 0.9012 (t0)
REVERT: I   75 LYS cc_start: 0.9543 (mmtm) cc_final: 0.9081 (mmtp)
REVERT: I   76 THR cc_start: 0.9291 (m) cc_final: 0.9010 (p)
REVERT: I   87 VAL cc_start: 0.9687 (m) cc_final: 0.9464 (m)
REVERT: I   90 ASP cc_start: 0.9125 (t0) cc_final: 0.8701 (t0)
REVERT: I   94 ASN cc_start: 0.9097 (t0) cc_final: 0.8574 (t0)
REVERT: I   95 LYS cc_start: 0.9622 (tptt) cc_final: 0.9355 (tppt)
REVERT: J   32 GLU cc_start: 0.9288 (pp20) cc_final: 0.9001 (pp20)
REVERT: J   44 GLN cc_start: 0.8974 (tm-30) cc_final: 0.8595 (tm-30)
REVERT: J   65 ASP cc_start: 0.8730 (t70) cc_final: 0.8528 (t0)
REVERT: J   68 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8793 (mm-30)
REVERT: J   76 ARG cc_start: 0.9169 (ttm110) cc_final: 0.8831 (ttm110)
REVERT: J   77 LEU cc_start: 0.9643 (tp) cc_final: 0.9378 (tp)
REVERT: J   81 ASN cc_start: 0.9161 (m-40) cc_final: 0.8204 (p0)
REVERT: J   93 THR cc_start: 0.9749 (m) cc_final: 0.9510 (p)
REVERT: J   98 LEU cc_start: 0.9274 (tt) cc_final: 0.8925 (tt)
REVERT: K   41 TYR cc_start: 0.8928 (m-80) cc_final: 0.8549 (m-80)
REVERT: K   50 GLU cc_start: 0.8454 (tp30) cc_final: 0.7917 (tp30)
REVERT: K   52 ARG cc_start: 0.9259 (mtt90) cc_final: 0.8893 (mtm-85)
REVERT: K   64 LYS cc_start: 0.9201 (mtmt) cc_final: 0.8724 (pttt)
REVERT: K   85 GLN cc_start: 0.9391 (mm110) cc_final: 0.9142 (mm110)
REVERT: K   97 GLU cc_start: 0.8882 (tt0) cc_final: 0.8665 (tt0)
REVERT: K  120 MET cc_start: 0.9195 (mmp) cc_final: 0.8893 (mmm)
REVERT: K  124 ILE cc_start: 0.9615 (mm) cc_final: 0.9394 (mm)
REVERT: M   35 ARG cc_start: 0.8408 (ttm-80) cc_final: 0.7928 (ttm-80)
REVERT: M   36 LYS cc_start: 0.9152 (mttm) cc_final: 0.8896 (pttt)
REVERT: M   64 GLU cc_start: 0.9478 (tt0) cc_final: 0.8998 (tm-30)
REVERT: M   68 ASN cc_start: 0.9535 (m-40) cc_final: 0.8082 (m-40)
REVERT: M  112 GLN cc_start: 0.9144 (mm-40) cc_final: 0.8738 (mp10)
REVERT: N   44 GLN cc_start: 0.9384 (tm-30) cc_final: 0.9074 (tm-30)
REVERT: N   65 ASP cc_start: 0.9255 (t0) cc_final: 0.8812 (t0)
REVERT: N   83 ARG cc_start: 0.8820 (mmt90) cc_final: 0.8536 (mmm160)
REVERT: N   86 ILE cc_start: 0.9392 (mt) cc_final: 0.9079 (mt)
REVERT: N   96 ARG cc_start: 0.8963 (mtp180) cc_final: 0.8522 (ttm110)
REVERT: N  110 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8576 (mt-10)
REVERT: L   43 VAL cc_start: 0.9750 (t) cc_final: 0.9548 (m)
REVERT: L   53 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8026 (tm-30)
REVERT: L   63 GLU cc_start: 0.8886 (tp30) cc_final: 0.8531 (tp30)
REVERT: L   79 LYS cc_start: 0.8539 (mmtt) cc_final: 0.7971 (mtmm)
REVERT: L   88 TYR cc_start: 0.9432 (m-10) cc_final: 0.8843 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 366
  average time/residue: 0.2955
  time to fit residues: 152.2998
Evaluate side-chains
  312 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 312
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 23 optimal weight:    0.0050
   chunk 36 optimal weight:    0.5980
   chunk 2 optimal weight:   20.0000
   chunk 72 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 130 optimal weight:    0.9980
   chunk 67 optimal weight:    0.3980
   chunk 60 optimal weight:    0.7980
   chunk 101 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
A 274 HIS
G  68 GLN
G  76 GLN
H  25 ASN
K  93 GLN
** N  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.057909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.042988 restraints weight = 76556.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.044496 restraints weight = 35391.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.045493 restraints weight = 21614.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.2974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  15271  Z= 0.160
  Angle     :  0.605   7.606  21915  Z= 0.352
  Chirality :  0.038   0.154   2509
  Planarity :  0.004   0.057   1765
  Dihedral  : 30.182 133.769   4372
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.26), residues: 1056
  helix:  1.54 (0.21), residues: 546
  sheet: -1.70 (0.42), residues: 155
  loop : -1.56 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 279 
 HIS   0.007   0.001   HIS H  75 
 PHE   0.028   0.002   PHE A 206 
 TYR   0.049   0.002   TYR H  88 
 ARG   0.005   0.000   ARG L  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05410 (  856)
  hydrogen bonds       : angle       3.70755 ( 2148)
  covalent geometry    : bond        0.00348 (15271)
  covalent geometry    : angle       0.60504 (21915)

*********************** 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
  354 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 354
  time to evaluate  : 1.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 MET cc_start: 0.8368 (mtp) cc_final: 0.8128 (mmp)
REVERT: A   81 LEU cc_start: 0.8837 (mt) cc_final: 0.8488 (pp)
REVERT: A  134 MET cc_start: 0.7780 (ttp) cc_final: 0.6668 (mpp)
REVERT: A  251 ARG cc_start: 0.8983 (mmt90) cc_final: 0.8544 (mmt90)
REVERT: A  259 PHE cc_start: 0.6655 (m-80) cc_final: 0.6228 (m-80)
REVERT: A  265 TYR cc_start: 0.7601 (m-80) cc_final: 0.7377 (m-80)
REVERT: A  280 GLU cc_start: 0.8614 (tt0) cc_final: 0.8017 (tt0)
REVERT: G   41 TYR cc_start: 0.8723 (m-80) cc_final: 0.8461 (m-80)
REVERT: G   50 GLU cc_start: 0.8624 (tp30) cc_final: 0.8375 (tp30)
REVERT: G   55 GLN cc_start: 0.9448 (mt0) cc_final: 0.9233 (mt0)
REVERT: G   63 ARG cc_start: 0.8286 (mmt-90) cc_final: 0.7543 (mmm-85)
REVERT: G   67 PHE cc_start: 0.9731 (t80) cc_final: 0.9478 (t80)
REVERT: G   73 GLU cc_start: 0.8883 (tt0) cc_final: 0.8128 (tt0)
REVERT: G   77 ASP cc_start: 0.9134 (t70) cc_final: 0.8870 (t70)
REVERT: G   93 GLN cc_start: 0.9428 (tt0) cc_final: 0.8884 (tt0)
REVERT: G  113 HIS cc_start: 0.9045 (t-170) cc_final: 0.8702 (t-170)
REVERT: H   25 ASN cc_start: 0.8737 (t160) cc_final: 0.8269 (m110)
