Starting phenix.real_space_refine
on Fri Feb 14 18:58:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6bx3_7303/02_2025/6bx3_7303.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6bx3_7303/02_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_7303/02_2025/6bx3_7303.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6bx3_7303/02_2025/6bx3_7303.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6bx3_7303/02_2025/6bx3_7303.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6bx3_7303/02_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-5592/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: 6.64, per 1000 atoms: 0.64
  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: 2.50
  Conformation dependent library (CDL) restraints added in 1.5 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: 1.07
  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: 2.69

  Time building geometry restraints manager: 2.91 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:             2.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     25.680
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.010
-------------------------------------------------------------------------------
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= 0.499
  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 

*********************** 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  : 1.243 
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: 0.2507
  time to fit residues: 99.3942
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  : 1.310 
-------------------------------------------------------------------------------
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 = 59367.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.069651 restraints weight = 38515.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.071066 restraints weight = 27864.512|
|-----------------------------------------------------------------------------|
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= 0.269
  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 

*********************** 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  : 1.285 
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: 0.8151 (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: 0.8658 (t60) cc_final: 0.8339 (t60)
REVERT: K  199 PHE cc_start: 0.9336 (t80) cc_final: 0.9065 (t80)
REVERT: K  439 THR cc_start: 0.5765 (OUTLIER) cc_final: 0.5565 (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: 0.7931 (p)
REVERT: F  291 LYS cc_start: 0.7819 (pttp) cc_final: 0.6499 (mmmt)
REVERT: B   83 ASP cc_start: 0.8190 (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: 0.6540 (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: 0.8417 (m100) cc_final: 0.8046 (m100)
REVERT: B  354 ASP cc_start: 0.8954 (m-30) cc_final: 0.8119 (t0)
REVERT: A   26 GLN cc_start: 0.9177 (mp10) cc_final: 0.8907 (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: 0.8188 (tp)
REVERT: A  194 GLN cc_start: 0.8952 (mt0) cc_final: 0.8651 (mt0)
REVERT: A  195 VAL cc_start: 0.8530 (m) cc_final: 0.7709 (p)
REVERT: A  199 GLU cc_start: 0.8545 (pm20) cc_final: 0.8059 (pm20)
REVERT: A  233 GLU cc_start: 0.7715 (tp30) cc_final: 0.7376 (tp30)
REVERT: A  291 MET cc_start: 0.8309 (tpp) cc_final: 0.7346 (mmp)
  outliers start: 4
  outliers final: 0
  residues processed: 240
  average time/residue: 0.2279
  time to fit residues: 77.1127
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  : 1.192 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 38 optimal weight:    7.9990
   chunk 127 optimal weight:    8.9990
   chunk 92 optimal weight:    9.9990
   chunk 122 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 107 optimal weight:   20.0000
   overall best weight:    2.6384

-------------------------------------------------------------------------------
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 = 0.3721 r_free = 0.3721 target = 0.079564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.067985 restraints weight = 62755.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.069745 restraints weight = 41450.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.071067 restraints weight = 30291.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3519
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3519 r_free = 0.3519    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 = 0.3519 r_free = 0.3519    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3519
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.3426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073  10658  Z= 0.276
  Angle     :  0.828  12.777  14519  Z= 0.430
  Chirality :  0.051   0.326   1686
  Planarity :  0.005   0.045   1879
  Dihedral  :  8.198  45.804   1491
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 20.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.76 %
    Favored  : 82.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  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: -4.08 (0.19), residues: 1385
  helix: -1.31 (0.30), residues: 248
  sheet: -2.75 (0.37), residues: 152
  loop : -3.35 (0.17), residues: 985

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP K 135 
 HIS   0.009   0.002   HIS B  71 
 PHE   0.019   0.002   PHE B  58 
 TYR   0.020   0.002   TYR F 344 
 ARG   0.005   0.001   ARG E 980 

