Starting phenix.real_space_refine
on Thu Jul 24 10:05:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6y9a_10734/07_2025/6y9a_10734.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6y9a_10734/07_2025/6y9a_10734.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/6y9a_10734/07_2025/6y9a_10734.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6y9a_10734/07_2025/6y9a_10734.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6y9a_10734/07_2025/6y9a_10734.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6y9a_10734/07_2025/6y9a_10734.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=   0.002 sd=   0.040
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    3829      2.51       5
     N     965      2.21       5
     O    1113      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5948
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1310
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 1310
          Classifications: {'peptide': 169}
          Link IDs: {'PTRANS': 7, 'TRANS': 161}
    Chain: "B"
      Number of atoms: 1310
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 1310
          Classifications: {'peptide': 169}
          Link IDs: {'PTRANS': 7, 'TRANS': 161}
    Chain: "H"
      Number of atoms: 1644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1644
          Classifications: {'peptide': 219}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206}
          Unresolved chain link angles: 2
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 2
    Chain: "L"
      Number of atoms: 1684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1684
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 205}
  Time building chain proxies: 4.85, per 1000 atoms: 0.82
  Number of scatterers: 5948
  At special positions: 0
  Unit cell: (61.864, 70.004, 154.66, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      41     16.00
     O    1113      8.00
     N     965      7.00
     C    3829      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 167 " - pdb=" SG  CYS A 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 167 " - pdb=" SG  CYS B 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 146 " - pdb=" SG  CYS H 202 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 139 " - pdb=" SG  CYS L 199 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.40
  Conformation dependent library (CDL) restraints added in 902.4 milliseconds
  

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1430

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 11 sheets defined
      37.8% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 51
      removed outlier: 5.150A  pdb=" N   LYS A  50 " --> pdb=" O   ARG A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 71
    Processing helix  chain 'A' and resid 79 through 84
      removed outlier: 3.617A  pdb=" N   THR A  83 " --> pdb=" O   PRO A  79 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   VAL A  84 " --> pdb=" O   ILE A  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 79 through 84'
    Processing helix  chain 'A' and resid 85 through 103
      removed outlier: 3.865A  pdb=" N   TRP A  89 " --> pdb=" O   TRP A  85 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   LEU A 101 " --> pdb=" O   SER A  97 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ALA A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 143
      removed outlier: 3.917A  pdb=" N   LEU A 139 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 157
    Processing helix  chain 'A' and resid 171 through 176
      removed outlier: 4.401A  pdb=" N   ASN A 176 " --> pdb=" O   SER A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 210
    Processing helix  chain 'B' and resid 45 through 51
      removed outlier: 5.825A  pdb=" N   LYS B  50 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 71
    Processing helix  chain 'B' and resid 79 through 84
      removed outlier: 3.646A  pdb=" N   VAL B  84 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 100
      removed outlier: 4.051A  pdb=" N   TRP B  89 " --> pdb=" O   TRP B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 143
      removed outlier: 3.710A  pdb=" N   LYS B 114 " --> pdb=" O   LYS B 110 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   LEU B 139 " --> pdb=" O   ILE B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 157
    Processing helix  chain 'B' and resid 171 through 176
      removed outlier: 4.078A  pdb=" N   ASN B 176 " --> pdb=" O   SER B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 212
      removed outlier: 3.585A  pdb=" N   GLN B 181 " --> pdb=" O   SER B 177 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 162 through 164
      No H-bonds generated for 'chain 'H' and resid 162 through 164'
    Processing helix  chain 'H' and resid 193 through 195
      No H-bonds generated for 'chain 'H' and resid 193 through 195'
    Processing helix  chain 'L' and resid 126 through 133
    Processing helix  chain 'L' and resid 188 through 193
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.723A  pdb=" N   LYS H  12 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   TRP H  36 " --> pdb=" O   GLY H  49 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.546A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ASP H  59 " --> pdb=" O   ARG H  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 19 through 21
      removed outlier: 3.900A  pdb=" N   VAL H  20 " --> pdb=" O   MET H  81 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   MET H  81 " --> pdb=" O   VAL H  20 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   TYR H  80 " --> pdb=" O   THR H  71 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   THR H  71 " --> pdb=" O   TYR H  80 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   GLU H  82 " --> pdb=" O   THR H  69 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   THR H  69 " --> pdb=" O   GLU H  82 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 126 through 130
      removed outlier: 3.563A  pdb=" N   LEU H 130 " --> pdb=" O   GLY H 145 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   GLY H 145 " --> pdb=" O   LEU H 130 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   ALA H 143 " --> pdb=" O   VAL H 190 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   VAL H 190 " --> pdb=" O   ALA H 143 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   GLY H 145 " --> pdb=" O   VAL H 188 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   VAL H 188 " --> pdb=" O   GLY H 145 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   LEU H 147 " --> pdb=" O   SER H 186 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   SER H 186 " --> pdb=" O   LEU H 147 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   LYS H 149 " --> pdb=" O   LEU H 184 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   LEU H 184 " --> pdb=" O   LYS H 149 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 157 through 160
      removed outlier: 3.635A  pdb=" N   THR H 157 " --> pdb=" O   ASN H 205 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   VAL H 204 " --> pdb=" O   VAL H 213 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   VAL H 213 " --> pdb=" O   VAL H 204 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 7
      removed outlier: 4.739A  pdb=" N   THR L   5 " --> pdb=" O   ARG L  24 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ARG L  24 " --> pdb=" O   THR L   5 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   THR L   7 " --> pdb=" O   SER L  22 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   SER L  22 " --> pdb=" O   THR L   7 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.572A  pdb=" N   LEU L  11 " --> pdb=" O   LYS L 108 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLU L 110 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   GLY L  89 " --> pdb=" O   VAL L 109 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   TYR L  39 " --> pdb=" O   ALA L  94 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   TRP L  40 " --> pdb=" O   LEU L  52 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.572A  pdb=" N   LEU L  11 " --> pdb=" O   LYS L 108 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLU L 110 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   GLY L  89 " --> pdb=" O   VAL L 109 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLN L  95 " --> pdb=" O   THR L 102 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   THR L 102 " --> pdb=" O   GLN L  95 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 68 through 71
    Processing sheet with id=AB1, first strand: chain 'L' and resid 120 through 123
      removed outlier: 3.646A  pdb=" N   PHE L 123 " --> pdb=" O   VAL L 138 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   VAL L 138 " --> pdb=" O   PHE L 123 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU L 184 " --> pdb=" O   VAL L 137 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   CYS L 139 " --> pdb=" O   SER L 182 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   SER L 182 " --> pdb=" O   CYS L 139 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LEU L 141 " --> pdb=" O   LEU L 180 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   ASN L 143 " --> pdb=" O   TYR L 178 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   TYR L 178 " --> pdb=" O   ASN L 143 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 158 through 159
      removed outlier: 3.972A  pdb=" N   LYS L 150 " --> pdb=" O   THR L 202 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   THR L 202 " --> pdb=" O   LYS L 150 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLN L 152 " --> pdb=" O   GLU L 200 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU L 200 " --> pdb=" O   GLN L 152 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS L 154 " --> pdb=" O   ALA L 198 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   TYR L 197 " --> pdb=" O   PHE L 214 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   PHE L 214 " --> pdb=" O   TYR L 197 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LYS L 212 " --> pdb=" O   CYS L 199 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   VAL L 210 " --> pdb=" O   VAL L 201 " (cutoff:3.500A)

    267 hydrogen bonds defined for protein.