REVERT: H   30 THR cc_start: 0.9397 (p) cc_final: 0.8868 (t)
REVERT: H   59 LYS cc_start: 0.9353 (ttmm) cc_final: 0.8778 (ttmm)
REVERT: H   64 ASN cc_start: 0.9337 (m-40) cc_final: 0.9090 (m110)
REVERT: H   68 ASP cc_start: 0.9156 (m-30) cc_final: 0.8839 (m-30)
REVERT: H   74 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8797 (tm-30)
REVERT: I   42 ARG cc_start: 0.9217 (mtm180) cc_final: 0.8969 (ttm110)
REVERT: I   57 TYR cc_start: 0.9300 (t80) cc_final: 0.8576 (t80)
REVERT: I   61 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8572 (tp30)
REVERT: I   75 LYS cc_start: 0.9521 (mmtm) cc_final: 0.9079 (mmtp)
REVERT: I   76 THR cc_start: 0.9164 (m) cc_final: 0.8862 (p)
REVERT: I   87 VAL cc_start: 0.9677 (m) cc_final: 0.9456 (m)
REVERT: I   94 ASN cc_start: 0.9025 (t0) cc_final: 0.8513 (t0)
REVERT: I   95 LYS cc_start: 0.9591 (tptt) cc_final: 0.9277 (tppt)
REVERT: I  115 LEU cc_start: 0.9350 (mm) cc_final: 0.8936 (mm)
REVERT: J   32 GLU cc_start: 0.9256 (pp20) cc_final: 0.9003 (pp20)
REVERT: J   44 GLN cc_start: 0.9072 (tm-30) cc_final: 0.8614 (tm-30)
REVERT: J   65 ASP cc_start: 0.8673 (t70) cc_final: 0.8219 (t70)
REVERT: J   81 ASN cc_start: 0.9142 (m-40) cc_final: 0.8082 (p0)
REVERT: J   87 THR cc_start: 0.9061 (p) cc_final: 0.8570 (p)
REVERT: J   93 THR cc_start: 0.9749 (m) cc_final: 0.9533 (p)
REVERT: J   99 LEU cc_start: 0.9382 (mt) cc_final: 0.9087 (mp)
REVERT: J  103 LEU cc_start: 0.9288 (mm) cc_final: 0.8800 (mm)
REVERT: K   50 GLU cc_start: 0.8520 (tp30) cc_final: 0.7608 (tp30)
REVERT: K   52 ARG cc_start: 0.9262 (mtt90) cc_final: 0.8811 (mtm-85)
REVERT: K   54 TYR cc_start: 0.8637 (m-10) cc_final: 0.8395 (m-10)
REVERT: K   73 GLU cc_start: 0.7672 (mp0) cc_final: 0.6951 (mt-10)
REVERT: K   84 PHE cc_start: 0.9015 (m-80) cc_final: 0.8522 (m-10)
REVERT: K   85 GLN cc_start: 0.9386 (mm110) cc_final: 0.9144 (mm110)
REVERT: K  106 ASP cc_start: 0.9043 (m-30) cc_final: 0.8834 (m-30)
REVERT: K  120 MET cc_start: 0.9244 (mmp) cc_final: 0.8939 (mmm)
REVERT: M   36 LYS cc_start: 0.9131 (mttm) cc_final: 0.8869 (pttt)
REVERT: M   64 GLU cc_start: 0.9454 (tt0) cc_final: 0.9009 (tm-30)
REVERT: M   68 ASN cc_start: 0.9571 (m-40) cc_final: 0.8234 (m-40)
REVERT: N   39 TYR cc_start: 0.8484 (t80) cc_final: 0.8173 (t80)
REVERT: N   44 GLN cc_start: 0.9334 (tm-30) cc_final: 0.9026 (tm-30)
REVERT: N   65 ASP cc_start: 0.9221 (t0) cc_final: 0.8804 (t0)
REVERT: N   83 ARG cc_start: 0.8697 (mmt90) cc_final: 0.8315 (mmm-85)
REVERT: N  105 LYS cc_start: 0.9331 (mttt) cc_final: 0.8865 (mtpt)
REVERT: N  110 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8539 (mt-10)
REVERT: L   44 LYS cc_start: 0.9268 (mtpt) cc_final: 0.8640 (mttt)
REVERT: L   63 GLU cc_start: 0.8901 (tp30) cc_final: 0.8549 (tp30)
REVERT: L   79 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8052 (mmtm)
REVERT: L   88 TYR cc_start: 0.9178 (m-10) cc_final: 0.8496 (m-10)
REVERT: L   98 TYR cc_start: 0.8902 (m-80) cc_final: 0.8416 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 354
  average time/residue: 0.2601
  time to fit residues: 132.7506
Evaluate side-chains
  306 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 306
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 15 optimal weight:    9.9990
   chunk 25 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 8 optimal weight:    0.3980
   chunk 104 optimal weight:    4.9990
   chunk 102 optimal weight:    3.9990
   chunk 92 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 GLN
** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 113 HIS
H  25 ASN
** J  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 108 ASN
** N  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  92 GLN
** L  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.055553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.040681 restraints weight = 81140.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.042145 restraints weight = 37541.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.043110 restraints weight = 22959.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.3237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  15271  Z= 0.257
  Angle     :  0.659   6.778  21915  Z= 0.380
  Chirality :  0.039   0.140   2509
  Planarity :  0.005   0.057   1765
  Dihedral  : 30.073 135.991   4372
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.26), residues: 1056
  helix:  1.53 (0.21), residues: 536
  sheet: -1.63 (0.44), residues: 144
  loop : -1.63 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A  51 
 HIS   0.013   0.001   HIS H  75 
 PHE   0.022   0.002   PHE A 206 
 TYR   0.056   0.003   TYR H  88 
 ARG   0.009   0.001   ARG N  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06251 (  856)
  hydrogen bonds       : angle       3.97824 ( 2148)
  covalent geometry    : bond        0.00562 (15271)
  covalent geometry    : angle       0.65890 (21915)

*********************** 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
  348 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 348
  time to evaluate  : 1.172 
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   26 MET cc_start: 0.8379 (mtp) cc_final: 0.8065 (mtp)
REVERT: A   81 LEU cc_start: 0.8953 (mt) cc_final: 0.8576 (pp)
REVERT: A  134 MET cc_start: 0.7757 (ttp) cc_final: 0.6627 (mpp)
REVERT: A  242 MET cc_start: 0.7965 (ptp) cc_final: 0.7624 (mpp)
REVERT: A  251 ARG cc_start: 0.9039 (mmt90) cc_final: 0.8631 (mmt90)
REVERT: A  259 PHE cc_start: 0.6802 (m-80) cc_final: 0.5922 (m-80)
REVERT: A  265 TYR cc_start: 0.7605 (m-80) cc_final: 0.7211 (m-80)
REVERT: A  280 GLU cc_start: 0.8721 (tt0) cc_final: 0.8208 (tt0)
REVERT: G   55 GLN cc_start: 0.9446 (mt0) cc_final: 0.9171 (mt0)
REVERT: G   63 ARG cc_start: 0.8284 (mmt-90) cc_final: 0.7577 (mmm-85)
REVERT: G   73 GLU cc_start: 0.8866 (tt0) cc_final: 0.8182 (tt0)
