Starting phenix.real_space_refine
on Mon Jul 28 16:56:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6bx3_7303/07_2025/6bx3_7303.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6bx3_7303/07_2025/6bx3_7303.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6bx3_7303/07_2025/6bx3_7303.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6bx3_7303/07_2025/6bx3_7303.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6bx3_7303/07_2025/6bx3_7303.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6bx3_7303/07_2025/6bx3_7303.cif"
  }
  resolution = 4.3
  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=   0.001 sd=   0.030
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      47      5.16       5
     C    6608      2.51       5
     N    1786      2.21       5
     O    2015      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10456
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "E"
      Number of atoms: 1432
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1432
          Classifications: {'peptide': 192}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 6, 'TRANS': 185}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 109
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 72
    Chain: "K"
      Number of atoms: 1520
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1520
          Classifications: {'peptide': 211}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 6, 'TRANS': 204}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 148
          Unresolved non-hydrogen angles: 183
          Unresolved non-hydrogen dihedrals: 119
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 70
    Chain: "M"
      Number of atoms: 328
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 328
          Classifications: {'peptide': 42}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 3, 'TRANS': 38}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "N"
      Number of atoms: 304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 304
          Classifications: {'peptide': 40}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 3, 'TRANS': 36}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "F"
      Number of atoms: 1526
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1526
          Classifications: {'peptide': 215}
          Incomplete info: {'truncation_to_alanine': 68}
          Link IDs: {'PTRANS': 2, 'TRANS': 212}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 280
          Unresolved non-hydrogen angles: 346
          Unresolved non-hydrogen dihedrals: 236
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 168
    Chain: "B"
      Number of atoms: 3050
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 3050
          Classifications: {'peptide': 399}
          Incomplete info: {'truncation_to_alanine': 47}
          Link IDs: {'PTRANS': 16, 'TRANS': 382}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 159
          Unresolved non-hydrogen angles: 196
          Unresolved non-hydrogen dihedrals: 122
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 107
    Chain: "A"
      Number of atoms: 2296
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2296
          Classifications: {'peptide': 314}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 11, 'TRANS': 302}
          Unresolved non-hydrogen bonds: 138
          Unresolved non-hydrogen angles: 179
          Unresolved non-hydrogen dihedrals: 111
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 76
  Time building chain proxies: 7.38, per 1000 atoms: 0.71
  Number of scatterers: 10456
  At special positions: 0
  Unit cell: (137, 109, 155, 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      47     16.00
     O    2015      8.00
     N    1786      7.00
     C    6608      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.01
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2658

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 15 sheets defined
      19.6% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'E' and resid 799 through 824
      removed outlier: 4.384A  pdb=" N   ARG E 805 " --> pdb=" O   TRP E 801 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   SER E 814 " --> pdb=" O   GLU E 810 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   ASP E 815 " --> pdb=" O   GLU E 811 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLN E 817 " --> pdb=" O   ALA E 813 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   ILE E 818 " --> pdb=" O   SER E 814 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU E 824 " --> pdb=" O   LEU E 820 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 926 through 933
    Processing helix  chain 'E' and resid 974 through 988
      removed outlier: 3.570A  pdb=" N   ASN E 987 " --> pdb=" O   ARG E 983 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 98 through 106
      removed outlier: 3.659A  pdb=" N   LEU K 101 " --> pdb=" O   SER K  98 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   SER K 102 " --> pdb=" O   GLU K  99 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ILE K 103 " --> pdb=" O   GLY K 100 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   SER K 104 " --> pdb=" O   LEU K 101 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 196 through 200
    Processing helix  chain 'K' and resid 459 through 463
      removed outlier: 3.704A  pdb=" N   GLN K 462 " --> pdb=" O   TYR K 459 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 479 through 500
      removed outlier: 3.747A  pdb=" N   LYS K 483 " --> pdb=" O   ASP K 479 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 133 through 144
    Processing helix  chain 'M' and resid 152 through 162
      removed outlier: 3.523A  pdb=" N   LEU M 157 " --> pdb=" O   LEU M 153 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 123 through 129
    Processing helix  chain 'N' and resid 130 through 142
      removed outlier: 4.278A  pdb=" N   LEU N 134 " --> pdb=" O   VAL N 130 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 152 through 159
      removed outlier: 3.726A  pdb=" N   TYR N 156 " --> pdb=" O   VAL N 152 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 118 through 129
    Processing helix  chain 'F' and resid 135 through 145
      removed outlier: 3.574A  pdb=" N   GLU F 143 " --> pdb=" O   LYS F 139 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 150 through 158
      removed outlier: 3.858A  pdb=" N   PHE F 154 " --> pdb=" O   LYS F 150 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 164 through 171
      removed outlier: 3.653A  pdb=" N   ASP F 169 " --> pdb=" O   VAL F 165 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 191 through 200
      removed outlier: 4.713A  pdb=" N   GLU F 197 " --> pdb=" O   GLN F 193 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ILE F 198 " --> pdb=" O   GLU F 194 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   LEU F 200 " --> pdb=" O   GLN F 196 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 202 through 208
    Processing helix  chain 'F' and resid 208 through 241
      removed outlier: 4.844A  pdb=" N   LEU F 217 " --> pdb=" O   TYR F 213 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   ASP F 218 " --> pdb=" O   LEU F 214 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ASP F 228 " --> pdb=" O   MET F 224 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   ASP F 229 " --> pdb=" O   ARG F 225 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ASP F 230 " --> pdb=" O   LYS F 226 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   VAL F 235 " --> pdb=" O   ALA F 231 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 278 through 283
    Processing helix  chain 'F' and resid 311 through 349
      removed outlier: 3.698A  pdb=" N   TYR F 315 " --> pdb=" O   ASN F 311 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   ILE F 342 " --> pdb=" O   LYS F 338 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   TYR F 344 " --> pdb=" O   LEU F 340 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LEU F 349 " --> pdb=" O   TYR F 345 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 1023 through 1026
      removed outlier: 6.424A  pdb=" N   THR E1024 " --> pdb=" O   TYR E1039 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL E1037 " --> pdb=" O   LYS E1026 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'K' and resid 137 through 139
    Processing sheet with id=AA3, first strand: chain 'K' and resid 204 through 205
    Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 23
      removed outlier: 4.321A  pdb=" N   ASP B 317 " --> pdb=" O   ASN B 330 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 34
      removed outlier: 5.318A  pdb=" N   CYS B  31 " --> pdb=" O   GLY B  44 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   GLY B  44 " --> pdb=" O   CYS B  31 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 79 through 80
      removed outlier: 3.683A  pdb=" N   LEU B  98 " --> pdb=" O   LYS B 109 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LYS B 109 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 122
      removed outlier: 4.097A  pdb=" N   TYR B 141 " --> pdb=" O   ALA B 132 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 176
      removed outlier: 5.456A  pdb=" N   CYS B 174 " --> pdb=" O   GLY B 187 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   GLY B 187 " --> pdb=" O   CYS B 174 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   LEU B 193 " --> pdb=" O   SER B 209 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   SER B 209 " --> pdb=" O   LEU B 193 " (cutoff:3.500A)
      removed outlier: 4.963A  pdb=" N   PHE B 195 " --> pdb=" O   ILE B 207 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 269 through 274
      removed outlier: 6.431A  pdb=" N   SER B 285 " --> pdb=" O   ASN B 270 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   ILE B 272 " --> pdb=" O   VAL B 283 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   VAL B 283 " --> pdb=" O   ILE B 272 " (cutoff:3.500A)
      removed outlier: 5.358A  pdb=" N   PHE B 274 " --> pdb=" O   TYR B 281 " (cutoff:3.500A)
      removed outlier: 7.364A  pdb=" N   TYR B 281 " --> pdb=" O   PHE B 274 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 61 through 62
      removed outlier: 4.263A  pdb=" N   ALA A  71 " --> pdb=" O   CYS A  62 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 102 through 104
      removed outlier: 3.947A  pdb=" N   THR A 103 " --> pdb=" O   PHE A 112 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   PHE A 112 " --> pdb=" O   THR A 103 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   LYS A 121 " --> pdb=" O   THR A 113 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   ILE A 120 " --> pdb=" O   THR A 133 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   THR A 133 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   ILE A 122 " --> pdb=" O   MET A 131 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   MET A 131 " --> pdb=" O   ILE A 122 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 141 through 143
    Processing sheet with id=AB4, first strand: chain 'A' and resid 162 through 163
    Processing sheet with id=AB5, first strand: chain 'A' and resid 204 through 207
      removed outlier: 3.686A  pdb=" N   LEU A 204 " --> pdb=" O   TRP A 216 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   VAL A 206 " --> pdb=" O   LYS A 214 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   VAL A 213 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   THR A 226 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   ILE A 215 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 248 through 250