*********************** 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
  211 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 1.315 
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  934 ASN cc_start: 0.9201 (t0) cc_final: 0.8889 (p0)
REVERT: E  979 MET cc_start: 0.8817 (tpt) cc_final: 0.8516 (tpp)
REVERT: E  998 ASP cc_start: 0.7319 (m-30) cc_final: 0.6528 (m-30)
REVERT: K  199 PHE cc_start: 0.9315 (t80) cc_final: 0.9050 (t80)
REVERT: K  238 LEU cc_start: 0.8773 (tp) cc_final: 0.8552 (tp)
REVERT: M  135 LEU cc_start: 0.8599 (pp) cc_final: 0.8329 (pp)
REVERT: M  139 ARG cc_start: 0.8892 (mmp-170) cc_final: 0.8148 (mtt180)
REVERT: M  156 TYR cc_start: 0.8595 (t80) cc_final: 0.7858 (t80)
REVERT: F  266 CYS cc_start: 0.8404 (p) cc_final: 0.8126 (p)
REVERT: F  291 LYS cc_start: 0.7819 (pttp) cc_final: 0.6512 (mmmt)
REVERT: B   54 ASP cc_start: 0.8318 (p0) cc_final: 0.7383 (p0)
REVERT: B  106 LYS cc_start: 0.8682 (tttp) cc_final: 0.8417 (mtpp)
REVERT: B  319 ASN cc_start: 0.9082 (t0) cc_final: 0.8870 (t0)
REVERT: B  354 ASP cc_start: 0.9000 (m-30) cc_final: 0.7972 (t0)
REVERT: A  107 LYS cc_start: 0.8935 (mtpt) cc_final: 0.8715 (mtpt)
REVERT: A  109 ASN cc_start: 0.9216 (m110) cc_final: 0.8664 (m-40)
REVERT: A  149 ASN cc_start: 0.9238 (m-40) cc_final: 0.8750 (m-40)
REVERT: A  154 LEU cc_start: 0.8666 (tp) cc_final: 0.8230 (tp)
REVERT: A  183 TRP cc_start: 0.7708 (p-90) cc_final: 0.7292 (p-90)
REVERT: A  195 VAL cc_start: 0.8616 (m) cc_final: 0.7805 (p)
REVERT: A  199 GLU cc_start: 0.8616 (pm20) cc_final: 0.8278 (pm20)
REVERT: A  228 GLN cc_start: 0.7967 (mm110) cc_final: 0.7764 (mm110)
REVERT: A  291 MET cc_start: 0.8294 (tpp) cc_final: 0.7569 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 211
  average time/residue: 0.2152
  time to fit residues: 65.2410
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  : 1.296 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 36 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 27 optimal weight:   20.0000
   chunk 30 optimal weight:    6.9990
   chunk 26 optimal weight:    0.1980
   chunk 132 optimal weight:    3.9990
   chunk 63 optimal weight:    9.9990
   chunk 46 optimal weight:    0.0040
   chunk 77 optimal weight:    6.9990
   chunk 112 optimal weight:    7.9990
   overall best weight:    2.6398

-------------------------------------------------------------------------------
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**
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.079068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.066916 restraints weight = 59970.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.068753 restraints weight = 39189.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.070116 restraints weight = 28450.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3517
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    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 = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3517
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.4029

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= 0.252
  Angle     :  0.785  10.542  14519  Z= 0.411
  Chirality :  0.049   0.221   1686
  Planarity :  0.004   0.047   1879
  Dihedral  :  7.702  43.306   1491
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 18.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.62 %
    Favored  : 82.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  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: -3.86 (0.20), residues: 1385
  helix: -0.84 (0.31), residues: 249
  sheet: -2.75 (0.38), residues: 149
  loop : -3.26 (0.17), residues: 987

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP K 135 
 HIS   0.010   0.002   HIS B  71 
 PHE   0.022   0.002   PHE B  58 
 TYR   0.020   0.002   TYR F 213 
 ARG   0.006   0.001   ARG B  59 