REVERT: G   77 ASP cc_start: 0.9233 (t70) cc_final: 0.8966 (t70)
REVERT: G   90 MET cc_start: 0.9187 (mmm) cc_final: 0.8949 (mmp)
REVERT: G   93 GLN cc_start: 0.9451 (tt0) cc_final: 0.9231 (tt0)
REVERT: G  113 HIS cc_start: 0.9147 (t70) cc_final: 0.8765 (t-170)
REVERT: G  125 GLN cc_start: 0.9161 (mt0) cc_final: 0.8743 (mp10)
REVERT: H   25 ASN cc_start: 0.8947 (t160) cc_final: 0.8503 (m110)
REVERT: H   30 THR cc_start: 0.9492 (p) cc_final: 0.8962 (t)
REVERT: H   39 ARG cc_start: 0.9217 (mmt-90) cc_final: 0.8728 (mpp-170)
REVERT: H   44 LYS cc_start: 0.9046 (ttmt) cc_final: 0.8801 (ttmt)
REVERT: H   74 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8824 (tm-30)
REVERT: H   75 HIS cc_start: 0.8880 (t-90) cc_final: 0.8543 (t-90)
REVERT: H   77 LYS cc_start: 0.9423 (mmtt) cc_final: 0.9082 (mmtm)
REVERT: I   57 TYR cc_start: 0.9347 (t80) cc_final: 0.8693 (t80)
REVERT: I   61 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8614 (tp30)
REVERT: I   75 LYS cc_start: 0.9625 (mmtm) cc_final: 0.9158 (mmtp)
REVERT: I   76 THR cc_start: 0.8969 (m) cc_final: 0.8711 (p)
REVERT: I   87 VAL cc_start: 0.9685 (m) cc_final: 0.9295 (m)
REVERT: I   90 ASP cc_start: 0.9019 (t70) cc_final: 0.8700 (t0)
REVERT: I   94 ASN cc_start: 0.9053 (t0) cc_final: 0.8345 (m-40)
REVERT: I   95 LYS cc_start: 0.9620 (tptt) cc_final: 0.9291 (tppt)
REVERT: I  115 LEU cc_start: 0.9423 (mm) cc_final: 0.9009 (mm)
REVERT: J   32 GLU cc_start: 0.9303 (pp20) cc_final: 0.9035 (pp20)
REVERT: J   44 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8657 (tm-30)
REVERT: J   65 ASP cc_start: 0.8714 (t70) cc_final: 0.8224 (t70)
REVERT: J   76 ARG cc_start: 0.9135 (ttm110) cc_final: 0.8800 (ttm110)
REVERT: J   81 ASN cc_start: 0.9058 (m-40) cc_final: 0.8063 (p0)
REVERT: J   93 THR cc_start: 0.9792 (m) cc_final: 0.9457 (p)
REVERT: J   99 LEU cc_start: 0.9492 (mt) cc_final: 0.9210 (mp)
REVERT: K   50 GLU cc_start: 0.8818 (tp30) cc_final: 0.8134 (tp30)
REVERT: K   52 ARG cc_start: 0.9250 (mtt90) cc_final: 0.8857 (mtm-85)
REVERT: K   64 LYS cc_start: 0.9133 (mtmt) cc_final: 0.8636 (pttt)
REVERT: K   70 LEU cc_start: 0.9563 (tt) cc_final: 0.9214 (tt)
REVERT: K   74 ILE cc_start: 0.9621 (tp) cc_final: 0.9399 (tp)
REVERT: K   79 LYS cc_start: 0.8444 (tppp) cc_final: 0.7889 (tptm)
REVERT: K   85 GLN cc_start: 0.9406 (mm110) cc_final: 0.9147 (mm110)
REVERT: K   93 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8574 (tm-30)
REVERT: K   97 GLU cc_start: 0.8714 (tt0) cc_final: 0.8466 (tt0)
REVERT: K  120 MET cc_start: 0.9310 (mmp) cc_final: 0.8920 (mmm)
REVERT: M   36 LYS cc_start: 0.9158 (mttm) cc_final: 0.8811 (tttt)
REVERT: M   56 GLU cc_start: 0.9438 (tt0) cc_final: 0.9196 (mt-10)
REVERT: M   64 GLU cc_start: 0.9474 (tt0) cc_final: 0.9012 (tm-30)
REVERT: M   68 ASN cc_start: 0.9541 (m-40) cc_final: 0.8129 (m-40)
REVERT: N   44 GLN cc_start: 0.9399 (tm-30) cc_final: 0.9052 (tm-30)
REVERT: N   65 ASP cc_start: 0.9281 (t0) cc_final: 0.8955 (t0)
REVERT: N   83 ARG cc_start: 0.8743 (mmt90) cc_final: 0.8343 (mtp85)
REVERT: N  102 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8618 (mm-30)
REVERT: N  110 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8437 (tp30)
REVERT: L   44 LYS cc_start: 0.9513 (mtpt) cc_final: 0.8880 (mttt)
REVERT: L   51 TYR cc_start: 0.8720 (m-80) cc_final: 0.8391 (m-80)
REVERT: L   53 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7712 (tm-30)
REVERT: L   63 GLU cc_start: 0.8899 (tp30) cc_final: 0.8427 (tp30)
REVERT: L   79 LYS cc_start: 0.8417 (mmtt) cc_final: 0.7967 (mmtm)
REVERT: L   98 TYR cc_start: 0.8891 (m-80) cc_final: 0.8364 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 348
  average time/residue: 0.2830
  time to fit residues: 139.2406
Evaluate side-chains
  301 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 301
  time to evaluate  : 1.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 4 optimal weight:   20.0000
   chunk 100 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 117 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0670
   chunk 56 optimal weight:    0.7980
   chunk 20 optimal weight:    6.9990
   chunk 118 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 12 optimal weight:    8.9990
   overall best weight:    1.9724

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

Flipped N/Q/H residues before XYZ refinement:
** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 GLN
G  76 GLN
H  25 ASN
** J  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 125 GLN
M  24 GLN
** L  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.055468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.040584 restraints weight = 80310.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.042055 restraints weight = 37168.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.043012 restraints weight = 22825.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.3413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  15271  Z= 0.250
  Angle     :  0.654   6.850  21915  Z= 0.378
  Chirality :  0.039   0.158   2509
  Planarity :  0.005   0.062   1765
  Dihedral  : 30.074 132.637   4372
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 15.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.00 (0.26), residues: 1056
  helix:  1.48 (0.21), residues: 536
  sheet: -1.58 (0.44), residues: 144
  loop : -1.51 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 279 
 HIS   0.012   0.001   HIS H  75 
 PHE   0.039   0.002   PHE G  67 
 TYR   0.065   0.003   TYR H  88 
 ARG   0.011   0.001   ARG N  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06030 (  856)
  hydrogen bonds       : angle       3.99665 ( 2148)
  covalent geometry    : bond        0.00550 (15271)
  covalent geometry    : angle       0.65391 (21915)