    223 hydrogen bonds defined for protein.
    627 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: 2.98

  Time building geometry restraints manager: 3.42 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2172
        1.33 -     1.45: 2588
        1.45 -     1.58: 5836
        1.58 -     1.70: 0
        1.70 -     1.83: 62
  Bond restraints: 10658
  Sorted by residual:
  bond pdb=" CA  HIS A  90 "
       pdb=" CB  HIS A  90 "
    ideal  model  delta    sigma   weight residual
    1.523  1.438  0.085 1.35e-02 5.49e+03 4.00e+01
  bond pdb=" C   THR N 131 "
       pdb=" N   PRO N 132 "
    ideal  model  delta    sigma   weight residual
    1.336  1.386 -0.050 1.20e-02 6.94e+03 1.76e+01
  bond pdb=" C   ALA E 943 "
       pdb=" O   ALA E 943 "
    ideal  model  delta    sigma   weight residual
    1.234  1.200  0.034 1.24e-02 6.50e+03 7.42e+00
  bond pdb=" CB  TRP A 312 "
       pdb=" CG  TRP A 312 "
    ideal  model  delta    sigma   weight residual
    1.498  1.415  0.083 3.10e-02 1.04e+03 7.11e+00
  bond pdb=" N   SER K 102 "
       pdb=" CA  SER K 102 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.031 1.20e-02 6.94e+03 6.89e+00
  ... (remaining 10653 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.04: 13799
        3.04 -     6.08: 585
        6.08 -     9.12: 105
        9.12 -    12.16: 24
       12.16 -    15.19: 6
  Bond angle restraints: 14519
  Sorted by residual:
  angle pdb=" N   ILE E 972 "
        pdb=" CA  ILE E 972 "
        pdb=" C   ILE E 972 "
      ideal   model   delta    sigma   weight residual
     110.72  124.94  -14.22 1.01e+00 9.80e-01 1.98e+02
  angle pdb=" N   ALA B 350 "
        pdb=" CA  ALA B 350 "
        pdb=" C   ALA B 350 "
      ideal   model   delta    sigma   weight residual
     111.07  123.29  -12.22 1.07e+00 8.73e-01 1.30e+02
  angle pdb=" C   ASN B  25 "
        pdb=" N   PRO B  26 "
        pdb=" CA  PRO B  26 "
      ideal   model   delta    sigma   weight residual
     119.05  131.02  -11.97 1.11e+00 8.12e-01 1.16e+02
  angle pdb=" N   GLU B 356 "
        pdb=" CA  GLU B 356 "
        pdb=" C   GLU B 356 "
      ideal   model   delta    sigma   weight residual
     109.59   94.40   15.19 1.47e+00 4.63e-01 1.07e+02
  angle pdb=" C   LYS B 103 "
        pdb=" N   PRO B 104 "
        pdb=" CA  PRO B 104 "
      ideal   model   delta    sigma   weight residual
     119.87  129.81   -9.94 1.04e+00 9.25e-01 9.13e+01
  ... (remaining 14514 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.94: 5702
       14.94 -    29.87: 484
       29.87 -    44.81: 97
       44.81 -    59.74: 19
       59.74 -    74.68: 11
  Dihedral angle restraints: 6313
    sinusoidal: 2210
      harmonic: 4103
  Sorted by residual:
  dihedral pdb=" CA  HIS A 286 "
           pdb=" C   HIS A 286 "
           pdb=" N   SER A 287 "
           pdb=" CA  SER A 287 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -120.35  -59.65     0      5.00e+00 4.00e-02 1.42e+02
  dihedral pdb=" CA  ASN B  66 "
           pdb=" C   ASN B  66 "
           pdb=" N   MET B  67 "
           pdb=" CA  MET B  67 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -125.42  -54.58     0      5.00e+00 4.00e-02 1.19e+02
  dihedral pdb=" CA  ILE E 947 "
           pdb=" C   ILE E 947 "
           pdb=" N   HIS E 948 "
           pdb=" CA  HIS E 948 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -127.07  -52.93     0      5.00e+00 4.00e-02 1.12e+02
  ... (remaining 6310 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 1420
       0.098 -    0.196: 218
       0.196 -    0.294: 33
       0.294 -    0.392: 12
       0.392 -    0.490: 3
  Chirality restraints: 1686
  Sorted by residual:
  chirality pdb=" CB  THR K 439 "
            pdb=" CA  THR K 439 "
            pdb=" OG1 THR K 439 "
            pdb=" CG2 THR K 439 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.06    0.49 2.00e-01 2.50e+01 5.99e+00
  chirality pdb=" CG  LEU B 154 "
            pdb=" CB  LEU B 154 "
            pdb=" CD1 LEU B 154 "
            pdb=" CD2 LEU B 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.18   -0.41 2.00e-01 2.50e+01 4.23e+00
  chirality pdb=" CA  PRO B  26 "
            pdb=" N   PRO B  26 "
            pdb=" C   PRO B  26 "
            pdb=" CB  PRO B  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.33    0.39 2.00e-01 2.50e+01 3.84e+00
  ... (remaining 1683 not shown)