    717 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.55

  Time building geometry restraints manager: 1.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1839
        1.34 -     1.46: 1465
        1.46 -     1.58: 2714
        1.58 -     1.70: 2
        1.70 -     1.82: 65
  Bond restraints: 6085
  Sorted by residual:
  bond pdb=" CB  PRO A  79 "
       pdb=" CG  PRO A  79 "
    ideal  model  delta    sigma   weight residual
    1.492  1.599 -0.107 5.00e-02 4.00e+02 4.61e+00
  bond pdb=" CB  PRO A  73 "
       pdb=" CG  PRO A  73 "
    ideal  model  delta    sigma   weight residual
    1.492  1.588 -0.096 5.00e-02 4.00e+02 3.70e+00
  bond pdb=" CG1 ILE A 141 "
       pdb=" CD1 ILE A 141 "
    ideal  model  delta    sigma   weight residual
    1.513  1.465  0.048 3.90e-02 6.57e+02 1.50e+00
  bond pdb=" CA  THR B 180 "
       pdb=" C   THR B 180 "
    ideal  model  delta    sigma   weight residual
    1.520  1.504  0.015 1.40e-02 5.10e+03 1.21e+00
  bond pdb=" N   PRO B  73 "
       pdb=" CA  PRO B  73 "
    ideal  model  delta    sigma   weight residual
    1.469  1.482 -0.013 1.28e-02 6.10e+03 1.10e+00
  ... (remaining 6080 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 7992
        2.04 -     4.09: 221
        4.09 -     6.13: 35
        6.13 -     8.18: 7
        8.18 -    10.22: 2
  Bond angle restraints: 8257
  Sorted by residual:
  angle pdb=" CA  PRO A  79 "
        pdb=" N   PRO A  79 "
        pdb=" CD  PRO A  79 "
      ideal   model   delta    sigma   weight residual
     112.00  105.14    6.86 1.40e+00 5.10e-01 2.40e+01
  angle pdb=" CA  PRO A  73 "
        pdb=" N   PRO A  73 "
        pdb=" CD  PRO A  73 "
      ideal   model   delta    sigma   weight residual
     112.00  105.64    6.36 1.40e+00 5.10e-01 2.06e+01
  angle pdb=" N   LYS B 148 "
        pdb=" CA  LYS B 148 "
        pdb=" C   LYS B 148 "
      ideal   model   delta    sigma   weight residual
     111.03  115.64   -4.61 1.11e+00 8.12e-01 1.73e+01
  angle pdb=" N   GLN A 181 "
        pdb=" CA  GLN A 181 "
        pdb=" C   GLN A 181 "
      ideal   model   delta    sigma   weight residual
     111.28  106.77    4.51 1.09e+00 8.42e-01 1.71e+01
  angle pdb=" N   GLN B 181 "
        pdb=" CA  GLN B 181 "
        pdb=" C   GLN B 181 "
      ideal   model   delta    sigma   weight residual
     111.28  107.01    4.27 1.09e+00 8.42e-01 1.54e+01
  ... (remaining 8252 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.24: 3284
       17.24 -    34.48: 278
       34.48 -    51.72: 61
       51.72 -    68.96: 10
       68.96 -    86.20: 7
  Dihedral angle restraints: 3640
    sinusoidal: 1404
      harmonic: 2236
  Sorted by residual:
  dihedral pdb=" CB  CYS L 139 "
           pdb=" SG  CYS L 139 "
           pdb=" SG  CYS L 199 "
           pdb=" CB  CYS L 199 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  176.92  -83.92     1      1.00e+01 1.00e-02 8.58e+01
  dihedral pdb=" CB  CYS H 146 "
           pdb=" SG  CYS H 146 "
           pdb=" SG  CYS H 202 "
           pdb=" CB  CYS H 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   16.07   76.93     1      1.00e+01 1.00e-02 7.43e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   18.32   74.68     1      1.00e+01 1.00e-02 7.06e+01
  ... (remaining 3637 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 750
       0.058 -    0.116: 171
       0.116 -    0.175: 20
       0.175 -    0.233: 3
       0.233 -    0.291: 1
  Chirality restraints: 945
  Sorted by residual:
  chirality pdb=" CG  LEU B 122 "
            pdb=" CB  LEU B 122 "
            pdb=" CD1 LEU B 122 "
            pdb=" CD2 LEU B 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.30   -0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CB  VAL H 190 "
            pdb=" CA  VAL H 190 "
            pdb=" CG1 VAL H 190 "
            pdb=" CG2 VAL H 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  GLN L  55 "
            pdb=" N   GLN L  55 "
            pdb=" C   GLN L  55 "
            pdb=" CB  GLN L  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.98e-01
  ... (remaining 942 not shown)

  Planarity restraints: 1030
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 179 "    0.031 2.00e-02 2.50e+03   6.11e-02 3.73e+01
        pdb=" C   SER B 179 "   -0.106 2.00e-02 2.50e+03
        pdb=" O   SER B 179 "    0.038 2.00e-02 2.50e+03
        pdb=" N   THR B 180 "    0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 179 "   -0.028 2.00e-02 2.50e+03   5.47e-02 3.00e+01
        pdb=" C   SER A 179 "    0.095 2.00e-02 2.50e+03
        pdb=" O   SER A 179 "   -0.035 2.00e-02 2.50e+03
        pdb=" N   THR A 180 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 116 "   -0.026 2.00e-02 2.50e+03   5.19e-02 2.69e+01
        pdb=" C   LYS B 116 "    0.090 2.00e-02 2.50e+03
        pdb=" O   LYS B 116 "   -0.034 2.00e-02 2.50e+03
        pdb=" N   MET B 117 "   -0.030 2.00e-02 2.50e+03
  ... (remaining 1027 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 566
        2.75 -     3.29: 6136
        3.29 -     3.82: 9405
        3.82 -     4.36: 10399
        4.36 -     4.90: 17289
  Nonbonded interactions: 43795
  Sorted by model distance:
  nonbonded pdb=" O   GLY H 103 "
            pdb=" OH  TYR L  39 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   TYR L 191 "
            pdb=" OH  TYR L 197 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" O   HIS L 194 "
            pdb=" NH2 ARG L 216 "
     model   vdw
     2.281 3.120
  nonbonded pdb=" OG1 THR H 199 "
            pdb=" OE2 GLU H 218 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" ND2 ASN A 163 "
            pdb=" OD1 ASN A 166 "
     model   vdw
     2.328 3.120
  ... (remaining 43790 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 'A'
  selection = chain 'B'
}

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:             3.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.660