*********************** 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
  343 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 343
  time to evaluate  : 1.198 
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   26 MET cc_start: 0.8293 (mtp) cc_final: 0.8089 (mmp)
REVERT: A   81 LEU cc_start: 0.8962 (mt) cc_final: 0.8581 (pp)
REVERT: A  134 MET cc_start: 0.7762 (ttp) cc_final: 0.6533 (mpp)
REVERT: A  242 MET cc_start: 0.7940 (ptp) cc_final: 0.7644 (mpp)
REVERT: A  251 ARG cc_start: 0.9044 (mmt90) cc_final: 0.8633 (mmt90)
REVERT: A  259 PHE cc_start: 0.6823 (m-80) cc_final: 0.5889 (m-80)
REVERT: A  265 TYR cc_start: 0.7584 (m-80) cc_final: 0.7306 (m-80)
REVERT: A  280 GLU cc_start: 0.8707 (tt0) cc_final: 0.8404 (tt0)
REVERT: G   55 GLN cc_start: 0.9384 (mt0) cc_final: 0.9086 (mt0)
REVERT: G   60 LEU cc_start: 0.9358 (mp) cc_final: 0.8047 (mp)
REVERT: G   63 ARG cc_start: 0.8327 (mmt-90) cc_final: 0.7542 (mmm-85)
REVERT: G   73 GLU cc_start: 0.8813 (tt0) cc_final: 0.8183 (tt0)
REVERT: G   77 ASP cc_start: 0.9251 (t70) cc_final: 0.8989 (t70)
REVERT: G   85 GLN cc_start: 0.9095 (mt0) cc_final: 0.8812 (mt0)
REVERT: G   93 GLN cc_start: 0.9561 (tt0) cc_final: 0.9132 (tm-30)
REVERT: H   25 ASN cc_start: 0.8931 (t160) cc_final: 0.8652 (m-40)
REVERT: H   30 THR cc_start: 0.9526 (p) cc_final: 0.8972 (t)
REVERT: H   51 TYR cc_start: 0.8927 (m-10) cc_final: 0.8412 (m-10)
REVERT: H   52 GLU cc_start: 0.8897 (pm20) cc_final: 0.8241 (pp20)
REVERT: H   74 GLU cc_start: 0.9290 (mt-10) cc_final: 0.8844 (tm-30)
REVERT: H   75 HIS cc_start: 0.8931 (t-90) cc_final: 0.8697 (t-90)
REVERT: H   85 ASP cc_start: 0.9252 (m-30) cc_final: 0.9028 (m-30)
REVERT: I   42 ARG cc_start: 0.9220 (mtm180) cc_final: 0.9018 (ttm110)
REVERT: I   57 TYR cc_start: 0.9365 (t80) cc_final: 0.8641 (t80)
REVERT: I   61 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8590 (tp30)
REVERT: I   75 LYS cc_start: 0.9614 (mmtm) cc_final: 0.9156 (mmtp)
REVERT: I   76 THR cc_start: 0.8929 (m) cc_final: 0.8673 (p)
REVERT: I   87 VAL cc_start: 0.9679 (m) cc_final: 0.9400 (m)
REVERT: I   90 ASP cc_start: 0.9089 (t70) cc_final: 0.8800 (t0)
REVERT: I   94 ASN cc_start: 0.8966 (t0) cc_final: 0.8338 (m-40)
REVERT: I   95 LYS cc_start: 0.9611 (tptt) cc_final: 0.9280 (tppt)
REVERT: J   44 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8727 (tm-30)
REVERT: J   65 ASP cc_start: 0.8759 (t70) cc_final: 0.8273 (t70)
REVERT: J   68 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8817 (mm-30)
REVERT: J   81 ASN cc_start: 0.8959 (m-40) cc_final: 0.8064 (p0)
REVERT: J   85 THR cc_start: 0.9014 (p) cc_final: 0.8439 (p)
REVERT: J   93 THR cc_start: 0.9766 (m) cc_final: 0.9491 (p)
REVERT: J   99 LEU cc_start: 0.9455 (mt) cc_final: 0.9162 (mp)
REVERT: K   50 GLU cc_start: 0.8766 (tp30) cc_final: 0.8183 (tp30)
REVERT: K   52 ARG cc_start: 0.9231 (mtt90) cc_final: 0.8831 (mtm-85)
REVERT: K   68 GLN cc_start: 0.9353 (pt0) cc_final: 0.9036 (pp30)
REVERT: K   70 LEU cc_start: 0.9601 (tt) cc_final: 0.9260 (tt)
REVERT: K   74 ILE cc_start: 0.9618 (tp) cc_final: 0.9349 (tp)
REVERT: K   79 LYS cc_start: 0.8378 (tppp) cc_final: 0.7824 (tptm)
REVERT: K   85 GLN cc_start: 0.9387 (mm110) cc_final: 0.9142 (mm-40)
REVERT: K   93 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8926 (tm-30)
REVERT: K  120 MET cc_start: 0.9380 (mmp) cc_final: 0.8952 (mmm)
REVERT: M   36 LYS cc_start: 0.9076 (mttm) cc_final: 0.8859 (pttt)
REVERT: M   56 GLU cc_start: 0.9391 (tt0) cc_final: 0.9100 (mt-10)
REVERT: M   64 GLU cc_start: 0.9476 (tt0) cc_final: 0.9003 (tm-30)
REVERT: M   68 ASN cc_start: 0.9530 (m-40) cc_final: 0.8147 (m-40)
REVERT: N   65 ASP cc_start: 0.9320 (t0) cc_final: 0.8859 (t0)
REVERT: N   80 TYR cc_start: 0.8238 (m-80) cc_final: 0.8031 (m-10)
REVERT: N   83 ARG cc_start: 0.8718 (mmt90) cc_final: 0.8421 (mtp85)
REVERT: N   85 THR cc_start: 0.8816 (p) cc_final: 0.8211 (p)
REVERT: N  102 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8627 (mm-30)
REVERT: N  110 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8394 (tp30)
REVERT: N  113 LYS cc_start: 0.9494 (tmmt) cc_final: 0.9212 (ttpp)
REVERT: L   31 LYS cc_start: 0.9385 (ttmt) cc_final: 0.9142 (ttmm)
REVERT: L   63 GLU cc_start: 0.8941 (tp30) cc_final: 0.8432 (tp30)
REVERT: L   77 LYS cc_start: 0.9429 (mmtp) cc_final: 0.9180 (mmtm)
REVERT: L   79 LYS cc_start: 0.8289 (mmtt) cc_final: 0.7829 (mmtm)
REVERT: L   98 TYR cc_start: 0.8732 (m-80) cc_final: 0.8132 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 343
  average time/residue: 0.2981
  time to fit residues: 142.9767
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  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 95 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 46 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 90 optimal weight:    1.9990
   chunk 109 optimal weight:    3.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 274 HIS
A 328 ASN
G  68 GLN
** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  68 ASN
** J  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 108 ASN
** L  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.056688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.041797 restraints weight = 78961.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.043297 restraints weight = 36428.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.044274 restraints weight = 22290.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15271  Z= 0.202
  Angle     :  0.643   8.394  21915  Z= 0.370
  Chirality :  0.039   0.205   2509
  Planarity :  0.005   0.086   1765
  Dihedral  : 30.010 133.226   4372
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.26), residues: 1056
  helix:  1.49 (0.22), residues: 536
  sheet: -1.71 (0.43), residues: 157
  loop : -1.32 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP A  51 
 HIS   0.009   0.001   HIS H  75 