  Planarity restraints: 1879
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE F 164 "   -0.022 2.00e-02 2.50e+03   4.44e-02 1.97e+01
        pdb=" C   ILE F 164 "    0.077 2.00e-02 2.50e+03
        pdb=" O   ILE F 164 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   VAL F 165 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 113 "    0.020 2.00e-02 2.50e+03   4.07e-02 1.65e+01
        pdb=" C   PHE B 113 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   PHE B 113 "    0.027 2.00e-02 2.50e+03
        pdb=" N   ASP B 114 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA E 943 "   -0.018 2.00e-02 2.50e+03   3.52e-02 1.24e+01
        pdb=" C   ALA E 943 "    0.061 2.00e-02 2.50e+03
        pdb=" O   ALA E 943 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ARG E 944 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1876 not shown)

  Histogram of nonbonded interaction distances:
        1.09 -     1.86: 3
        1.86 -     2.62: 230
        2.62 -     3.38: 14421
        3.38 -     4.14: 24674
        4.14 -     4.90: 41121
  Nonbonded interactions: 80449
  Sorted by model distance:
  nonbonded pdb=" CB  ASP K 125 "
            pdb=" OH  TYR K 482 "
     model   vdw
     1.094 3.440
  nonbonded pdb=" O   CYS F 263 "
            pdb=" OG1 THR F 297 "
     model   vdw
     1.520 3.040
  nonbonded pdb=" CB  ASP K 125 "
            pdb=" CZ  TYR K 482 "
     model   vdw
     1.775 3.660
  nonbonded pdb=" O   ASP K  96 "
            pdb=" CB  ARG K 123 "
     model   vdw
     1.917 3.440
  nonbonded pdb=" CG2 THR F 297 "
            pdb=" CE1 HIS F 304 "
     model   vdw
     1.955 3.680
  ... (remaining 80444 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 'M' and (resid 122 through 138 or (resid 139 through 140 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 141 through 146 or (resid 147  \ 
and (name N or name CA or name C or name O or name CB )) or resid 148 through 16 \ 
1))
  selection = (chain 'N' and (resid 122 through 125 or (resid 126 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 127 through 142 or (resid 143 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 144 through 161))
}

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=0.07 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:             1.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     28.310
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
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      :  0.007   0.085  10658  Z= 0.397
  Angle     :  1.492  15.194  14519  Z= 0.898
  Chirality :  0.079   0.490   1686
  Planarity :  0.008   0.072   1879
  Dihedral  : 12.650  74.679   3655
  Min Nonbonded Distance : 1.094

Molprobity Statistics.
  All-atom Clashscore : 24.88
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 18.77 %
    Favored  : 81.16 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  9.17 %
    Favored  : 89.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.17 %
    Twisted General : 1.26 %

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: -5.00 (0.17), residues: 1385
  helix: -2.80 (0.24), residues: 229
  sheet: -2.94 (0.34), residues: 173
  loop : -3.83 (0.15), residues: 983

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.004   TRP K 135 
 HIS   0.015   0.003   HIS A 286 
 PHE   0.030   0.004   PHE F 283 
 TYR   0.031   0.004   TYR K 202 
 ARG   0.009   0.001   ARG E 841 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21959 (  223)
  hydrogen bonds       : angle       8.86331 (  627)
  covalent geometry    : bond        0.00743 (10658)
  covalent geometry    : angle       1.49184 (14519)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 283
  time to evaluate  : 1.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  819 GLU cc_start: 0.9393 (mm-30) cc_final: 0.9165 (mm-30)
REVERT: E  934 ASN cc_start: 0.9318 (t160) cc_final: 0.8889 (p0)
REVERT: E  975 PRO cc_start: 0.8494 (Cg_exo) cc_final: 0.8142 (Cg_endo)
REVERT: E  979 MET cc_start: 0.8978 (tpt) cc_final: 0.8650 (tpp)
REVERT: E  998 ASP cc_start: 0.7816 (m-30) cc_final: 0.6241 (p0)
REVERT: E 1026 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8197 (mtmm)
REVERT: E 1039 TYR cc_start: 0.8089 (t80) cc_final: 0.7490 (t80)
REVERT: K  194 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8301 (tm-30)
REVERT: K  199 PHE cc_start: 0.9470 (t80) cc_final: 0.8996 (t80)
REVERT: K  469 VAL cc_start: 0.6236 (t) cc_final: 0.5743 (t)
REVERT: K  483 LYS cc_start: 0.9018 (mptt) cc_final: 0.8808 (mmtt)
REVERT: M  139 ARG cc_start: 0.8745 (mmp-170) cc_final: 0.7931 (mtt180)
REVERT: M  147 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7057 (mp0)
REVERT: N  123 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7781 (mtt180)
REVERT: F  120 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8239 (mm-30)
REVERT: F  204 LYS cc_start: 0.9089 (ttpm) cc_final: 0.8748 (ptpp)
REVERT: F  223 GLU cc_start: 0.9661 (tt0) cc_final: 0.9441 (tm-30)
REVERT: F  228 ASP cc_start: 0.8918 (m-30) cc_final: 0.8712 (t0)
REVERT: F  291 LYS cc_start: 0.8185 (pttp) cc_final: 0.7087 (mmmt)
REVERT: B   54 ASP cc_start: 0.8339 (p0) cc_final: 0.7381 (p0)
REVERT: B   59 ARG cc_start: 0.8741 (mtt-85) cc_final: 0.8394 (mmm-85)
REVERT: B   67 MET cc_start: 0.9076 (mpm) cc_final: 0.8741 (mmm)
REVERT: B  144 ASP cc_start: 0.9572 (m-30) cc_final: 0.9095 (t70)
REVERT: B  258 HIS cc_start: 0.7965 (t-90) cc_final: 0.7657 (t-170)
REVERT: B  268 GLN cc_start: 0.8249 (pp30) cc_final: 0.8009 (pp30)
REVERT: B  319 ASN cc_start: 0.9046 (t0) cc_final: 0.8768 (t0)
REVERT: B  320 TRP cc_start: 0.8524 (m100) cc_final: 0.8259 (m100)
REVERT: B  354 ASP cc_start: 0.8753 (m-30) cc_final: 0.7945 (t0)
REVERT: A  116 MET cc_start: 0.7837 (tmt) cc_final: 0.7478 (tmm)
REVERT: A  127 ASN cc_start: 0.9137 (t160) cc_final: 0.8848 (t0)
REVERT: A  149 ASN cc_start: 0.9139 (m-40) cc_final: 0.8871 (m-40)
REVERT: A  196 LYS cc_start: 0.8564 (tttp) cc_final: 0.8238 (ttmm)
REVERT: A  249 GLU cc_start: 0.7906 (mp0) cc_final: 0.7594 (mp0)
REVERT: A  291 MET cc_start: 0.8426 (tpp) cc_final: 0.7926 (mmm)
  outliers start: 10
  outliers final: 3
  residues processed: 291
  average time/residue: 0.2487
  time to fit residues: 98.7050
Evaluate side-chains
  176 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 172
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 117 optimal weight:    0.8980
   chunk 105 optimal weight:    0.0770
   chunk 58 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   chunk 56 optimal weight:    7.9990
   chunk 108 optimal weight:    8.9990
   chunk 42 optimal weight:   20.0000
   chunk 66 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9980
   chunk 126 optimal weight:   10.0000
   overall best weight:    2.3942