*********************** 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
  199 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 1.296 
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  934 ASN cc_start: 0.9109 (t0) cc_final: 0.8798 (p0)
REVERT: K  135 TRP cc_start: 0.8732 (t60) cc_final: 0.8496 (t60)
REVERT: K  483 LYS cc_start: 0.9181 (mptt) cc_final: 0.8548 (mtpt)
REVERT: M  139 ARG cc_start: 0.8929 (mmp-170) cc_final: 0.8250 (mtt180)
REVERT: M  156 TYR cc_start: 0.8688 (t80) cc_final: 0.8020 (t80)
REVERT: F  224 MET cc_start: 0.8550 (mmm) cc_final: 0.8300 (mmm)
REVERT: F  266 CYS cc_start: 0.8621 (p) cc_final: 0.8393 (p)
REVERT: F  291 LYS cc_start: 0.7875 (pttp) cc_final: 0.6495 (mmmt)
REVERT: B   54 ASP cc_start: 0.8328 (p0) cc_final: 0.7371 (p0)
REVERT: B  106 LYS cc_start: 0.8678 (tttp) cc_final: 0.8357 (mtpp)
REVERT: B  319 ASN cc_start: 0.9123 (t0) cc_final: 0.8918 (t0)
REVERT: B  354 ASP cc_start: 0.9040 (m-30) cc_final: 0.8124 (t0)
REVERT: A  107 LYS cc_start: 0.9345 (mtpt) cc_final: 0.8777 (mtpt)
REVERT: A  109 ASN cc_start: 0.9330 (m110) cc_final: 0.8722 (m110)
REVERT: A  149 ASN cc_start: 0.9265 (m-40) cc_final: 0.8715 (m-40)
REVERT: A  154 LEU cc_start: 0.8695 (tp) cc_final: 0.8397 (tp)
REVERT: A  183 TRP cc_start: 0.7676 (p-90) cc_final: 0.7280 (p-90)
REVERT: A  195 VAL cc_start: 0.8605 (m) cc_final: 0.7909 (p)
REVERT: A  199 GLU cc_start: 0.8233 (pm20) cc_final: 0.7999 (pm20)
REVERT: A  238 HIS cc_start: 0.7664 (p-80) cc_final: 0.7463 (p-80)
REVERT: A  291 MET cc_start: 0.8493 (tpp) cc_final: 0.7284 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.2176
  time to fit residues: 62.4252
Evaluate side-chains
  143 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 118 optimal weight:    3.9990
   chunk 135 optimal weight:    0.2980
   chunk 106 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 123 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 61 optimal weight:    7.9990
   chunk 112 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    1.0186

-------------------------------------------------------------------------------
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 932 GLN
** 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 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 = 0.3763 r_free = 0.3763 target = 0.081382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.069704 restraints weight = 60293.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.071523 restraints weight = 39438.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.072905 restraints weight = 28602.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3568
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3568 r_free = 0.3568    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3568 r_free = 0.3568    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3568
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
moved from start:          0.4421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10658  Z= 0.198
  Angle     :  0.757  11.341  14519  Z= 0.390
  Chirality :  0.048   0.240   1686
  Planarity :  0.004   0.035   1879
  Dihedral  :  7.252  41.139   1491
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 16.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.39 %
    Favored  : 83.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  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: -3.73 (0.20), residues: 1385
  helix: -0.55 (0.32), residues: 248
  sheet: -2.72 (0.38), residues: 151
  loop : -3.22 (0.17), residues: 986

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP K 135 
 HIS   0.009   0.001   HIS B  71 
 PHE   0.022   0.002   PHE B  58 
 TYR   0.016   0.002   TYR B 281 
 ARG   0.004   0.000   ARG B  85 