 PHE   0.016   0.002   PHE K  67 
 TYR   0.073   0.003   TYR H  88 
 ARG   0.013   0.001   ARG J  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05618 (  856)
  hydrogen bonds       : angle       3.85060 ( 2148)
  covalent geometry    : bond        0.00445 (15271)
  covalent geometry    : angle       0.64264 (21915)

*********************** 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
  353 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 353
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.8926 (mt) cc_final: 0.8524 (pp)
REVERT: A  134 MET cc_start: 0.7785 (ttp) cc_final: 0.6654 (mpp)
REVERT: A  242 MET cc_start: 0.7917 (ptp) cc_final: 0.7618 (mpp)
REVERT: A  251 ARG cc_start: 0.9012 (mmt90) cc_final: 0.8592 (mmt90)
REVERT: A  259 PHE cc_start: 0.6967 (m-80) cc_final: 0.6394 (m-80)
REVERT: A  265 TYR cc_start: 0.7486 (m-10) cc_final: 0.7221 (m-80)
REVERT: A  280 GLU cc_start: 0.8602 (tt0) cc_final: 0.8120 (tt0)
REVERT: G   63 ARG cc_start: 0.8300 (mmt-90) cc_final: 0.7507 (mmm-85)
REVERT: G   73 GLU cc_start: 0.8846 (tt0) cc_final: 0.8207 (tt0)
REVERT: G   77 ASP cc_start: 0.9273 (t70) cc_final: 0.9072 (t70)
REVERT: G   93 GLN cc_start: 0.9569 (tt0) cc_final: 0.9234 (tm-30)
REVERT: G  113 HIS cc_start: 0.9059 (t-170) cc_final: 0.8619 (t-170)
REVERT: G  125 GLN cc_start: 0.9217 (mt0) cc_final: 0.8776 (mp10)
REVERT: H   30 THR cc_start: 0.9462 (p) cc_final: 0.8942 (t)
REVERT: H   39 ARG cc_start: 0.9295 (mmt-90) cc_final: 0.9078 (mmt-90)
REVERT: H   63 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8142 (mp0)
REVERT: H   74 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8856 (tm-30)
REVERT: H   75 HIS cc_start: 0.8894 (t-90) cc_final: 0.7857 (t-90)
REVERT: I   75 LYS cc_start: 0.9603 (mmtm) cc_final: 0.9186 (mmtp)
REVERT: I   76 THR cc_start: 0.8857 (m) cc_final: 0.8627 (p)
REVERT: I   87 VAL cc_start: 0.9668 (m) cc_final: 0.9209 (m)
REVERT: I   90 ASP cc_start: 0.9081 (t70) cc_final: 0.8710 (t0)
REVERT: I   94 ASN cc_start: 0.9003 (t0) cc_final: 0.8236 (m-40)
REVERT: I   95 LYS cc_start: 0.9601 (tptt) cc_final: 0.9245 (tppt)
REVERT: J   44 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8740 (tm-30)
REVERT: J   81 ASN cc_start: 0.8892 (m-40) cc_final: 0.8537 (m-40)
REVERT: J   85 THR cc_start: 0.9056 (p) cc_final: 0.8462 (p)
REVERT: J   93 THR cc_start: 0.9758 (m) cc_final: 0.9515 (p)
REVERT: K   50 GLU cc_start: 0.8791 (tp30) cc_final: 0.8173 (tp30)
REVERT: K   52 ARG cc_start: 0.9217 (mtt90) cc_final: 0.8681 (mtm-85)
REVERT: K   68 GLN cc_start: 0.9351 (pt0) cc_final: 0.8972 (pp30)
REVERT: K   84 PHE cc_start: 0.8935 (m-10) cc_final: 0.8548 (m-10)
REVERT: K   93 GLN cc_start: 0.9197 (tm-30) cc_final: 0.8872 (tm-30)
REVERT: K   97 GLU cc_start: 0.8953 (tt0) cc_final: 0.8681 (tt0)
REVERT: K  120 MET cc_start: 0.9466 (mmp) cc_final: 0.9037 (mmm)
REVERT: M   35 ARG cc_start: 0.8751 (mtm110) cc_final: 0.8442 (mtm110)
REVERT: M   36 LYS cc_start: 0.9058 (mttm) cc_final: 0.8779 (pttt)
REVERT: M   56 GLU cc_start: 0.9375 (tt0) cc_final: 0.9076 (mt-10)
REVERT: M   64 GLU cc_start: 0.9456 (tt0) cc_final: 0.9015 (tm-30)
REVERT: M   68 ASN cc_start: 0.9561 (m-40) cc_final: 0.8110 (m-40)
REVERT: N   65 ASP cc_start: 0.9237 (t0) cc_final: 0.8738 (t0)
REVERT: N   80 TYR cc_start: 0.8331 (m-80) cc_final: 0.7145 (m-10)
REVERT: N   83 ARG cc_start: 0.8748 (mmt90) cc_final: 0.8456 (mmm160)
REVERT: N  102 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8139 (mm-30)
REVERT: N  105 LYS cc_start: 0.9286 (mttt) cc_final: 0.8380 (mtmm)
REVERT: N  110 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8445 (tp30)
REVERT: N  113 LYS cc_start: 0.9524 (tmmt) cc_final: 0.9247 (ttpp)
REVERT: L   43 VAL cc_start: 0.9657 (m) cc_final: 0.9373 (m)
REVERT: L   44 LYS cc_start: 0.9552 (mtpt) cc_final: 0.8804 (ttmm)
REVERT: L   51 TYR cc_start: 0.8659 (m-80) cc_final: 0.7557 (m-80)
REVERT: L   63 GLU cc_start: 0.8908 (tp30) cc_final: 0.8555 (tp30)
REVERT: L   77 LYS cc_start: 0.9419 (mmtp) cc_final: 0.9070 (mmtp)
REVERT: L   88 TYR cc_start: 0.9088 (m-10) cc_final: 0.7838 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 353
  average time/residue: 0.2893
  time to fit residues: 142.4968
Evaluate side-chains
  298 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 298
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 57 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 63 optimal weight:    0.7980
   chunk 90 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   chunk 128 optimal weight:    1.9990
   chunk 48 optimal weight:    0.3980
   chunk 122 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 114 GLN
A 274 HIS
G  68 GLN
G  76 GLN
** J  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 108 ASN
K 125 GLN
** 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 = 0.3232 r_free = 0.3232 target = 0.057325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.042397 restraints weight = 78463.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.043874 restraints weight = 36432.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.044827 restraints weight = 22403.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.3785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15271  Z= 0.192
  Angle     :  0.655  11.291  21915  Z= 0.372
  Chirality :  0.039   0.154   2509
  Planarity :  0.005   0.072   1765
  Dihedral  : 29.956 133.649   4372
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 14.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.26), residues: 1056
  helix:  1.60 (0.22), residues: 530
  sheet: -1.49 (0.44), residues: 146
  loop : -1.37 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 279 
 HIS   0.007   0.001   HIS H  75 
 PHE   0.016   0.002   PHE K  67 
 TYR   0.025   0.003   TYR N  80 
 ARG   0.011   0.001   ARG N  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05532 (  856)