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

Flipped N/Q/H residues before XYZ refinement:
** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 215 HIS
** M 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 145 GLN
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 193 GLN
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 343 GLN
B   6 GLN
** B  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 ASN
** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 ASN
B 336 ASN
** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 172 HIS
A 294 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.080012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.067740 restraints weight = 59367.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.069651 restraints weight = 38516.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.071067 restraints weight = 27865.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3538
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3538 r_free = 0.3538    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3537 r_free = 0.3537    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3537
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.2785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10658  Z= 0.185
  Angle     :  0.870  15.201  14519  Z= 0.457
  Chirality :  0.052   0.397   1686
  Planarity :  0.005   0.047   1879
  Dihedral  :  8.808  48.084   1491
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 19.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.82 %
    Favored  : 83.18 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  4.54 %
    Favored  : 95.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.67 %

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: -4.37 (0.19), residues: 1385
  helix: -1.89 (0.28), residues: 253
  sheet: -3.05 (0.34), residues: 182
  loop : -3.40 (0.17), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP K 135 
 HIS   0.010   0.002   HIS A  95 
 PHE   0.023   0.002   PHE B 355 
 TYR   0.024   0.002   TYR M 156 
 ARG   0.004   0.001   ARG A 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04861 (  223)
  hydrogen bonds       : angle       6.56296 (  627)
  covalent geometry    : bond        0.00394 (10658)
  covalent geometry    : angle       0.86959 (14519)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 238
  time to evaluate  : 1.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  934 ASN cc_start: 0.9216 (t0) cc_final: 0.8916 (p0)
REVERT: E  975 PRO cc_start: 0.8150 (Cg_exo) cc_final: 0.7925 (Cg_endo)
REVERT: E  979 MET cc_start: 0.8956 (tpt) cc_final: 0.8674 (tpp)
REVERT: E  998 ASP cc_start: 0.7602 (m-30) cc_final: 0.6802 (m-30)
REVERT: K  135 TRP cc_start: 0.8657 (t60) cc_final: 0.8339 (t60)
REVERT: K  199 PHE cc_start: 0.9336 (t80) cc_final: 0.9064 (t80)
REVERT: K  439 THR cc_start: 0.5766 (OUTLIER) cc_final: 0.5566 (p)
REVERT: K  483 LYS cc_start: 0.9303 (mptt) cc_final: 0.8583 (mtpt)
REVERT: M  139 ARG cc_start: 0.8911 (mmp-170) cc_final: 0.8136 (mtt180)
REVERT: F  266 CYS cc_start: 0.8179 (p) cc_final: 0.7930 (p)
REVERT: F  291 LYS cc_start: 0.7819 (pttp) cc_final: 0.6499 (mmmt)
REVERT: B   83 ASP cc_start: 0.8189 (t0) cc_final: 0.7803 (t0)
REVERT: B  106 LYS cc_start: 0.8685 (tttp) cc_final: 0.8300 (mtmm)
REVERT: B  199 HIS cc_start: 0.6539 (m90) cc_final: 0.6330 (t70)
REVERT: B  319 ASN cc_start: 0.9125 (t0) cc_final: 0.8913 (t0)
REVERT: B  320 TRP cc_start: 0.8416 (m100) cc_final: 0.8046 (m100)
REVERT: B  354 ASP cc_start: 0.8954 (m-30) cc_final: 0.8118 (t0)
REVERT: A   26 GLN cc_start: 0.9175 (mp10) cc_final: 0.8906 (mp10)
REVERT: A  149 ASN cc_start: 0.9170 (m-40) cc_final: 0.8754 (m-40)
REVERT: A  154 LEU cc_start: 0.8653 (tp) cc_final: 0.8189 (tp)
REVERT: A  194 GLN cc_start: 0.8953 (mt0) cc_final: 0.8651 (mt0)
REVERT: A  195 VAL cc_start: 0.8529 (m) cc_final: 0.7709 (p)
REVERT: A  199 GLU cc_start: 0.8546 (pm20) cc_final: 0.8059 (pm20)
REVERT: A  233 GLU cc_start: 0.7715 (tp30) cc_final: 0.7377 (tp30)
REVERT: A  291 MET cc_start: 0.8308 (tpp) cc_final: 0.7346 (mmp)
  outliers start: 4
  outliers final: 0
  residues processed: 240
  average time/residue: 0.2642
  time to fit residues: 90.2523
Evaluate side-chains
  162 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 16 optimal weight:   20.0000
   chunk 36 optimal weight:   10.0000
   chunk 100 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 127 optimal weight:    7.9990
   chunk 92 optimal weight:   10.0000
   chunk 122 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 62 optimal weight:    0.4980
   chunk 107 optimal weight:   20.0000
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 145 GLN
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 240 GLN
B 330 ASN
B 405 ASN
A  48 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.080303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.068603 restraints weight = 63012.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.070386 restraints weight = 41769.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.071718 restraints weight = 30553.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3536
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3536 r_free = 0.3536    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3536 r_free = 0.3536    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3536
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.3485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10658  Z= 0.164
  Angle     :  0.813  12.251  14519  Z= 0.420
  Chirality :  0.051   0.313   1686
  Planarity :  0.005   0.047   1879
  Dihedral  :  8.081  45.136   1491
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 19.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.04 %
    Favored  : 82.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.59 %

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: -4.04 (0.19), residues: 1385
  helix: -1.22 (0.30), residues: 249
  sheet: -2.64 (0.38), residues: 140
  loop : -3.36 (0.17), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP K 135 
 HIS   0.007   0.002   HIS B  71 
 PHE   0.021   0.002   PHE E 942 
 TYR   0.019   0.002   TYR F 344 
 ARG   0.019   0.001   ARG E 980 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04339 (  223)
  hydrogen bonds       : angle       6.04487 (  627)
  covalent geometry    : bond        0.00348 (10658)
  covalent geometry    : angle       0.81306 (14519)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 1.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  934 ASN cc_start: 0.9189 (t0) cc_final: 0.8883 (p0)
REVERT: E  979 MET cc_start: 0.8809 (tpt) cc_final: 0.8491 (tpp)
REVERT: K  199 PHE cc_start: 0.9295 (t80) cc_final: 0.9023 (t80)
REVERT: K  238 LEU cc_start: 0.8765 (tp) cc_final: 0.8503 (tp)
REVERT: K  483 LYS cc_start: 0.9261 (mptt) cc_final: 0.8595 (mtpt)
REVERT: M  135 LEU cc_start: 0.8585 (pp) cc_final: 0.8309 (pp)
REVERT: M  139 ARG cc_start: 0.8871 (mmp-170) cc_final: 0.8141 (mtt180)
REVERT: M  156 TYR cc_start: 0.8574 (t80) cc_final: 0.7843 (t80)
REVERT: F  291 LYS cc_start: 0.7829 (pttp) cc_final: 0.6492 (mmmt)
REVERT: B   54 ASP cc_start: 0.8314 (p0) cc_final: 0.7376 (p0)
REVERT: B  106 LYS cc_start: 0.8668 (tttp) cc_final: 0.8404 (mtpp)
REVERT: B  319 ASN cc_start: 0.9076 (t0) cc_final: 0.8868 (t0)
REVERT: B  354 ASP cc_start: 0.9002 (m-30) cc_final: 0.7902 (t0)
REVERT: A  107 LYS cc_start: 0.8954 (mtpt) cc_final: 0.8642 (mtpt)
REVERT: A  109 ASN cc_start: 0.9238 (m110) cc_final: 0.8745 (m110)
REVERT: A  149 ASN cc_start: 0.9220 (m-40) cc_final: 0.8700 (m-40)
REVERT: A  154 LEU cc_start: 0.8665 (tp) cc_final: 0.8379 (tp)
REVERT: A  195 VAL cc_start: 0.8570 (m) cc_final: 0.7724 (p)
REVERT: A  199 GLU cc_start: 0.8603 (pm20) cc_final: 0.8266 (pm20)
REVERT: A  238 HIS cc_start: 0.7475 (p-80) cc_final: 0.7068 (p-80)
REVERT: A  291 MET cc_start: 0.8291 (tpp) cc_final: 0.7522 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.2862
  time to fit residues: 88.8159
Evaluate side-chains
  152 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 1.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 111 optimal weight:    0.0770
   chunk 36 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 132 optimal weight:    0.2980
   chunk 63 optimal weight:    8.9990
   chunk 46 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 112 optimal weight:    1.9990
   overall best weight:    1.4744