*********************** 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
  214 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 1.261 
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: 0.7204 (m-10) cc_final: 0.6982 (m-80)
REVERT: E  934 ASN cc_start: 0.9039 (t0) cc_final: 0.8765 (p0)
REVERT: K  117 TYR cc_start: 0.5583 (m-10) cc_final: 0.5259 (m-80)
REVERT: K  135 TRP cc_start: 0.8516 (t60) cc_final: 0.8238 (t60)
REVERT: K  237 PHE cc_start: 0.7891 (m-80) cc_final: 0.7534 (m-80)
REVERT: K  483 LYS cc_start: 0.9132 (mptt) cc_final: 0.8476 (mtpt)
REVERT: M  139 ARG cc_start: 0.8910 (mmp-170) cc_final: 0.8209 (mtt180)
REVERT: F  291 LYS cc_start: 0.7756 (pttp) cc_final: 0.6337 (mmmt)
REVERT: B   54 ASP cc_start: 0.8369 (p0) cc_final: 0.7434 (p0)
REVERT: B  354 ASP cc_start: 0.8997 (m-30) cc_final: 0.8132 (t0)
REVERT: A  107 LYS cc_start: 0.9304 (mtpt) cc_final: 0.8723 (mtpt)
REVERT: A  109 ASN cc_start: 0.9241 (m110) cc_final: 0.8725 (m110)
REVERT: A  149 ASN cc_start: 0.9246 (m-40) cc_final: 0.8734 (m-40)
REVERT: A  154 LEU cc_start: 0.8591 (tp) cc_final: 0.8308 (tp)
REVERT: A  195 VAL cc_start: 0.8598 (m) cc_final: 0.7896 (p)
REVERT: A  291 MET cc_start: 0.8493 (tpp) cc_final: 0.7260 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.2135
  time to fit residues: 65.7718
Evaluate side-chains
  148 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 1.198 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 73 optimal weight:    6.9990
   chunk 113 optimal weight:    0.9980
   chunk 50 optimal weight:    9.9990
   chunk 77 optimal weight:    9.9990
   chunk 10 optimal weight:    8.9990
   chunk 43 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0050
   chunk 79 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   overall best weight:    0.7594

-------------------------------------------------------------------------------
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**
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.082529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.070279 restraints weight = 59862.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.072196 restraints weight = 39471.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.073572 restraints weight = 28596.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
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:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3587
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.4916

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= 0.188
  Angle     :  0.735  10.226  14519  Z= 0.375
  Chirality :  0.047   0.275   1686
  Planarity :  0.004   0.040   1879
  Dihedral  :  6.823  38.659   1491
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 15.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.52 %
    Favored  : 84.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  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: -3.59 (0.20), residues: 1385
  helix: -0.48 (0.33), residues: 243
  sheet: -2.36 (0.37), residues: 166
  loop : -3.14 (0.18), residues: 976

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP K 119 
 HIS   0.009   0.001   HIS B  71 
 PHE   0.024   0.001   PHE B  58 
 TYR   0.016   0.001   TYR B 281 
 ARG   0.003   0.000   ARG E 973 