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4803
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      :  0.004   0.107   6091  Z= 0.153
  Angle     :  0.809  10.221   8269  Z= 0.443
  Chirality :  0.050   0.291    945
  Planarity :  0.008   0.127   1030
  Dihedral  : 13.593  86.201   2192
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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: -1.17 (0.29), residues: 766
  helix: -0.51 (0.30), residues: 228
  sheet:  0.10 (0.38), residues: 174
  loop : -1.35 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP H 109 
 HIS   0.005   0.001   HIS B  63 
 PHE   0.040   0.002   PHE B  62 
 TYR   0.014   0.001   TYR L 197 
 ARG   0.005   0.001   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19682 (  263)
  hydrogen bonds       : angle       6.69154 (  717)
  SS BOND              : bond        0.00433 (    6)
  SS BOND              : angle       1.14637 (   12)
  covalent geometry    : bond        0.00353 ( 6085)
  covalent geometry    : angle       0.80880 ( 8257)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 MET cc_start: 0.4432 (mmm) cc_final: 0.4113 (mmm)
REVERT: A  117 MET cc_start: 0.8031 (ptt) cc_final: 0.6042 (tpt)
REVERT: B  149 MET cc_start: 0.7266 (mpp) cc_final: 0.6631 (mpp)
REVERT: L   42 LEU cc_start: 0.6631 (tt) cc_final: 0.6234 (tt)
REVERT: L   56 MET cc_start: 0.7262 (tmm) cc_final: 0.7059 (tmm)
REVERT: L  146 PRO cc_start: 0.6978 (Cg_endo) cc_final: 0.6457 (Cg_exo)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.1484
  time to fit residues: 38.4377
Evaluate side-chains
  155 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 56 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0270
   chunk 37 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0870
   chunk 22 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 43 optimal weight:    7.9990
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
A 204 GLN
B 120 ASN
H  39 GLN
H 161 ASN
L  47 GLN
L 194 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.157036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.123958 restraints weight = 15121.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.129228 restraints weight = 10284.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.133422 restraints weight = 7458.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6393
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6091  Z= 0.119
  Angle     :  0.612   6.655   8269  Z= 0.318
  Chirality :  0.044   0.167    945
  Planarity :  0.006   0.068   1030
  Dihedral  :  4.564  18.461    824
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  4.80 %
    Favored  : 95.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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: -0.10 (0.30), residues: 766
  helix:  0.91 (0.32), residues: 245
  sheet:  0.76 (0.42), residues: 157
  loop : -1.13 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP H  33 
 HIS   0.003   0.001   HIS B 158 
 PHE   0.024   0.002   PHE B  62 
 TYR   0.017   0.001   TYR L  54 
 ARG   0.010   0.001   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03632 (  263)
  hydrogen bonds       : angle       4.70063 (  717)
  SS BOND              : bond        0.00420 (    6)
  SS BOND              : angle       0.90064 (   12)
  covalent geometry    : bond        0.00258 ( 6085)
  covalent geometry    : angle       0.61175 ( 8257)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 192
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.7781 (ptt) cc_final: 0.6449 (tpt)
REVERT: A  119 MET cc_start: 0.8975 (mmp) cc_final: 0.8731 (mmm)
REVERT: A  164 ILE cc_start: 0.8093 (mt) cc_final: 0.7821 (mp)
REVERT: A  176 ASN cc_start: 0.8105 (m-40) cc_final: 0.7667 (m-40)
REVERT: A  190 PHE cc_start: 0.8884 (m-10) cc_final: 0.8492 (m-80)
REVERT: B   58 MET cc_start: 0.8733 (ttm) cc_final: 0.8364 (ttt)
REVERT: B   62 PHE cc_start: 0.8592 (m-80) cc_final: 0.8161 (m-80)
REVERT: B  119 MET cc_start: 0.8560 (tpt) cc_final: 0.8332 (tpt)
REVERT: B  131 MET cc_start: 0.7654 (mmp) cc_final: 0.7332 (mmm)
REVERT: B  149 MET cc_start: 0.7360 (mpp) cc_final: 0.6688 (mpp)
REVERT: B  150 GLU cc_start: 0.7708 (pp20) cc_final: 0.7346 (pp20)
REVERT: B  184 TYR cc_start: 0.8219 (m-10) cc_final: 0.7776 (m-10)
REVERT: B  211 ILE cc_start: 0.7435 (mm) cc_final: 0.7226 (mm)
REVERT: H   36 TRP cc_start: 0.8072 (m100) cc_final: 0.7474 (m100)
REVERT: H   73 ASP cc_start: 0.9286 (t0) cc_final: 0.8995 (t0)
REVERT: H   99 ASN cc_start: 0.8303 (t0) cc_final: 0.7592 (p0)
REVERT: H  100 VAL cc_start: 0.8881 (t) cc_final: 0.8290 (t)
REVERT: H  128 PHE cc_start: 0.8829 (m-80) cc_final: 0.8627 (m-80)
REVERT: H  201 ILE cc_start: 0.8364 (tp) cc_final: 0.8065 (tp)
REVERT: L   79 LYS cc_start: 0.7885 (tptt) cc_final: 0.7266 (tppt)
REVERT: L   80 ILE cc_start: 0.7223 (mp) cc_final: 0.6794 (mm)
REVERT: L   91 TYR cc_start: 0.9095 (m-10) cc_final: 0.8430 (m-80)
REVERT: L  123 PHE cc_start: 0.8136 (m-80) cc_final: 0.7710 (m-80)
REVERT: L  175 ASP cc_start: 0.8709 (m-30) cc_final: 0.8467 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 192
  average time/residue: 0.1386
  time to fit residues: 36.5412
Evaluate side-chains
  158 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 6 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 34 optimal weight:   20.0000
   chunk 31 optimal weight:    3.9990
   chunk 55 optimal weight:    8.9990
   chunk 69 optimal weight:    6.9990
   chunk 40 optimal weight:    8.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 145 HIS
** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  58 ASN
L  95 GLN
L 143 ASN