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

Flipped N/Q/H residues before XYZ refinement:
** E 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E1022 ASN
** M 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 240 GLN
B 330 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.080986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.069071 restraints weight = 60097.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.070949 restraints weight = 39561.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.072294 restraints weight = 28527.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3555
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3555
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.4076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10658  Z= 0.142
  Angle     :  0.760  10.000  14519  Z= 0.395
  Chirality :  0.048   0.213   1686
  Planarity :  0.004   0.047   1879
  Dihedral  :  7.476  42.093   1491
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 16.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.04 %
    Favored  : 82.96 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.54 %
    Favored  : 95.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

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: -3.79 (0.20), residues: 1385
  helix: -0.73 (0.32), residues: 249
  sheet: -2.59 (0.38), residues: 154
  loop : -3.26 (0.17), residues: 982

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP K 135 
 HIS   0.010   0.001   HIS B  71 
 PHE   0.022   0.001   PHE B  58 
 TYR   0.018   0.002   TYR F 213 
 ARG   0.003   0.000   ARG B  85 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03905 (  223)
  hydrogen bonds       : angle       5.61295 (  627)
  covalent geometry    : bond        0.00308 (10658)
  covalent geometry    : angle       0.75990 (14519)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 211
  time to evaluate  : 1.622 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  934 ASN cc_start: 0.9160 (t0) cc_final: 0.8873 (p0)
REVERT: E  979 MET cc_start: 0.8856 (tpt) cc_final: 0.8593 (tpp)
REVERT: K  117 TYR cc_start: 0.5649 (m-10) cc_final: 0.5269 (m-80)
REVERT: K  135 TRP cc_start: 0.8651 (t60) cc_final: 0.8398 (t60)
REVERT: K  199 PHE cc_start: 0.9188 (t80) cc_final: 0.8904 (t80)
REVERT: K  439 THR cc_start: 0.4822 (OUTLIER) cc_final: 0.4385 (p)
REVERT: K  450 ILE cc_start: 0.9240 (pt) cc_final: 0.9039 (mm)
REVERT: K  483 LYS cc_start: 0.9134 (mptt) cc_final: 0.8506 (mtpt)
REVERT: M  139 ARG cc_start: 0.8883 (mmp-170) cc_final: 0.8163 (mtt180)
REVERT: M  156 TYR cc_start: 0.8550 (t80) cc_final: 0.7836 (t80)
REVERT: F  224 MET cc_start: 0.8544 (mmm) cc_final: 0.8285 (mmm)
REVERT: F  291 LYS cc_start: 0.7727 (pttp) cc_final: 0.6406 (mmmt)
REVERT: B   54 ASP cc_start: 0.8302 (p0) cc_final: 0.7333 (p0)
REVERT: B  106 LYS cc_start: 0.8666 (tttp) cc_final: 0.8350 (mtpp)
REVERT: B  199 HIS cc_start: 0.6650 (t70) cc_final: 0.6264 (t70)
REVERT: B  354 ASP cc_start: 0.8964 (m-30) cc_final: 0.7906 (t0)
REVERT: A   42 ASN cc_start: 0.9119 (m-40) cc_final: 0.8145 (m110)
REVERT: A  107 LYS cc_start: 0.9295 (mtpt) cc_final: 0.8736 (mtpt)
REVERT: A  109 ASN cc_start: 0.9285 (m110) cc_final: 0.8722 (m110)
REVERT: A  149 ASN cc_start: 0.9221 (m-40) cc_final: 0.8693 (m-40)
REVERT: A  154 LEU cc_start: 0.8670 (tp) cc_final: 0.8396 (tp)
REVERT: A  195 VAL cc_start: 0.8622 (m) cc_final: 0.7975 (p)
REVERT: A  291 MET cc_start: 0.8407 (tpp) cc_final: 0.7268 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 212
  average time/residue: 0.3515
  time to fit residues: 110.3175
Evaluate side-chains
  151 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 2.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 129 optimal weight:    6.9990
   chunk 118 optimal weight:    6.9990
   chunk 135 optimal weight:    7.9990
   chunk 106 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 123 optimal weight:    4.9990
   chunk 64 optimal weight:    0.0970
   chunk 61 optimal weight:    6.9990
   chunk 112 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
** E 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 ASN
** A  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 127 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.080538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.068212 restraints weight = 60559.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.070119 restraints weight = 39491.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.071479 restraints weight = 28509.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3544
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3544 r_free = 0.3544    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3544 r_free = 0.3544    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3544
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.4426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10658  Z= 0.158
  Angle     :  0.764  10.250  14519  Z= 0.397
  Chirality :  0.048   0.232   1686
  Planarity :  0.004   0.048   1879
  Dihedral  :  7.289  41.215   1491
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 18.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.46 %
    Favored  : 83.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

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: -3.69 (0.20), residues: 1385
  helix: -0.55 (0.32), residues: 248
  sheet: -2.58 (0.38), residues: 161
  loop : -3.19 (0.18), residues: 976