*********************** 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
  208 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 1.285 
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: K  478 LEU cc_start: 0.8746 (mt) cc_final: 0.7813 (tp)
REVERT: K  483 LYS cc_start: 0.9162 (mptt) cc_final: 0.8469 (mttm)
REVERT: M  139 ARG cc_start: 0.9002 (mmp-170) cc_final: 0.8532 (mmt180)
REVERT: M  156 TYR cc_start: 0.8508 (t80) cc_final: 0.8134 (t80)
REVERT: F  120 GLU cc_start: 0.8243 (mp0) cc_final: 0.7870 (pm20)
REVERT: F  199 SER cc_start: 0.9107 (t) cc_final: 0.8875 (m)
REVERT: F  291 LYS cc_start: 0.7757 (pttp) cc_final: 0.6312 (mmmt)
REVERT: B   54 ASP cc_start: 0.8312 (p0) cc_final: 0.7349 (p0)
REVERT: B  325 MET cc_start: 0.8419 (mmp) cc_final: 0.7237 (ppp)
REVERT: B  347 LYS cc_start: 0.8462 (mttt) cc_final: 0.8148 (mppt)
REVERT: B  354 ASP cc_start: 0.9005 (m-30) cc_final: 0.8196 (t0)
REVERT: A   42 ASN cc_start: 0.9152 (m110) cc_final: 0.8248 (m110)
REVERT: A   54 HIS cc_start: 0.7387 (m90) cc_final: 0.7028 (m90)
REVERT: A   88 LEU cc_start: 0.6657 (tt) cc_final: 0.6391 (tt)
REVERT: A  107 LYS cc_start: 0.9260 (mtpt) cc_final: 0.8093 (mtpt)
REVERT: A  109 ASN cc_start: 0.9215 (m110) cc_final: 0.8722 (m110)
REVERT: A  142 VAL cc_start: 0.9395 (p) cc_final: 0.9076 (m)
REVERT: A  149 ASN cc_start: 0.9250 (m-40) cc_final: 0.8886 (m-40)
REVERT: A  154 LEU cc_start: 0.8419 (tp) cc_final: 0.8086 (tp)
REVERT: A  155 SER cc_start: 0.7139 (p) cc_final: 0.6937 (p)
REVERT: A  195 VAL cc_start: 0.8489 (m) cc_final: 0.7797 (p)
REVERT: A  233 GLU cc_start: 0.8108 (tp30) cc_final: 0.7790 (tp30)
REVERT: A  241 CYS cc_start: 0.8261 (p) cc_final: 0.7375 (m)
REVERT: A  291 MET cc_start: 0.8502 (tpp) cc_final: 0.7188 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.2322
  time to fit residues: 69.2284
Evaluate side-chains
  150 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 1.338 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 85 optimal weight:    8.9990
   chunk 23 optimal weight:    2.9990
   chunk 88 optimal weight:   10.0000
   chunk 66 optimal weight:    5.9990
   chunk 114 optimal weight:    0.9980
   chunk 101 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0270
   chunk 41 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.9842

-------------------------------------------------------------------------------
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**
K 225 ASN
K 444 ASN
** M 160 GLN ** 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 319 ASN ** 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 = 0.3789 r_free = 0.3789 target = 0.083270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.071100 restraints weight = 60641.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.072951 restraints weight = 40169.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.074315 restraints weight = 29314.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3595
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3595 r_free = 0.3595    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3595 r_free = 0.3595    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3595
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.5176

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= 0.193
  Angle     :  0.731  10.676  14519  Z= 0.375
  Chirality :  0.048   0.250   1686
  Planarity :  0.004   0.044   1879
  Dihedral  :  6.638  37.785   1491
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 15.44
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 14.15 %
    Favored  : 85.78 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.74 %
    Favored  : 98.17 %
  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: -3.51 (0.20), residues: 1385
  helix: -0.41 (0.32), residues: 247
  sheet: -2.27 (0.38), residues: 166
  loop : -3.11 (0.18), residues: 972

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 183 
 HIS   0.009   0.001   HIS B  71 
 PHE   0.029   0.002   PHE A  58 
 TYR   0.019   0.001   TYR K 202 
 ARG   0.005   0.000   ARG K 188 