** L 171 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 = 0.3970 r_free = 0.3970 target = 0.122352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.092193 restraints weight = 15588.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.096711 restraints weight = 9978.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.100175 restraints weight = 7019.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6896
moved from start:          0.5316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.075   6091  Z= 0.333
  Angle     :  0.910   8.787   8269  Z= 0.481
  Chirality :  0.050   0.224    945
  Planarity :  0.007   0.059   1030
  Dihedral  :  5.906  26.108    824
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 27.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  6.30 %
    Favored  : 93.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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: -0.80 (0.30), residues: 766
  helix:  0.05 (0.30), residues: 256
  sheet: -0.13 (0.36), residues: 195
  loop : -1.17 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.004   TRP B  89 
 HIS   0.012   0.002   HIS L  31 
 PHE   0.032   0.003   PHE L 103 
 TYR   0.027   0.003   TYR L 197 
 ARG   0.010   0.001   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04864 (  263)
  hydrogen bonds       : angle       5.72691 (  717)
  SS BOND              : bond        0.00512 (    6)
  SS BOND              : angle       1.94025 (   12)
  covalent geometry    : bond        0.00709 ( 6085)
  covalent geometry    : angle       0.90812 ( 8257)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 180
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 ASN cc_start: 0.8737 (m-40) cc_final: 0.8391 (m-40)
REVERT: A  184 TYR cc_start: 0.8058 (m-10) cc_final: 0.7647 (m-10)
REVERT: A  190 PHE cc_start: 0.9548 (m-10) cc_final: 0.9219 (m-80)
REVERT: B  119 MET cc_start: 0.8961 (tpt) cc_final: 0.8638 (tpt)
REVERT: B  131 MET cc_start: 0.8434 (mmp) cc_final: 0.8218 (mmm)
REVERT: B  140 ASN cc_start: 0.8113 (m110) cc_final: 0.7911 (m-40)
REVERT: B  149 MET cc_start: 0.7149 (mpp) cc_final: 0.6899 (mpp)
REVERT: B  158 HIS cc_start: 0.6529 (t-170) cc_final: 0.6295 (p-80)
REVERT: B  161 TYR cc_start: 0.8205 (m-80) cc_final: 0.7571 (m-80)
REVERT: B  174 GLU cc_start: 0.9195 (mp0) cc_final: 0.8856 (mp0)
REVERT: B  184 TYR cc_start: 0.8382 (m-10) cc_final: 0.8158 (m-10)
REVERT: B  188 SER cc_start: 0.9247 (t) cc_final: 0.8914 (p)
REVERT: H    3 GLN cc_start: 0.8652 (mp10) cc_final: 0.8365 (mp10)
REVERT: H   22 CYS cc_start: 0.6365 (p) cc_final: 0.6055 (p)
REVERT: H   36 TRP cc_start: 0.8732 (m100) cc_final: 0.7860 (m100)
REVERT: H   47 TRP cc_start: 0.9144 (t60) cc_final: 0.8202 (t60)
REVERT: H   57 ASP cc_start: 0.8474 (m-30) cc_final: 0.8215 (m-30)
REVERT: H   73 ASP cc_start: 0.9302 (t0) cc_final: 0.9020 (t0)
REVERT: H  101 PHE cc_start: 0.8627 (m-80) cc_final: 0.7979 (m-80)
REVERT: H  216 LYS cc_start: 0.8554 (tmtt) cc_final: 0.8342 (pttt)
REVERT: L   40 TRP cc_start: 0.8080 (m100) cc_final: 0.7507 (m100)
REVERT: L   76 PHE cc_start: 0.8123 (m-80) cc_final: 0.7862 (m-80)
REVERT: L   93 CYS cc_start: 0.3970 (m) cc_final: 0.1743 (m)
REVERT: L  101 TYR cc_start: 0.8009 (m-10) cc_final: 0.7757 (m-10)
REVERT: L  150 LYS cc_start: 0.8551 (tttm) cc_final: 0.8255 (tmtt)
  outliers start: 1
  outliers final: 0
  residues processed: 181
  average time/residue: 0.1541
  time to fit residues: 37.9156
Evaluate side-chains
  147 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0670
   chunk 69 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   chunk 16 optimal weight:    0.3980
   chunk 42 optimal weight:    0.9980
   chunk 0 optimal weight:    9.9990
   chunk 71 optimal weight:    9.9990
   chunk 58 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.8922

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

Flipped N/Q/H residues before XYZ refinement:
** A  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  47 GLN
L 143 ASN
** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.129843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.098715 restraints weight = 15882.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.103674 restraints weight = 10162.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.107515 restraints weight = 7200.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6731
moved from start:          0.5177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6091  Z= 0.126
  Angle     :  0.636   7.092   8269  Z= 0.327
  Chirality :  0.044   0.186    945
  Planarity :  0.005   0.058   1030
  Dihedral  :  4.831  18.847    824
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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: -0.23 (0.30), residues: 766
  helix:  0.76 (0.32), residues: 260
  sheet:  0.02 (0.37), residues: 197
  loop : -0.98 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  89 
 HIS   0.008   0.001   HIS A  63 
 PHE   0.016   0.001   PHE B  62 
 TYR   0.018   0.002   TYR A  86 
 ARG   0.008   0.001   ARG H  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03781 (  263)
  hydrogen bonds       : angle       4.62918 (  717)
  SS BOND              : bond        0.00503 (    6)
  SS BOND              : angle       1.21636 (   12)
  covalent geometry    : bond        0.00281 ( 6085)
  covalent geometry    : angle       0.63506 ( 8257)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 TRP cc_start: 0.8839 (m-10) cc_final: 0.8575 (m100)
REVERT: A  190 PHE cc_start: 0.9438 (m-10) cc_final: 0.9134 (m-80)
REVERT: B  119 MET cc_start: 0.8666 (tpt) cc_final: 0.8191 (tpt)
REVERT: B  140 ASN cc_start: 0.8112 (m110) cc_final: 0.7882 (m110)
REVERT: B  149 MET cc_start: 0.6609 (mpp) cc_final: 0.5965 (mpp)
REVERT: B  150 GLU cc_start: 0.7219 (pp20) cc_final: 0.6716 (pp20)
REVERT: B  161 TYR cc_start: 0.8004 (m-80) cc_final: 0.7540 (m-80)
REVERT: B  168 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8219 (mm-30)
REVERT: B  176 ASN cc_start: 0.7909 (m-40) cc_final: 0.7298 (p0)
REVERT: B  184 TYR cc_start: 0.8473 (m-10) cc_final: 0.8124 (m-10)