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 183 
 HIS   0.006   0.001   HIS B  71 
 PHE   0.023   0.002   PHE B  58 
 TYR   0.017   0.002   TYR F 344 
 ARG   0.003   0.000   ARG B  85 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03932 (  223)
  hydrogen bonds       : angle       5.53506 (  627)
  covalent geometry    : bond        0.00343 (10658)
  covalent geometry    : angle       0.76411 (14519)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 1.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  117 TYR cc_start: 0.5684 (m-10) cc_final: 0.5378 (m-80)
REVERT: K  202 TYR cc_start: 0.7095 (p90) cc_final: 0.6229 (p90)
REVERT: K  483 LYS cc_start: 0.9140 (mptt) cc_final: 0.8495 (mtpt)
REVERT: M  135 LEU cc_start: 0.8656 (pp) cc_final: 0.8396 (pp)
REVERT: M  139 ARG cc_start: 0.8947 (mmp-170) cc_final: 0.8192 (mtt180)
REVERT: F  291 LYS cc_start: 0.7756 (pttp) cc_final: 0.6352 (mmmt)
REVERT: B   54 ASP cc_start: 0.8443 (p0) cc_final: 0.7475 (p0)
REVERT: B  354 ASP cc_start: 0.9010 (m-30) cc_final: 0.7985 (t0)
REVERT: A  107 LYS cc_start: 0.9354 (mtpt) cc_final: 0.8788 (mtpt)
REVERT: A  109 ASN cc_start: 0.9330 (m110) cc_final: 0.8784 (m110)
REVERT: A  149 ASN cc_start: 0.9230 (m-40) cc_final: 0.8775 (m-40)
REVERT: A  154 LEU cc_start: 0.8513 (tp) cc_final: 0.8249 (tp)
REVERT: A  155 SER cc_start: 0.7373 (p) cc_final: 0.7171 (p)
REVERT: A  195 VAL cc_start: 0.8651 (m) cc_final: 0.7991 (p)
REVERT: A  233 GLU cc_start: 0.8097 (tp30) cc_final: 0.7752 (tp30)
REVERT: A  291 MET cc_start: 0.8517 (tpp) cc_final: 0.7128 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 197
  average time/residue: 0.3004
  time to fit residues: 83.7396
Evaluate side-chains
  144 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 113 optimal weight:    0.1980
   chunk 50 optimal weight:   10.0000
   chunk 77 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 43 optimal weight:    0.8980
   chunk 75 optimal weight:    6.9990
   chunk 29 optimal weight:    0.0030
   chunk 79 optimal weight:    0.8980
   chunk 5 optimal weight:    7.9990
   overall best weight:    0.5992

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

Flipped N/Q/H residues before XYZ refinement:
** E 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E1022 ASN
** M 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 144 GLN
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 ASN
A 127 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.082954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.070729 restraints weight = 61112.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.072642 restraints weight = 40152.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.074047 restraints weight = 29003.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3587
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3587 r_free = 0.3587    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3587 r_free = 0.3587    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3587
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.4826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10658  Z= 0.127
  Angle     :  0.740  11.218  14519  Z= 0.378
  Chirality :  0.047   0.264   1686
  Planarity :  0.004   0.049   1879
  Dihedral  :  6.907  38.779   1491
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.88 %
    Favored  : 84.12 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.90 %
    Favored  : 97.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -3.54 (0.20), residues: 1385
  helix: -0.40 (0.33), residues: 243
  sheet: -2.28 (0.38), residues: 162
  loop : -3.14 (0.17), residues: 980

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 183 
 HIS   0.005   0.001   HIS B  71 
 PHE   0.023   0.002   PHE B  58 
 TYR   0.019   0.002   TYR K 436 
 ARG   0.004   0.000   ARG E 973 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03462 (  223)
  hydrogen bonds       : angle       5.30947 (  627)
  covalent geometry    : bond        0.00280 (10658)
  covalent geometry    : angle       0.74040 (14519)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 206
  time to evaluate  : 1.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  113 VAL cc_start: 0.7137 (t) cc_final: 0.6874 (t)
REVERT: K  117 TYR cc_start: 0.5550 (m-10) cc_final: 0.5231 (m-10)
REVERT: M  135 LEU cc_start: 0.8672 (pp) cc_final: 0.8380 (pp)
REVERT: M  139 ARG cc_start: 0.8943 (mmp-170) cc_final: 0.8158 (mtt180)
REVERT: F  120 GLU cc_start: 0.8300 (mp0) cc_final: 0.8061 (mp0)
REVERT: F  199 SER cc_start: 0.9101 (t) cc_final: 0.8854 (m)
REVERT: F  291 LYS cc_start: 0.7715 (pttp) cc_final: 0.6294 (mmmt)
REVERT: B   54 ASP cc_start: 0.8314 (p0) cc_final: 0.7455 (p0)
REVERT: B  325 MET cc_start: 0.8664 (mmp) cc_final: 0.7445 (ppp)
REVERT: B  347 LYS cc_start: 0.8451 (mttt) cc_final: 0.8140 (mppt)
REVERT: B  354 ASP cc_start: 0.8970 (m-30) cc_final: 0.8010 (t0)
REVERT: A   42 ASN cc_start: 0.9029 (m-40) cc_final: 0.8073 (m-40)
REVERT: A   54 HIS cc_start: 0.7127 (m90) cc_final: 0.6623 (m-70)
REVERT: A   88 LEU cc_start: 0.6541 (tt) cc_final: 0.6208 (tt)
REVERT: A  107 LYS cc_start: 0.9299 (mtpt) cc_final: 0.7967 (mtpt)
REVERT: A  109 ASN cc_start: 0.9216 (m110) cc_final: 0.8619 (m110)
REVERT: A  142 VAL cc_start: 0.9405 (p) cc_final: 0.9078 (m)
REVERT: A  149 ASN cc_start: 0.9241 (m-40) cc_final: 0.8920 (m-40)
REVERT: A  154 LEU cc_start: 0.8551 (tp) cc_final: 0.8349 (tp)
REVERT: A  173 CYS cc_start: 0.9080 (m) cc_final: 0.8799 (m)
REVERT: A  195 VAL cc_start: 0.8583 (m) cc_final: 0.7939 (p)
REVERT: A  233 GLU cc_start: 0.7882 (tp30) cc_final: 0.7484 (tp30)
REVERT: A  241 CYS cc_start: 0.8286 (p) cc_final: 0.7366 (m)
REVERT: A  291 MET cc_start: 0.8467 (tpp) cc_final: 0.7135 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 206
  average time/residue: 0.2192
  time to fit residues: 65.2815
Evaluate side-chains
  152 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 1.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 85 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 88 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 114 optimal weight:    0.8980
   chunk 101 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 6 optimal weight:    9.9990
   chunk 41 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** E 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 225 ASN
K 444 ASN
** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 144 GLN
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 ASN
A 127 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.079659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.067595 restraints weight = 61863.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.069474 restraints weight = 40853.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.070797 restraints weight = 29665.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3511
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3511 r_free = 0.3511    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3510 r_free = 0.3510    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3510
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.4972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10658  Z= 0.176
  Angle     :  0.769  10.721  14519  Z= 0.399
  Chirality :  0.049   0.247   1686
  Planarity :  0.005   0.048   1879
  Dihedral  :  7.015  38.777   1491
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 19.84
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 16.32 %
    Favored  : 83.61 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.83 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -3.66 (0.20), residues: 1385
  helix: -0.66 (0.31), residues: 251
  sheet: -2.47 (0.38), residues: 158
  loop : -3.16 (0.18), residues: 976