  hydrogen bonds       : angle       3.82498 ( 2148)
  covalent geometry    : bond        0.00425 (15271)
  covalent geometry    : angle       0.65496 (21915)

*********************** 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
  343 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 343
  time to evaluate  : 1.209 
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: 0.7669 (t60) cc_final: 0.7388 (t60)
REVERT: A   81 LEU cc_start: 0.8910 (mt) cc_final: 0.8487 (pp)
REVERT: A  134 MET cc_start: 0.7778 (ttp) cc_final: 0.6650 (mpp)
REVERT: A  251 ARG cc_start: 0.8963 (mmt90) cc_final: 0.8561 (mmt90)
REVERT: A  280 GLU cc_start: 0.8593 (tt0) cc_final: 0.8035 (tt0)
REVERT: G   41 TYR cc_start: 0.8703 (m-80) cc_final: 0.8471 (m-80)
REVERT: G   55 GLN cc_start: 0.9361 (mt0) cc_final: 0.9091 (tt0)
REVERT: G   63 ARG cc_start: 0.8231 (mmt-90) cc_final: 0.7730 (mmm-85)
REVERT: G   73 GLU cc_start: 0.8842 (tt0) cc_final: 0.8076 (tt0)
REVERT: G   93 GLN cc_start: 0.9545 (tt0) cc_final: 0.9230 (tm-30)
REVERT: H   25 ASN cc_start: 0.8639 (m-40) cc_final: 0.8191 (m110)
REVERT: H   30 THR cc_start: 0.9423 (p) cc_final: 0.8821 (t)
REVERT: H   31 LYS cc_start: 0.9173 (tptp) cc_final: 0.8929 (tptp)
REVERT: H   39 ARG cc_start: 0.9195 (mmt-90) cc_final: 0.8978 (mmt-90)
REVERT: H   63 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8095 (mp0)
REVERT: H   68 ASP cc_start: 0.8941 (m-30) cc_final: 0.8684 (m-30)
REVERT: H   74 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8794 (pt0)
REVERT: H   75 HIS cc_start: 0.8791 (t-90) cc_final: 0.8541 (t-90)
REVERT: I   76 THR cc_start: 0.8798 (m) cc_final: 0.8595 (p)
REVERT: I   87 VAL cc_start: 0.9647 (m) cc_final: 0.9402 (m)
REVERT: I   90 ASP cc_start: 0.9098 (t70) cc_final: 0.8623 (t0)
REVERT: I   94 ASN cc_start: 0.8956 (t0) cc_final: 0.8312 (m-40)
REVERT: I   95 LYS cc_start: 0.9591 (tptt) cc_final: 0.9223 (tppt)
REVERT: J   44 GLN cc_start: 0.9126 (tm-30) cc_final: 0.8733 (tm-30)
REVERT: J   65 ASP cc_start: 0.8635 (t70) cc_final: 0.8286 (t70)
REVERT: K   50 GLU cc_start: 0.8807 (tp30) cc_final: 0.8168 (tp30)
REVERT: K   52 ARG cc_start: 0.9207 (mtt90) cc_final: 0.8676 (mtm-85)
REVERT: K   68 GLN cc_start: 0.9317 (pt0) cc_final: 0.8977 (pp30)
REVERT: K   84 PHE cc_start: 0.8983 (m-10) cc_final: 0.8655 (m-10)
REVERT: K   93 GLN cc_start: 0.9201 (tm-30) cc_final: 0.8846 (tm-30)
REVERT: K   97 GLU cc_start: 0.8946 (tt0) cc_final: 0.8680 (tt0)
REVERT: K  120 MET cc_start: 0.9378 (mmp) cc_final: 0.8770 (mmm)
REVERT: K  123 ASP cc_start: 0.9334 (m-30) cc_final: 0.8675 (m-30)
REVERT: M   35 ARG cc_start: 0.8838 (mtm110) cc_final: 0.8510 (mtm110)
REVERT: M   36 LYS cc_start: 0.9066 (mttm) cc_final: 0.8714 (tttt)
REVERT: M   56 GLU cc_start: 0.9357 (tt0) cc_final: 0.9058 (mt-10)
REVERT: M   64 GLU cc_start: 0.9437 (tt0) cc_final: 0.9004 (tm-30)
REVERT: M   68 ASN cc_start: 0.9516 (m-40) cc_final: 0.8234 (m-40)
REVERT: M   99 ARG cc_start: 0.8048 (tpt170) cc_final: 0.7790 (tpt170)
REVERT: N   65 ASP cc_start: 0.9274 (t0) cc_final: 0.8817 (t0)
REVERT: N   68 GLU cc_start: 0.8417 (tp30) cc_final: 0.8190 (tp30)
REVERT: N   80 TYR cc_start: 0.8343 (m-80) cc_final: 0.7687 (m-10)
REVERT: N   83 ARG cc_start: 0.8721 (mmt90) cc_final: 0.8415 (mmm160)
REVERT: N  110 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8415 (tp30)
REVERT: N  113 LYS cc_start: 0.9470 (tmmt) cc_final: 0.9222 (ttpp)
REVERT: L   43 VAL cc_start: 0.9659 (m) cc_final: 0.9379 (m)
REVERT: L   44 LYS cc_start: 0.9556 (mtpt) cc_final: 0.9311 (mttt)
REVERT: L   63 GLU cc_start: 0.8854 (tp30) cc_final: 0.8534 (tp30)
REVERT: L   77 LYS cc_start: 0.9422 (mmtp) cc_final: 0.9122 (mmtp)
REVERT: L   79 LYS cc_start: 0.8024 (mmtm) cc_final: 0.7394 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 343
  average time/residue: 0.2891
  time to fit residues: 140.6792
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  : 1.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0980
   chunk 113 optimal weight:    4.9990
   chunk 129 optimal weight:    4.9990
   chunk 64 optimal weight:    0.4980
   chunk 116 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 114 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 274 HIS
G  68 GLN
G  85 GLN
** J  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 108 ASN
K 125 GLN
** L  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.058370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.043584 restraints weight = 77376.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.045046 restraints weight = 35933.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.046021 restraints weight = 22132.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.3989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  15271  Z= 0.177
  Angle     :  0.655  13.536  21915  Z= 0.371
  Chirality :  0.038   0.151   2509
  Planarity :  0.005   0.070   1765
  Dihedral  : 29.896 134.022   4372
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 14.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.26), residues: 1056
  helix:  1.59 (0.22), residues: 530
  sheet: -1.47 (0.43), residues: 157
  loop : -1.34 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 279 
 HIS   0.007   0.001   HIS G 113 
 PHE   0.018   0.002   PHE J  62 
 TYR   0.032   0.003   TYR H  88 
 ARG   0.014   0.001   ARG N  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05384 (  856)
  hydrogen bonds       : angle       3.81477 ( 2148)
  covalent geometry    : bond        0.00393 (15271)
  covalent geometry    : angle       0.65532 (21915)

*********************** 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
  344 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 343
  time to evaluate  : 1.203 
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   26 MET cc_start: 0.8369 (tpp) cc_final: 0.7378 (ptp)