REVERT: B  188 SER cc_start: 0.9174 (t) cc_final: 0.8861 (p)
REVERT: B  211 ILE cc_start: 0.7691 (mm) cc_final: 0.7454 (mm)
REVERT: H    3 GLN cc_start: 0.8627 (mp10) cc_final: 0.8343 (pm20)
REVERT: H   36 TRP cc_start: 0.8832 (m100) cc_final: 0.7719 (m100)
REVERT: H   47 TRP cc_start: 0.8877 (t60) cc_final: 0.7570 (t60)
REVERT: H   73 ASP cc_start: 0.9280 (t0) cc_final: 0.8990 (t0)
REVERT: H  101 PHE cc_start: 0.8773 (m-80) cc_final: 0.8213 (m-80)
REVERT: L   40 TRP cc_start: 0.8182 (m100) cc_final: 0.7579 (m100)
REVERT: L   56 MET cc_start: 0.8876 (tmm) cc_final: 0.8467 (tmm)
REVERT: L   70 SER cc_start: 0.8597 (p) cc_final: 0.8357 (p)
REVERT: L   79 LYS cc_start: 0.8262 (tptt) cc_final: 0.8060 (tptt)
REVERT: L   87 ASP cc_start: 0.7471 (p0) cc_final: 0.6942 (p0)
REVERT: L  123 PHE cc_start: 0.9016 (m-80) cc_final: 0.8730 (m-80)
REVERT: L  148 GLU cc_start: 0.9521 (mp0) cc_final: 0.9298 (mp0)
REVERT: L  150 LYS cc_start: 0.8472 (tttm) cc_final: 0.8226 (tmtt)
REVERT: L  175 ASP cc_start: 0.8912 (m-30) cc_final: 0.8662 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.1381
  time to fit residues: 37.2665
Evaluate side-chains
  160 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 1.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 52 optimal weight:   20.0000
   chunk 34 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 143 ASN
** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.119794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.089936 restraints weight = 16615.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.094607 restraints weight = 10380.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.098119 restraints weight = 7209.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.6297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.084   6091  Z= 0.241
  Angle     :  0.745   7.476   8269  Z= 0.391
  Chirality :  0.046   0.174    945
  Planarity :  0.006   0.060   1030
  Dihedral  :  5.356  21.643    824
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 23.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.66 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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: -0.61 (0.30), residues: 766
  helix:  0.35 (0.31), residues: 256
  sheet: -0.34 (0.36), residues: 197
  loop : -0.97 (0.37), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP B  89 
 HIS   0.006   0.001   HIS L  31 
 PHE   0.019   0.002   PHE L  76 
 TYR   0.023   0.002   TYR L  54 
 ARG   0.004   0.001   ARG H  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04437 (  263)
  hydrogen bonds       : angle       5.27059 (  717)
  SS BOND              : bond        0.00870 (    6)
  SS BOND              : angle       2.97919 (   12)
  covalent geometry    : bond        0.00515 ( 6085)
  covalent geometry    : angle       0.73722 ( 8257)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 HIS cc_start: 0.8977 (m-70) cc_final: 0.7746 (m-70)
REVERT: A   85 TRP cc_start: 0.8993 (m-10) cc_final: 0.8652 (m100)
REVERT: A  176 ASN cc_start: 0.8756 (m-40) cc_final: 0.8501 (m-40)
REVERT: A  184 TYR cc_start: 0.8231 (m-10) cc_final: 0.7920 (m-10)
REVERT: A  190 PHE cc_start: 0.9570 (m-10) cc_final: 0.9243 (m-80)
REVERT: B   58 MET cc_start: 0.9228 (ttp) cc_final: 0.8902 (ttp)
REVERT: B  149 MET cc_start: 0.6862 (mpp) cc_final: 0.6648 (mpp)
REVERT: B  161 TYR cc_start: 0.8371 (m-80) cc_final: 0.7867 (m-80)
REVERT: B  176 ASN cc_start: 0.7855 (m-40) cc_final: 0.7256 (p0)
REVERT: B  184 TYR cc_start: 0.8863 (m-10) cc_final: 0.8438 (m-10)
REVERT: B  188 SER cc_start: 0.9221 (t) cc_final: 0.8880 (p)
REVERT: H    3 GLN cc_start: 0.8761 (mp10) cc_final: 0.8370 (mp10)
REVERT: H   36 TRP cc_start: 0.8806 (m100) cc_final: 0.7796 (m100)
REVERT: H   47 TRP cc_start: 0.8900 (t60) cc_final: 0.7984 (t60)
REVERT: H   57 ASP cc_start: 0.8527 (m-30) cc_final: 0.8303 (m-30)
REVERT: H   73 ASP cc_start: 0.9293 (t0) cc_final: 0.8989 (t0)
REVERT: H  101 PHE cc_start: 0.8784 (m-80) cc_final: 0.7959 (m-80)
REVERT: H  216 LYS cc_start: 0.8758 (tmtt) cc_final: 0.8453 (ptpt)
REVERT: L   40 TRP cc_start: 0.8276 (m100) cc_final: 0.7727 (m100)
REVERT: L   76 PHE cc_start: 0.8237 (m-80) cc_final: 0.7921 (m-80)
REVERT: L   87 ASP cc_start: 0.7255 (p0) cc_final: 0.7050 (p0)
REVERT: L   93 CYS cc_start: 0.5786 (t) cc_final: 0.4736 (t)
REVERT: L  123 PHE cc_start: 0.9052 (m-80) cc_final: 0.8819 (m-80)
REVERT: L  148 GLU cc_start: 0.9515 (mp0) cc_final: 0.9210 (mp0)
REVERT: L  150 LYS cc_start: 0.8616 (tttm) cc_final: 0.8403 (tmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1612
  time to fit residues: 40.9989
Evaluate side-chains
  147 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0170
   chunk 32 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.9624

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.121341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.090469 restraints weight = 15883.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.095254 restraints weight = 9988.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.098910 restraints weight = 6998.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6847
moved from start:          0.6590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6091  Z= 0.163
  Angle     :  0.671   8.215   8269  Z= 0.349
  Chirality :  0.044   0.179    945
  Planarity :  0.005   0.061   1030
  Dihedral  :  5.065  20.785    824
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 17.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.31), residues: 766
  helix:  0.36 (0.32), residues: 256
  sheet: -0.34 (0.36), residues: 199
  loop : -1.16 (0.37), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  89 
 HIS   0.002   0.001   HIS A  63 
 PHE   0.013   0.002   PHE A  62 
 TYR   0.019   0.002   TYR L  54 
 ARG   0.004   0.001   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04180 (  263)