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 183 
 HIS   0.014   0.002   HIS B  71 
 PHE   0.023   0.002   PHE B  58 
 TYR   0.021   0.002   TYR A 284 
 ARG   0.005   0.001   ARG K 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03765 (  223)
  hydrogen bonds       : angle       5.31728 (  627)
  covalent geometry    : bond        0.00381 (10658)
  covalent geometry    : angle       0.76908 (14519)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 189
  time to evaluate  : 1.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  825 PHE cc_start: 0.7185 (m-10) cc_final: 0.6791 (m-10)
REVERT: K  483 LYS cc_start: 0.9081 (mptt) cc_final: 0.8413 (mttm)
REVERT: M  135 LEU cc_start: 0.8759 (pp) cc_final: 0.8393 (pp)
REVERT: M  139 ARG cc_start: 0.9004 (mmp-170) cc_final: 0.8223 (mtt180)
REVERT: F  199 SER cc_start: 0.9208 (t) cc_final: 0.8970 (m)
REVERT: F  291 LYS cc_start: 0.7727 (pttp) cc_final: 0.7390 (pttm)
REVERT: B  354 ASP cc_start: 0.8939 (m-30) cc_final: 0.7793 (t70)
REVERT: A   54 HIS cc_start: 0.7107 (m90) cc_final: 0.6525 (m170)
REVERT: A  109 ASN cc_start: 0.9372 (m110) cc_final: 0.9169 (m-40)
REVERT: A  149 ASN cc_start: 0.9281 (m-40) cc_final: 0.8822 (m-40)
REVERT: A  241 CYS cc_start: 0.8301 (p) cc_final: 0.7351 (m)
REVERT: A  291 MET cc_start: 0.8558 (tpp) cc_final: 0.7152 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 190
  average time/residue: 0.2830
  time to fit residues: 78.5468
Evaluate side-chains
  147 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 102 optimal weight:    9.9990
   chunk 68 optimal weight:    4.9990
   chunk 115 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 93 optimal weight:    8.9990
   chunk 80 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 44 optimal weight:    7.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** E 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 144 GLN
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 ASN
A 127 ASN
A 194 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.080576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.069081 restraints weight = 62103.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.070867 restraints weight = 41436.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.072142 restraints weight = 30264.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3537
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3537 r_free = 0.3537    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3537 r_free = 0.3537    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3537
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.5190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10658  Z= 0.149
  Angle     :  0.763  11.153  14519  Z= 0.392
  Chirality :  0.048   0.250   1686
  Planarity :  0.004   0.049   1879
  Dihedral  :  6.852  37.814   1491
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 18.24
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 15.74 %
    Favored  : 84.19 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.54 %
    Favored  : 98.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -3.54 (0.20), residues: 1385
  helix: -0.28 (0.32), residues: 239
  sheet: -2.50 (0.38), residues: 152
  loop : -3.12 (0.18), residues: 994

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP K 135 
 HIS   0.013   0.001   HIS B  71 
 PHE   0.022   0.002   PHE B  58 
 TYR   0.026   0.002   TYR A 260 
 ARG   0.004   0.000   ARG E 973 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03557 (  223)
  hydrogen bonds       : angle       5.20685 (  627)
  covalent geometry    : bond        0.00327 (10658)
  covalent geometry    : angle       0.76280 (14519)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 182
  time to evaluate  : 1.682 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  825 PHE cc_start: 0.7032 (m-10) cc_final: 0.6550 (m-10)
REVERT: K  483 LYS cc_start: 0.9082 (mptt) cc_final: 0.8398 (mttm)
REVERT: M  139 ARG cc_start: 0.9010 (mmp-170) cc_final: 0.8604 (mmt180)
REVERT: F  199 SER cc_start: 0.9091 (t) cc_final: 0.8851 (m)
REVERT: F  291 LYS cc_start: 0.7602 (pttp) cc_final: 0.7217 (pttm)
REVERT: B   54 ASP cc_start: 0.8464 (p0) cc_final: 0.7481 (p0)
REVERT: B  106 LYS cc_start: 0.8663 (tttp) cc_final: 0.8410 (mtpp)
REVERT: B  325 MET cc_start: 0.8672 (mmp) cc_final: 0.7481 (ppp)
REVERT: B  354 ASP cc_start: 0.8893 (m-30) cc_final: 0.7748 (t70)
REVERT: A   42 ASN cc_start: 0.9078 (m-40) cc_final: 0.8045 (m-40)
REVERT: A   54 HIS cc_start: 0.7149 (m90) cc_final: 0.6589 (m170)
REVERT: A  109 ASN cc_start: 0.9320 (m110) cc_final: 0.9103 (m-40)
REVERT: A  241 CYS cc_start: 0.8284 (p) cc_final: 0.7338 (m)
REVERT: A  291 MET cc_start: 0.8525 (tpp) cc_final: 0.7100 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 182
  average time/residue: 0.2625
  time to fit residues: 71.1125
Evaluate side-chains
  142 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 1.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 83 optimal weight:    8.9990
   chunk 76 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   chunk 80 optimal weight:    4.9990
   chunk 92 optimal weight:   10.0000
   chunk 100 optimal weight:    0.1980
   chunk 60 optimal weight:   10.0000
   chunk 132 optimal weight:    0.9990
   chunk 129 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 102 optimal weight:    0.6980
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** E 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 144 GLN
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 ASN
A 127 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.081126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.069675 restraints weight = 61659.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.071473 restraints weight = 40936.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.072763 restraints weight = 29854.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3553
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3553
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.5363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10658  Z= 0.137
  Angle     :  0.750  11.320  14519  Z= 0.384
  Chirality :  0.048   0.256   1686
  Planarity :  0.004   0.060   1879
  Dihedral  :  6.718  36.302   1491
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 17.44
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 15.74 %
    Favored  : 84.19 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.16 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -3.47 (0.20), residues: 1385
  helix: -0.13 (0.32), residues: 239
  sheet: -2.46 (0.39), residues: 144
  loop : -3.10 (0.18), residues: 1002

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP K 135 
 HIS   0.007   0.001   HIS B  71 
 PHE   0.026   0.002   PHE B  58 
 TYR   0.014   0.002   TYR B 281 
 ARG   0.004   0.000   ARG K 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03451 (  223)
  hydrogen bonds       : angle       5.13802 (  627)
  covalent geometry    : bond        0.00306 (10658)
  covalent geometry    : angle       0.75030 (14519)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 192
  time to evaluate  : 1.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  825 PHE cc_start: 0.6914 (m-10) cc_final: 0.6549 (m-10)
REVERT: K  483 LYS cc_start: 0.9036 (mptt) cc_final: 0.8367 (mttm)
REVERT: M  139 ARG cc_start: 0.9000 (mmp-170) cc_final: 0.8604 (mmt180)
REVERT: F  199 SER cc_start: 0.9055 (t) cc_final: 0.8802 (m)
REVERT: F  291 LYS cc_start: 0.7614 (pttp) cc_final: 0.7254 (pttm)
REVERT: B   54 ASP cc_start: 0.8449 (p0) cc_final: 0.7453 (p0)
REVERT: B   83 ASP cc_start: 0.8072 (t0) cc_final: 0.7694 (t0)
REVERT: B  106 LYS cc_start: 0.8652 (tttp) cc_final: 0.8378 (mtpp)
REVERT: B  148 ASP cc_start: 0.7582 (m-30) cc_final: 0.7325 (m-30)
REVERT: B  325 MET cc_start: 0.8750 (mmp) cc_final: 0.7227 (ppp)
REVERT: B  354 ASP cc_start: 0.8950 (m-30) cc_final: 0.7860 (t70)
REVERT: A   42 ASN cc_start: 0.9040 (m-40) cc_final: 0.8033 (m-40)
REVERT: A   54 HIS cc_start: 0.7173 (m90) cc_final: 0.6720 (m170)
REVERT: A   68 GLN cc_start: 0.8485 (tt0) cc_final: 0.8208 (tm-30)
REVERT: A  154 LEU cc_start: 0.8278 (tp) cc_final: 0.8064 (tt)
REVERT: A  241 CYS cc_start: 0.8292 (p) cc_final: 0.7323 (m)
REVERT: A  291 MET cc_start: 0.8489 (tpp) cc_final: 0.7100 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 192
  average time/residue: 0.2236
  time to fit residues: 63.6134
Evaluate side-chains
  142 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 1.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 119 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0970
   chunk 9 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0370
   chunk 53 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 47 optimal weight:    0.0570
   chunk 22 optimal weight:    8.9990
   chunk 17 optimal weight:   10.0000
   overall best weight:    0.4174