REVERT: A   51 TRP cc_start: 0.7715 (t60) cc_final: 0.7394 (t60)
REVERT: A   81 LEU cc_start: 0.8822 (mt) cc_final: 0.8408 (pp)
REVERT: A  134 MET cc_start: 0.7560 (ttp) cc_final: 0.6640 (mpp)
REVERT: A  242 MET cc_start: 0.7982 (ptp) cc_final: 0.7597 (mpp)
REVERT: A  280 GLU cc_start: 0.8572 (tt0) cc_final: 0.8242 (tt0)
REVERT: G   41 TYR cc_start: 0.8697 (m-80) cc_final: 0.8492 (m-80)
REVERT: G   55 GLN cc_start: 0.9318 (mt0) cc_final: 0.9066 (tt0)
REVERT: G   63 ARG cc_start: 0.8208 (mmt-90) cc_final: 0.7675 (mmm-85)
REVERT: G   73 GLU cc_start: 0.8866 (tt0) cc_final: 0.8432 (tt0)
REVERT: G   93 GLN cc_start: 0.9466 (tt0) cc_final: 0.9215 (tm-30)
REVERT: G  125 GLN cc_start: 0.9209 (mt0) cc_final: 0.8783 (mp10)
REVERT: H   25 ASN cc_start: 0.8708 (m-40) cc_final: 0.8393 (m110)
REVERT: H   30 THR cc_start: 0.9452 (p) cc_final: 0.8866 (t)
REVERT: H   31 LYS cc_start: 0.9350 (tmtt) cc_final: 0.9137 (tptp)
REVERT: H   39 ARG cc_start: 0.9127 (mmt-90) cc_final: 0.8687 (mmt-90)
REVERT: H   63 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8078 (mp0)
REVERT: H   75 HIS cc_start: 0.8818 (t-90) cc_final: 0.8451 (t70)
REVERT: I   87 VAL cc_start: 0.9629 (m) cc_final: 0.9241 (m)
REVERT: I   90 ASP cc_start: 0.9038 (t70) cc_final: 0.8520 (t0)
REVERT: I   94 ASN cc_start: 0.8878 (t0) cc_final: 0.8147 (m-40)
REVERT: I   95 LYS cc_start: 0.9542 (tptt) cc_final: 0.9271 (ttmm)
REVERT: I  115 LEU cc_start: 0.9396 (mm) cc_final: 0.9053 (mm)
REVERT: J   43 LYS cc_start: 0.9255 (mmtt) cc_final: 0.9019 (mmtp)
REVERT: J   44 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8698 (tm-30)
REVERT: J   65 ASP cc_start: 0.8509 (t70) cc_final: 0.8139 (t70)
REVERT: J   81 ASN cc_start: 0.8881 (m-40) cc_final: 0.8550 (m-40)
REVERT: K   50 GLU cc_start: 0.8796 (tp30) cc_final: 0.8188 (tp30)
REVERT: K   52 ARG cc_start: 0.9193 (mtt90) cc_final: 0.8697 (mtm-85)
REVERT: K   68 GLN cc_start: 0.9313 (pt0) cc_final: 0.9008 (pp30)
REVERT: K   82 LEU cc_start: 0.9361 (mt) cc_final: 0.9135 (mt)
REVERT: K   84 PHE cc_start: 0.9054 (m-10) cc_final: 0.8806 (m-10)
REVERT: K   93 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8708 (tm-30)
REVERT: K   97 GLU cc_start: 0.8935 (tt0) cc_final: 0.8576 (mt-10)
REVERT: K  120 MET cc_start: 0.9382 (mmp) cc_final: 0.8661 (mmm)
REVERT: K  123 ASP cc_start: 0.9317 (m-30) cc_final: 0.8683 (m-30)
REVERT: M   35 ARG cc_start: 0.8839 (mtm110) cc_final: 0.8452 (mtm110)
REVERT: M   36 LYS cc_start: 0.9061 (mttm) cc_final: 0.8704 (tttt)
REVERT: M   56 GLU cc_start: 0.9323 (tt0) cc_final: 0.9047 (mt-10)
REVERT: M   64 GLU cc_start: 0.9444 (tt0) cc_final: 0.9019 (tm-30)
REVERT: M   68 ASN cc_start: 0.9507 (m-40) cc_final: 0.8246 (m-40)
REVERT: M   84 GLN cc_start: 0.9189 (tp40) cc_final: 0.8909 (tp40)
REVERT: M   99 ARG cc_start: 0.8044 (tpt170) cc_final: 0.7808 (tpt170)
REVERT: M  102 ILE cc_start: 0.9692 (tp) cc_final: 0.9418 (tp)
REVERT: N   65 ASP cc_start: 0.9238 (t0) cc_final: 0.8882 (t0)
REVERT: N   68 GLU cc_start: 0.8312 (tp30) cc_final: 0.8085 (tp30)
REVERT: N   80 TYR cc_start: 0.8236 (m-80) cc_final: 0.7642 (m-10)
REVERT: N   83 ARG cc_start: 0.8697 (mmt90) cc_final: 0.8404 (mmm160)
REVERT: N  110 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8462 (tp30)
REVERT: N  113 LYS cc_start: 0.9473 (tmmt) cc_final: 0.9176 (ttpp)
REVERT: L   44 LYS cc_start: 0.9534 (mtpt) cc_final: 0.9012 (mttt)
REVERT: L   63 GLU cc_start: 0.8835 (tp30) cc_final: 0.8485 (tp30)
REVERT: L   77 LYS cc_start: 0.9415 (mmtp) cc_final: 0.9118 (mmtp)
  outliers start: 1
  outliers final: 0
  residues processed: 343
  average time/residue: 0.2803
  time to fit residues: 136.7553
Evaluate side-chains
  306 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 306
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 80 optimal weight:    0.6980
   chunk 60 optimal weight:    0.4980
   chunk 63 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 5 optimal weight:    0.1980
   chunk 113 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 2 optimal weight:    8.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 274 HIS
G  68 GLN
G  76 GLN
G  85 GLN
** J  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 125 GLN
** L  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.059436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.044620 restraints weight = 76300.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.046144 restraints weight = 35685.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.047128 restraints weight = 21851.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.4227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  15271  Z= 0.163
  Angle     :  0.644  13.037  21915  Z= 0.364
  Chirality :  0.038   0.170   2509
  Planarity :  0.005   0.066   1765
  Dihedral  : 29.812 134.351   4372
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.26), residues: 1056
  helix:  1.67 (0.22), residues: 528
  sheet: -1.29 (0.44), residues: 157
  loop : -1.26 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 279 
 HIS   0.011   0.001   HIS G 113 
 PHE   0.018   0.002   PHE N  67 
 TYR   0.027   0.002   TYR A 225 
 ARG   0.014   0.001   ARG N  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05245 (  856)
  hydrogen bonds       : angle       3.67369 ( 2148)
  covalent geometry    : bond        0.00362 (15271)
  covalent geometry    : angle       0.64361 (21915)

********************** 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
  337 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 337
  time to evaluate  : 1.235 
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   26 MET cc_start: 0.8336 (tpp) cc_final: 0.7179 (ptp)
REVERT: A   51 TRP cc_start: 0.7685 (t60) cc_final: 0.7290 (t60)
REVERT: A   81 LEU cc_start: 0.8804 (mt) cc_final: 0.8389 (pp)