*********************** 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
  204 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 203
  time to evaluate  : 1.231 
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: 0.7018 (m-10) cc_final: 0.6630 (m-10)
REVERT: K  202 TYR cc_start: 0.6814 (p90) cc_final: 0.6286 (p90)
REVERT: K  237 PHE cc_start: 0.7617 (m-10) cc_final: 0.7338 (m-80)
REVERT: K  483 LYS cc_start: 0.9077 (mptt) cc_final: 0.8381 (mttm)
REVERT: M  139 ARG cc_start: 0.9029 (mmp-170) cc_final: 0.8629 (mmt180)
REVERT: M  156 TYR cc_start: 0.8481 (t80) cc_final: 0.7922 (t80)
REVERT: M  160 GLN cc_start: 0.6757 (pt0) cc_final: 0.6483 (pt0)
REVERT: F  199 SER cc_start: 0.9078 (t) cc_final: 0.8835 (m)
REVERT: F  224 MET cc_start: 0.8584 (mmm) cc_final: 0.8308 (mmm)
REVERT: F  291 LYS cc_start: 0.7693 (pttp) cc_final: 0.6266 (mmmt)
REVERT: B   30 GLU cc_start: 0.7033 (tt0) cc_final: 0.6663 (tp30)
REVERT: B   54 ASP cc_start: 0.8425 (p0) cc_final: 0.7447 (p0)
REVERT: B  199 HIS cc_start: 0.7169 (t70) cc_final: 0.6579 (t70)
REVERT: B  347 LYS cc_start: 0.8362 (mttt) cc_final: 0.8078 (mppt)
REVERT: B  354 ASP cc_start: 0.9035 (m-30) cc_final: 0.8273 (t0)
REVERT: A   42 ASN cc_start: 0.9070 (m110) cc_final: 0.8189 (m110)
REVERT: A   54 HIS cc_start: 0.7043 (m90) cc_final: 0.6546 (m-70)
REVERT: A   68 GLN cc_start: 0.8398 (tt0) cc_final: 0.8182 (tm-30)
REVERT: A   88 LEU cc_start: 0.6499 (tt) cc_final: 0.6216 (tt)
REVERT: A  107 LYS cc_start: 0.8947 (mtpt) cc_final: 0.8283 (mtpt)
REVERT: A  109 ASN cc_start: 0.9211 (m110) cc_final: 0.8676 (m110)
REVERT: A  149 ASN cc_start: 0.9282 (m-40) cc_final: 0.8891 (m-40)
REVERT: A  154 LEU cc_start: 0.8505 (tp) cc_final: 0.8288 (tp)
REVERT: A  195 VAL cc_start: 0.8533 (m) cc_final: 0.7859 (p)
REVERT: A  233 GLU cc_start: 0.8103 (tp30) cc_final: 0.7741 (tp30)
REVERT: A  241 CYS cc_start: 0.8235 (p) cc_final: 0.7284 (m)
REVERT: A  291 MET cc_start: 0.8491 (tpp) cc_final: 0.7201 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 204
  average time/residue: 0.2115
  time to fit residues: 62.4707
Evaluate side-chains
  149 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.218 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 102 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 115 optimal weight:    3.9990
   chunk 12 optimal weight:   10.0000
   chunk 93 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0970
   chunk 13 optimal weight:    8.9990
   chunk 44 optimal weight:    7.9990
   overall best weight:    1.9782

-------------------------------------------------------------------------------
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 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 196 GLN
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 240 GLN
** B 319 ASN ** 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 = 0.3751 r_free = 0.3751 target = 0.081421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.069285 restraints weight = 60413.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.071221 restraints weight = 39251.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.072572 restraints weight = 28289.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3552
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3552 r_free = 0.3552    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 = 0.3552 r_free = 0.3552    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3552
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.5332

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= 0.220
  Angle     :  0.735  10.805  14519  Z= 0.378
  Chirality :  0.048   0.248   1686
  Planarity :  0.004   0.037   1879
  Dihedral  :  6.642  36.242   1491
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 17.24
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 15.52 %
    Favored  : 84.40 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.45 %
    Favored  : 98.46 %
  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: -3.43 (0.20), residues: 1385
  helix: -0.29 (0.32), residues: 245
  sheet: -2.07 (0.42), residues: 144
  loop : -3.09 (0.17), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 183 
 HIS   0.011   0.001   HIS B  71 
 PHE   0.026   0.002   PHE B  58 
 TYR   0.024   0.002   TYR A 260 
 ARG   0.005   0.001   ARG B 228 