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

Flipped N/Q/H residues before XYZ refinement:
** E 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 144 GLN
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 196 GLN
F 318 GLN
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 ASN
A 109 ASN
A 127 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.084315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.072701 restraints weight = 61500.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.074530 restraints weight = 40959.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.075875 restraints weight = 29858.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3627
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3627
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.5900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10658  Z= 0.129
  Angle     :  0.743  11.239  14519  Z= 0.379
  Chirality :  0.048   0.262   1686
  Planarity :  0.004   0.050   1879
  Dihedral  :  6.259  33.749   1491
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 14.22 %
    Favored  : 85.70 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.68 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -3.32 (0.20), residues: 1385
  helix:  0.25 (0.34), residues: 240
  sheet: -2.36 (0.39), residues: 138
  loop : -3.07 (0.17), residues: 1007

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 320 
 HIS   0.010   0.001   HIS B  71 
 PHE   0.026   0.002   PHE B  58 
 TYR   0.019   0.002   TYR K 117 
 ARG   0.005   0.000   ARG E 980 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03313 (  223)
  hydrogen bonds       : angle       4.90159 (  627)
  covalent geometry    : bond        0.00269 (10658)
  covalent geometry    : angle       0.74315 (14519)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 202
  time to evaluate  : 1.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  825 PHE cc_start: 0.6870 (m-10) cc_final: 0.6418 (m-10)
REVERT: K   92 MET cc_start: 0.4455 (pmm) cc_final: 0.3425 (pmm)
REVERT: K  117 TYR cc_start: 0.5782 (m-10) cc_final: 0.5491 (m-10)
REVERT: K  483 LYS cc_start: 0.9036 (mptt) cc_final: 0.8361 (mttm)
REVERT: M  139 ARG cc_start: 0.8980 (mmp-170) cc_final: 0.8340 (mmt180)
REVERT: F  120 GLU cc_start: 0.8279 (mp0) cc_final: 0.7862 (pm20)
REVERT: F  182 ASP cc_start: 0.7068 (t70) cc_final: 0.6342 (t70)
REVERT: F  183 MET cc_start: 0.8551 (mmp) cc_final: 0.8028 (pmm)
REVERT: F  199 SER cc_start: 0.8935 (t) cc_final: 0.8601 (m)
REVERT: F  269 TYR cc_start: 0.7440 (p90) cc_final: 0.7191 (p90)
REVERT: F  291 LYS cc_start: 0.7539 (pttp) cc_final: 0.6116 (mmmt)
REVERT: F  311 ASN cc_start: 0.8313 (t0) cc_final: 0.8089 (t0)
REVERT: B   54 ASP cc_start: 0.8340 (p0) cc_final: 0.7335 (p0)
REVERT: B   83 ASP cc_start: 0.7941 (t0) cc_final: 0.7535 (t0)
REVERT: B  148 ASP cc_start: 0.7481 (m-30) cc_final: 0.7222 (m-30)
REVERT: B  199 HIS cc_start: 0.7392 (t70) cc_final: 0.6834 (t70)
REVERT: B  229 LEU cc_start: 0.9552 (mt) cc_final: 0.9336 (mt)
REVERT: B  325 MET cc_start: 0.8633 (mmp) cc_final: 0.7286 (ppp)
REVERT: B  347 LYS cc_start: 0.8354 (mttt) cc_final: 0.8064 (mppt)
REVERT: B  354 ASP cc_start: 0.8958 (m-30) cc_final: 0.7943 (t0)
REVERT: A   42 ASN cc_start: 0.8923 (m-40) cc_final: 0.7976 (m-40)
REVERT: A   54 HIS cc_start: 0.7084 (m90) cc_final: 0.6592 (m170)
REVERT: A  116 MET cc_start: 0.6815 (tmm) cc_final: 0.6362 (tmm)
REVERT: A  142 VAL cc_start: 0.9328 (p) cc_final: 0.9048 (m)
REVERT: A  154 LEU cc_start: 0.8342 (tp) cc_final: 0.7889 (tp)
REVERT: A  241 CYS cc_start: 0.8145 (p) cc_final: 0.7157 (m)
REVERT: A  291 MET cc_start: 0.8264 (tpp) cc_final: 0.6934 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 203
  average time/residue: 0.2090
  time to fit residues: 62.4415
Evaluate side-chains
  152 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 1.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 111 optimal weight:    0.1980
   chunk 5 optimal weight:    8.9990
   chunk 60 optimal weight:   10.0000
   chunk 114 optimal weight:    0.3980
   chunk 116 optimal weight:    0.5980
   chunk 34 optimal weight:    4.9990
   chunk 136 optimal weight:    9.9990
   chunk 64 optimal weight:    0.0050
   chunk 14 optimal weight:    3.9990
   chunk 42 optimal weight:    9.9990
   overall best weight:    0.4394

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

Flipped N/Q/H residues before XYZ refinement:
E 821 ASN
** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 ASN
A 109 ASN
A 127 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.084188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.072480 restraints weight = 61133.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.074325 restraints weight = 40899.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.075649 restraints weight = 29798.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3624
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3624 r_free = 0.3624    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3624 r_free = 0.3624    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3624
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.6074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10658  Z= 0.123
  Angle     :  0.726  11.593  14519  Z= 0.369
  Chirality :  0.047   0.270   1686
  Planarity :  0.004   0.051   1879
  Dihedral  :  6.121  32.403   1491
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 13.57 %
    Favored  : 86.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -3.24 (0.20), residues: 1385
  helix:  0.26 (0.33), residues: 240
  sheet: -2.32 (0.40), residues: 137
  loop : -2.99 (0.17), residues: 1008

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 183 
 HIS   0.005   0.001   HIS B  71 
 PHE   0.027   0.001   PHE B  58 
 TYR   0.026   0.002   TYR K 117 
 ARG   0.011   0.001   ARG E 980 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03287 (  223)
  hydrogen bonds       : angle       4.85022 (  627)
  covalent geometry    : bond        0.00268 (10658)
  covalent geometry    : angle       0.72577 (14519)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4828.46 seconds
wall clock time: 89 minutes 36.56 seconds (5376.56 seconds total)