REVERT: A  134 MET cc_start: 0.7681 (ttp) cc_final: 0.6553 (mpp)
REVERT: A  242 MET cc_start: 0.7885 (ptp) cc_final: 0.7503 (mpp)
REVERT: A  265 TYR cc_start: 0.7419 (m-10) cc_final: 0.7013 (m-80)
REVERT: A  280 GLU cc_start: 0.8460 (tt0) cc_final: 0.7906 (tt0)
REVERT: G   55 GLN cc_start: 0.9396 (mt0) cc_final: 0.9067 (tt0)
REVERT: G   63 ARG cc_start: 0.8222 (mmt-90) cc_final: 0.7643 (mmm-85)
REVERT: G   73 GLU cc_start: 0.8926 (tt0) cc_final: 0.8519 (tt0)
REVERT: G   93 GLN cc_start: 0.9450 (tt0) cc_final: 0.9000 (tm-30)
REVERT: G   97 GLU cc_start: 0.9041 (tt0) cc_final: 0.8789 (mt-10)
REVERT: H   25 ASN cc_start: 0.8700 (m-40) cc_final: 0.8312 (m-40)
REVERT: H   31 LYS cc_start: 0.9369 (tmtt) cc_final: 0.9109 (tptp)
REVERT: H   52 GLU cc_start: 0.8802 (pm20) cc_final: 0.7735 (pp20)
REVERT: H   63 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8119 (mt-10)
REVERT: H   74 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8819 (tm-30)
REVERT: H   75 HIS cc_start: 0.8715 (t-90) cc_final: 0.8129 (t-90)
REVERT: I   61 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8661 (mm-30)
REVERT: I   73 ASN cc_start: 0.9217 (t0) cc_final: 0.8902 (t0)
REVERT: I   75 LYS cc_start: 0.9493 (mmtm) cc_final: 0.9050 (mmtp)
REVERT: I   87 VAL cc_start: 0.9611 (m) cc_final: 0.9230 (m)
REVERT: I   90 ASP cc_start: 0.8973 (t70) cc_final: 0.8575 (t0)
REVERT: I   94 ASN cc_start: 0.8871 (t0) cc_final: 0.8175 (m-40)
REVERT: I   95 LYS cc_start: 0.9530 (tptt) cc_final: 0.9288 (ttmm)
REVERT: J   44 GLN cc_start: 0.9091 (tm-30) cc_final: 0.8670 (tm-30)
REVERT: J   65 ASP cc_start: 0.8595 (t70) cc_final: 0.8259 (t70)
REVERT: J   81 ASN cc_start: 0.8855 (m-40) cc_final: 0.8449 (m-40)
REVERT: K   50 GLU cc_start: 0.8796 (tp30) cc_final: 0.8072 (tp30)
REVERT: K   52 ARG cc_start: 0.9192 (mtt90) cc_final: 0.8697 (mtm-85)
REVERT: K   56 LYS cc_start: 0.9469 (tptp) cc_final: 0.9183 (tppp)
REVERT: K   68 GLN cc_start: 0.9305 (pt0) cc_final: 0.8994 (pp30)
REVERT: K   82 LEU cc_start: 0.9386 (mt) cc_final: 0.9144 (mt)
REVERT: K   84 PHE cc_start: 0.9033 (m-10) cc_final: 0.8819 (m-10)
REVERT: K   90 MET cc_start: 0.9097 (mtm) cc_final: 0.8701 (mtt)
REVERT: K   93 GLN cc_start: 0.9179 (tm-30) cc_final: 0.8699 (tm-30)
REVERT: K   97 GLU cc_start: 0.8922 (tt0) cc_final: 0.8596 (mt-10)
REVERT: K  108 ASN cc_start: 0.9672 (t0) cc_final: 0.9416 (t0)
REVERT: K  120 MET cc_start: 0.9405 (mmp) cc_final: 0.8678 (mmm)
REVERT: K  123 ASP cc_start: 0.9359 (m-30) cc_final: 0.8750 (m-30)
REVERT: M   35 ARG cc_start: 0.8771 (mtm110) cc_final: 0.8417 (mtm110)
REVERT: M   36 LYS cc_start: 0.9050 (mttm) cc_final: 0.8715 (pttt)
REVERT: M   56 GLU cc_start: 0.9320 (tt0) cc_final: 0.9044 (mt-10)
REVERT: M   64 GLU cc_start: 0.9425 (tt0) cc_final: 0.9064 (tm-30)
REVERT: M   68 ASN cc_start: 0.9529 (m-40) cc_final: 0.8359 (m-40)
REVERT: M   84 GLN cc_start: 0.9178 (tp40) cc_final: 0.8971 (tp40)
REVERT: M   89 ASN cc_start: 0.9006 (m-40) cc_final: 0.8792 (m-40)
REVERT: M   99 ARG cc_start: 0.8046 (tpt170) cc_final: 0.7841 (tpt170)
REVERT: M  102 ILE cc_start: 0.9646 (tp) cc_final: 0.9402 (tp)
REVERT: N   65 ASP cc_start: 0.9256 (t0) cc_final: 0.8887 (t0)
REVERT: N   68 GLU cc_start: 0.8288 (tp30) cc_final: 0.8031 (tp30)
REVERT: N   80 TYR cc_start: 0.8285 (m-80) cc_final: 0.7570 (m-10)
REVERT: N   83 ARG cc_start: 0.8647 (mmt90) cc_final: 0.8371 (mmm160)
REVERT: N  102 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8130 (mm-30)
REVERT: N  105 LYS cc_start: 0.9228 (mttt) cc_final: 0.8449 (mtmm)
REVERT: N  110 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8446 (tp30)
REVERT: L   51 TYR cc_start: 0.8534 (m-80) cc_final: 0.7858 (m-80)
REVERT: L   59 LYS cc_start: 0.9470 (ttmm) cc_final: 0.9150 (ttmt)
REVERT: L   63 GLU cc_start: 0.8841 (tp30) cc_final: 0.8506 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 337
  average time/residue: 0.2931
  time to fit residues: 141.3804
Evaluate side-chains
  300 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 300
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 129 optimal weight:    0.7980
   chunk 125 optimal weight:    0.9980
   chunk 15 optimal weight:    8.9990
   chunk 53 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   chunk 108 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 274 HIS
G  68 GLN
G  85 GLN
G 108 ASN
** J  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 125 GLN
N  60 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 = 0.3272 r_free = 0.3272 target = 0.059060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.044147 restraints weight = 76746.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.045675 restraints weight = 35885.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.046654 restraints weight = 21931.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.4302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  15271  Z= 0.177
  Angle     :  0.647  14.182  21915  Z= 0.365
  Chirality :  0.038   0.168   2509
  Planarity :  0.005   0.067   1765
  Dihedral  : 29.786 138.361   4372
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.45 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.26), residues: 1056
  helix:  1.63 (0.22), residues: 526
  sheet: -1.25 (0.44), residues: 157
  loop : -1.13 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 279 
 HIS   0.007   0.001   HIS G 113 
 PHE   0.020   0.002   PHE J  62 
 TYR   0.038   0.003   TYR H  88 
 ARG   0.014   0.001   ARG N  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05314 (  856)
  hydrogen bonds       : angle       3.75057 ( 2148)
  covalent geometry    : bond        0.00394 (15271)
  covalent geometry    : angle       0.64675 (21915)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5153.39 seconds
wall clock time: 90 minutes 10.32 seconds (5410.32 seconds total)