  hydrogen bonds       : angle       4.95675 (  717)
  SS BOND              : bond        0.00360 (    6)
  SS BOND              : angle       1.39659 (   12)
  covalent geometry    : bond        0.00353 ( 6085)
  covalent geometry    : angle       0.66910 ( 8257)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.603 
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   63 HIS cc_start: 0.9066 (m-70) cc_final: 0.7794 (m90)
REVERT: A   85 TRP cc_start: 0.8918 (m-10) cc_final: 0.8568 (m100)
REVERT: A  176 ASN cc_start: 0.8431 (m-40) cc_final: 0.8133 (m-40)
REVERT: A  190 PHE cc_start: 0.9577 (m-10) cc_final: 0.9247 (m-80)
REVERT: B   58 MET cc_start: 0.9221 (ttp) cc_final: 0.8928 (ttp)
REVERT: B  161 TYR cc_start: 0.8393 (m-80) cc_final: 0.7640 (m-80)
REVERT: B  171 ASN cc_start: 0.8691 (p0) cc_final: 0.7861 (p0)
REVERT: B  176 ASN cc_start: 0.7974 (m-40) cc_final: 0.7252 (p0)
REVERT: B  184 TYR cc_start: 0.8577 (m-10) cc_final: 0.8109 (m-10)
REVERT: B  188 SER cc_start: 0.9182 (t) cc_final: 0.8893 (p)
REVERT: H    3 GLN cc_start: 0.8771 (mp10) cc_final: 0.8378 (mp10)
REVERT: H   47 TRP cc_start: 0.8877 (t60) cc_final: 0.7981 (t60)
REVERT: H   57 ASP cc_start: 0.8414 (m-30) cc_final: 0.8201 (m-30)
REVERT: H   73 ASP cc_start: 0.9211 (t0) cc_final: 0.8926 (t0)
REVERT: H   81 MET cc_start: 0.7042 (tpt) cc_final: 0.6841 (tpt)
REVERT: H  101 PHE cc_start: 0.8805 (m-80) cc_final: 0.8287 (m-80)
REVERT: H  102 ASP cc_start: 0.8733 (t70) cc_final: 0.8107 (t0)
REVERT: H  150 ASP cc_start: 0.7231 (m-30) cc_final: 0.7030 (m-30)
REVERT: H  216 LYS cc_start: 0.8745 (tmtt) cc_final: 0.8494 (ptpt)
REVERT: L   40 TRP cc_start: 0.8143 (m100) cc_final: 0.7656 (m100)
REVERT: L   56 MET cc_start: 0.8798 (tmm) cc_final: 0.8199 (tmm)
REVERT: L   76 PHE cc_start: 0.8296 (m-80) cc_final: 0.8084 (m-80)
REVERT: L   93 CYS cc_start: 0.5562 (t) cc_final: 0.4151 (t)
REVERT: L  101 TYR cc_start: 0.8852 (m-10) cc_final: 0.8274 (m-80)
REVERT: L  123 PHE cc_start: 0.8978 (m-80) cc_final: 0.8767 (m-80)
REVERT: L  148 GLU cc_start: 0.9512 (mp0) cc_final: 0.9204 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.1665
  time to fit residues: 41.8191
Evaluate side-chains
  151 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
** L  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.125421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.093393 restraints weight = 15491.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.098590 restraints weight = 9699.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.102439 restraints weight = 6745.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6864
moved from start:          0.6475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6091  Z= 0.123
  Angle     :  0.631   6.490   8269  Z= 0.323
  Chirality :  0.044   0.176    945
  Planarity :  0.005   0.056   1030
  Dihedral  :  4.732  19.064    824
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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 (0.30), residues: 766
  helix:  0.63 (0.32), residues: 258
  sheet: -0.25 (0.36), residues: 199
  loop : -1.17 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  89 
 HIS   0.004   0.001   HIS A  63 
 PHE   0.014   0.002   PHE B  62 
 TYR   0.014   0.001   TYR L  54 
 ARG   0.004   0.001   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03743 (  263)
  hydrogen bonds       : angle       4.62274 (  717)
  SS BOND              : bond        0.00257 (    6)
  SS BOND              : angle       1.19959 (   12)
  covalent geometry    : bond        0.00277 ( 6085)
  covalent geometry    : angle       0.62951 ( 8257)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.702 
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   85 TRP cc_start: 0.8805 (m-10) cc_final: 0.8525 (m100)
REVERT: A  149 MET cc_start: 0.7202 (tpt) cc_final: 0.6962 (tpt)
REVERT: A  176 ASN cc_start: 0.8572 (m-40) cc_final: 0.8073 (m-40)
REVERT: A  190 PHE cc_start: 0.9536 (m-10) cc_final: 0.9191 (m-80)
REVERT: B   58 MET cc_start: 0.9300 (ttp) cc_final: 0.8914 (ttp)
REVERT: B  161 TYR cc_start: 0.8336 (m-80) cc_final: 0.7162 (m-80)
REVERT: B  167 CYS cc_start: 0.3971 (p) cc_final: 0.3708 (p)
REVERT: B  174 GLU cc_start: 0.9555 (tp30) cc_final: 0.9119 (tp30)
REVERT: B  176 ASN cc_start: 0.7888 (m-40) cc_final: 0.7265 (p0)
REVERT: B  184 TYR cc_start: 0.8603 (m-10) cc_final: 0.8143 (m-10)
REVERT: B  188 SER cc_start: 0.9184 (t) cc_final: 0.8868 (p)
REVERT: H    3 GLN cc_start: 0.8666 (mp10) cc_final: 0.8303 (mp10)
REVERT: H   47 TRP cc_start: 0.8939 (t60) cc_final: 0.7942 (t60)
REVERT: H   57 ASP cc_start: 0.8410 (m-30) cc_final: 0.8129 (m-30)
REVERT: H   73 ASP cc_start: 0.9229 (t0) cc_final: 0.8935 (t0)
REVERT: H  101 PHE cc_start: 0.8880 (m-80) cc_final: 0.8342 (m-80)
REVERT: H  102 ASP cc_start: 0.8328 (t70) cc_final: 0.8078 (t0)
REVERT: H  216 LYS cc_start: 0.8705 (tmtt) cc_final: 0.8461 (ptpt)
REVERT: L   40 TRP cc_start: 0.8124 (m100) cc_final: 0.7437 (m100)
REVERT: L   76 PHE cc_start: 0.8299 (m-80) cc_final: 0.7900 (m-80)
REVERT: L   87 ASP cc_start: 0.7174 (p0) cc_final: 0.6958 (p0)
REVERT: L   93 CYS cc_start: 0.4903 (t) cc_final: 0.3284 (t)
REVERT: L  101 TYR cc_start: 0.8911 (m-10) cc_final: 0.8387 (m-80)
REVERT: L  148 GLU cc_start: 0.9513 (mp0) cc_final: 0.9177 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.1621
  time to fit residues: 41.8649
Evaluate side-chains
  157 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 73 optimal weight:    0.0670
   chunk 4 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0870
   chunk 65 optimal weight:    8.9990
   chunk 43 optimal weight:    8.9990
   overall best weight:    0.5696

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  47 GLN
L 143 ASN
** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.128539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.096464 restraints weight = 15721.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.101463 restraints weight = 9973.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.105291 restraints weight = 7043.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6835
moved from start:          0.6415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6091  Z= 0.115
  Angle     :  0.627   6.873   8269  Z= 0.319
  Chirality :  0.044   0.195    945
  Planarity :  0.005   0.055   1030
  Dihedral  :  4.573  18.491    824
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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: -0.29 (0.31), residues: 766
  helix:  0.77 (0.32), residues: 258
  sheet:  0.02 (0.38), residues: 191
  loop : -1.06 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  36 
 HIS   0.003   0.001   HIS B  63 
 PHE   0.018   0.001   PHE A 202 
 TYR   0.022   0.001   TYR L  54 
 ARG   0.004   0.001   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03603 (  263)
  hydrogen bonds       : angle       4.41661 (  717)
  SS BOND              : bond        0.00230 (    6)
  SS BOND              : angle       0.79504 (   12)
  covalent geometry    : bond        0.00250 ( 6085)
  covalent geometry    : angle       0.62651 ( 8257)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 TRP cc_start: 0.8710 (m-10) cc_final: 0.8424 (m100)
REVERT: A  149 MET cc_start: 0.7238 (tpt) cc_final: 0.7001 (tpt)
REVERT: A  176 ASN cc_start: 0.8577 (m-40) cc_final: 0.8050 (m-40)
REVERT: A  190 PHE cc_start: 0.9513 (m-10) cc_final: 0.9157 (m-80)
REVERT: B   58 MET cc_start: 0.9260 (ttp) cc_final: 0.8929 (ttp)
REVERT: B  140 ASN cc_start: 0.8486 (m110) cc_final: 0.8260 (m110)
REVERT: B  174 GLU cc_start: 0.9612 (tp30) cc_final: 0.9255 (tp30)
REVERT: B  176 ASN cc_start: 0.7873 (m-40) cc_final: 0.7292 (p0)
REVERT: B  184 TYR cc_start: 0.8609 (m-10) cc_final: 0.8159 (m-10)
REVERT: B  187 GLN cc_start: 0.8884 (mt0) cc_final: 0.8140 (mm-40)
REVERT: B  188 SER cc_start: 0.9186 (t) cc_final: 0.8882 (p)
REVERT: H    3 GLN cc_start: 0.8613 (mp10) cc_final: 0.8270 (mp10)
REVERT: H   36 TRP cc_start: 0.8660 (m100) cc_final: 0.7778 (m100)
REVERT: H   47 TRP cc_start: 0.8889 (t60) cc_final: 0.7951 (t60)
REVERT: H   57 ASP cc_start: 0.8416 (m-30) cc_final: 0.8075 (m-30)
REVERT: H   73 ASP cc_start: 0.9265 (t0) cc_final: 0.8967 (t0)
REVERT: H  101 PHE cc_start: 0.8897 (m-80) cc_final: 0.8345 (m-80)
REVERT: H  216 LYS cc_start: 0.8728 (tmtt) cc_final: 0.8451 (ptpt)
REVERT: L   33 ASN cc_start: 0.7225 (p0) cc_final: 0.7013 (p0)
REVERT: L   56 MET cc_start: 0.8489 (tmm) cc_final: 0.8278 (tmm)
REVERT: L   70 SER cc_start: 0.8696 (p) cc_final: 0.7996 (p)
REVERT: L   76 PHE cc_start: 0.8380 (m-80) cc_final: 0.7975 (m-80)
REVERT: L  101 TYR cc_start: 0.8828 (m-10) cc_final: 0.8524 (m-80)
REVERT: L  123 PHE cc_start: 0.8340 (m-80) cc_final: 0.8124 (m-80)
REVERT: L  148 GLU cc_start: 0.9506 (mp0) cc_final: 0.9219 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.1395
  time to fit residues: 35.6692
Evaluate side-chains
  151 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 16 optimal weight:    0.3980
   chunk 36 optimal weight:    0.6980
   chunk 55 optimal weight:    8.9990
   chunk 11 optimal weight:    4.9990
   chunk 46 optimal weight:    7.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  56 GLN
B 181 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.123868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.091332 restraints weight = 15832.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.096382 restraints weight = 9987.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.100218 restraints weight = 6993.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6876
moved from start:          0.6728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6091  Z= 0.139
  Angle     :  0.668   9.109   8269  Z= 0.341
  Chirality :  0.045   0.191    945
  Planarity :  0.006   0.063   1030
  Dihedral  :  4.661  18.804    824
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 15.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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: -0.25 (0.31), residues: 766
  helix:  0.94 (0.32), residues: 254
  sheet: -0.04 (0.38), residues: 197
  loop : -1.12 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  89 
 HIS   0.003   0.001   HIS L  31 
 PHE   0.021   0.002   PHE A 202 
 TYR   0.018   0.001   TYR L  54 
 ARG   0.015   0.001   ARG L 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03782 (  263)
  hydrogen bonds       : angle       4.52378 (  717)
  SS BOND              : bond        0.00348 (    6)
  SS BOND              : angle       1.19998 (   12)
  covalent geometry    : bond        0.00311 ( 6085)
  covalent geometry    : angle       0.66655 ( 8257)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.671 
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   64 ILE cc_start: 0.9157 (mm) cc_final: 0.8911 (mm)
REVERT: A   85 TRP cc_start: 0.8786 (m-10) cc_final: 0.8382 (m100)
REVERT: A  149 MET cc_start: 0.7192 (tpt) cc_final: 0.6988 (tpt)
REVERT: A  171 ASN cc_start: 0.9326 (p0) cc_final: 0.9078 (p0)
REVERT: A  190 PHE cc_start: 0.9549 (m-10) cc_final: 0.9178 (m-80)
REVERT: B   58 MET cc_start: 0.9358 (ttp) cc_final: 0.8957 (ttp)
REVERT: B  124 LEU cc_start: 0.8549 (mt) cc_final: 0.8013 (pt)
REVERT: B  131 MET cc_start: 0.8389 (mmm) cc_final: 0.8062 (mmm)
REVERT: B  167 CYS cc_start: 0.3901 (p) cc_final: 0.3663 (p)
REVERT: B  174 GLU cc_start: 0.9623 (tp30) cc_final: 0.9074 (tp30)
REVERT: B  176 ASN cc_start: 0.7828 (m-40) cc_final: 0.7239 (p0)
REVERT: B  184 TYR cc_start: 0.8596 (m-10) cc_final: 0.8058 (m-10)
REVERT: B  188 SER cc_start: 0.9241 (t) cc_final: 0.8937 (p)
REVERT: H    3 GLN cc_start: 0.8643 (mp10) cc_final: 0.8275 (mp10)
REVERT: H   47 TRP cc_start: 0.8862 (t60) cc_final: 0.8024 (t60)
REVERT: H   73 ASP cc_start: 0.9197 (t0) cc_final: 0.8923 (t0)
REVERT: H   81 MET cc_start: 0.6959 (tpt) cc_final: 0.6698 (tpt)
REVERT: H  101 PHE cc_start: 0.8914 (m-80) cc_final: 0.8584 (m-80)
REVERT: H  102 ASP cc_start: 0.8387 (t70) cc_final: 0.8069 (t0)
REVERT: H  216 LYS cc_start: 0.8769 (tmtt) cc_final: 0.8503 (ptpt)
REVERT: L   56 MET cc_start: 0.8821 (tmm) cc_final: 0.8586 (tmm)
REVERT: L   76 PHE cc_start: 0.8355 (m-80) cc_final: 0.8030 (m-80)
REVERT: L   87 ASP cc_start: 0.7349 (p0) cc_final: 0.7133 (p0)
REVERT: L  101 TYR cc_start: 0.8912 (m-10) cc_final: 0.8514 (m-80)
REVERT: L  148 GLU cc_start: 0.9510 (mp0) cc_final: 0.9114 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.1302
  time to fit residues: 31.8407
Evaluate side-chains
  149 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 73 optimal weight:    0.4980
   chunk 41 optimal weight:    0.6980
   chunk 25 optimal weight:    7.9990
   chunk 59 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   chunk 27 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 28 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0000
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  47 GLN
** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.128731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.097179 restraints weight = 15778.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.101920 restraints weight = 10148.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.105600 restraints weight = 7227.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6742
moved from start:          0.6638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6091  Z= 0.117
  Angle     :  0.672   9.291   8269  Z= 0.339
  Chirality :  0.045   0.193    945
  Planarity :  0.005   0.053   1030
  Dihedral  :  4.547  18.327    824
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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: -0.10 (0.31), residues: 766
  helix:  1.09 (0.33), residues: 254
  sheet:  0.01 (0.38), residues: 191
  loop : -1.01 (0.36), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP H  33 
 HIS   0.003   0.001   HIS A  63 
 PHE   0.021   0.001   PHE A 202 
 TYR   0.015   0.001   TYR L  54 
 ARG   0.013   0.001   ARG L 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03635 (  263)
  hydrogen bonds       : angle       4.43674 (  717)
  SS BOND              : bond        0.00236 (    6)
  SS BOND              : angle       0.87804 (   12)
  covalent geometry    : bond        0.00259 ( 6085)
  covalent geometry    : angle       0.67129 ( 8257)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.677 
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   63 HIS cc_start: 0.9086 (m-70) cc_final: 0.8028 (m-70)
REVERT: A  171 ASN cc_start: 0.9128 (p0) cc_final: 0.8858 (p0)
REVERT: A  190 PHE cc_start: 0.9501 (m-10) cc_final: 0.9144 (m-80)
REVERT: B   58 MET cc_start: 0.9275 (ttp) cc_final: 0.8941 (ttp)
REVERT: B  131 MET cc_start: 0.8252 (mmm) cc_final: 0.7982 (mmm)
REVERT: B  174 GLU cc_start: 0.9631 (tp30) cc_final: 0.9235 (tp30)
REVERT: B  176 ASN cc_start: 0.7838 (m-40) cc_final: 0.7237 (p0)
REVERT: B  184 TYR cc_start: 0.8545 (m-10) cc_final: 0.8078 (m-10)
REVERT: B  188 SER cc_start: 0.9210 (t) cc_final: 0.8922 (p)
REVERT: H    3 GLN cc_start: 0.8634 (mp10) cc_final: 0.8256 (mp10)
REVERT: H   36 TRP cc_start: 0.8845 (m100) cc_final: 0.7946 (m100)
REVERT: H   47 TRP cc_start: 0.8824 (t60) cc_final: 0.8009 (t60)
REVERT: H   73 ASP cc_start: 0.9195 (t0) cc_final: 0.8864 (t0)
REVERT: H  216 LYS cc_start: 0.8762 (tmtt) cc_final: 0.8466 (ptpt)
REVERT: L   70 SER cc_start: 0.8727 (p) cc_final: 0.8197 (p)
REVERT: L   76 PHE cc_start: 0.8499 (m-80) cc_final: 0.8014 (m-80)
REVERT: L   87 ASP cc_start: 0.7292 (p0) cc_final: 0.7050 (p0)
REVERT: L  101 TYR cc_start: 0.8878 (m-10) cc_final: 0.8500 (m-80)
REVERT: L  148 GLU cc_start: 0.9480 (mp0) cc_final: 0.9138 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.1374
  time to fit residues: 34.3180
Evaluate side-chains
  142 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 64 optimal weight:    0.0370
   chunk 65 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.7058

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

Flipped N/Q/H residues before XYZ refinement:
A 176 ASN
** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  47 GLN
L  55 GLN
** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.128201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.096569 restraints weight = 15917.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.101430 restraints weight = 10122.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.105194 restraints weight = 7156.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6732
moved from start:          0.6688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6091  Z= 0.116
  Angle     :  0.655   9.458   8269  Z= 0.329
  Chirality :  0.044   0.189    945
  Planarity :  0.005   0.053   1030
  Dihedral  :  4.500  17.850    824
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.82 %
    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 (0.31), residues: 766
  helix:  1.29 (0.33), residues: 242
  sheet:  0.04 (0.38), residues: 192
  loop : -0.93 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP L  40 
 HIS   0.002   0.001   HIS B  63 
 PHE   0.018   0.002   PHE A 202 
 TYR   0.013   0.001   TYR L  54 
 ARG   0.007   0.001   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03547 (  263)
  hydrogen bonds       : angle       4.34468 (  717)
  SS BOND              : bond        0.00437 (    6)
  SS BOND              : angle       1.00269 (   12)
  covalent geometry    : bond        0.00257 ( 6085)
  covalent geometry    : angle       0.65458 ( 8257)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2468.63 seconds
wall clock time: 44 minutes 50.25 seconds (2690.25 seconds total)