*********************** 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
  196 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 195
  time to evaluate  : 1.022 
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: 0.6986 (m-10) cc_final: 0.6563 (m-10)
REVERT: K  117 TYR cc_start: 0.5610 (m-10) cc_final: 0.5343 (m-10)
REVERT: K  483 LYS cc_start: 0.9116 (mptt) cc_final: 0.8445 (mttm)
REVERT: M  139 ARG cc_start: 0.9024 (mmp-170) cc_final: 0.8605 (mmt180)
REVERT: M  156 TYR cc_start: 0.8571 (t80) cc_final: 0.8001 (t80)
REVERT: M  160 GLN cc_start: 0.6886 (pt0) cc_final: 0.6635 (pt0)
REVERT: F  199 SER cc_start: 0.9073 (t) cc_final: 0.8758 (m)
REVERT: F  291 LYS cc_start: 0.7714 (pttp) cc_final: 0.6232 (mmmt)
REVERT: B   54 ASP cc_start: 0.8383 (p0) cc_final: 0.7366 (p0)
REVERT: B   83 ASP cc_start: 0.8107 (t0) cc_final: 0.7716 (t0)
REVERT: B  148 ASP cc_start: 0.7573 (m-30) cc_final: 0.7351 (m-30)
REVERT: B  229 LEU cc_start: 0.9653 (mt) cc_final: 0.9449 (mt)
REVERT: B  325 MET cc_start: 0.8526 (mmp) cc_final: 0.7509 (ppp)
REVERT: B  354 ASP cc_start: 0.9067 (m-30) cc_final: 0.8254 (t0)
REVERT: A   42 ASN cc_start: 0.9160 (m110) cc_final: 0.8322 (m110)
REVERT: A   54 HIS cc_start: 0.7122 (m90) cc_final: 0.6554 (m170)
REVERT: A  154 LEU cc_start: 0.8548 (tp) cc_final: 0.8335 (tp)
REVERT: A  233 GLU cc_start: 0.8221 (tp30) cc_final: 0.7834 (tp30)
REVERT: A  241 CYS cc_start: 0.8203 (p) cc_final: 0.7274 (m)
REVERT: A  291 MET cc_start: 0.8444 (tpp) cc_final: 0.7052 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 196
  average time/residue: 0.2022
  time to fit residues: 57.6200
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  : 1.297 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 18 optimal weight:   20.0000
   chunk 80 optimal weight:    1.9990
   chunk 92 optimal weight:    9.9990
   chunk 100 optimal weight:    7.9990
   chunk 60 optimal weight:    9.9990
   chunk 132 optimal weight:    3.9990
   chunk 129 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 102 optimal weight:    6.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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**
** E1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 160 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**
** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 127 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.077000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.065256 restraints weight = 62545.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.067002 restraints weight = 41579.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.068244 restraints weight = 30575.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3449
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3449
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.5362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  10658  Z= 0.361
  Angle     :  0.841  11.448  14519  Z= 0.439
  Chirality :  0.051   0.235   1686
  Planarity :  0.005   0.063   1879
  Dihedral  :  7.270  40.029   1491
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 24.29
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 18.77 %
    Favored  : 81.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    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: -3.63 (0.20), residues: 1385
  helix: -0.37 (0.31), residues: 239
  sheet: -2.58 (0.37), residues: 153
  loop : -3.16 (0.18), residues: 993

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP B 320 
 HIS   0.013   0.002   HIS B  71 
 PHE   0.024   0.002   PHE B  58 
 TYR   0.026   0.003   TYR F 344 
 ARG   0.006   0.001   ARG E 841 

*********************** 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
  177 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 1.109 
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: K  483 LYS cc_start: 0.9058 (mptt) cc_final: 0.8421 (mttm)
REVERT: M  139 ARG cc_start: 0.8996 (mmp-170) cc_final: 0.8611 (mmt180)
REVERT: M  156 TYR cc_start: 0.8668 (t80) cc_final: 0.8275 (t80)
REVERT: F  269 TYR cc_start: 0.7814 (p90) cc_final: 0.7520 (p90)
REVERT: F  291 LYS cc_start: 0.7698 (pttp) cc_final: 0.6439 (mmmt)
REVERT: B   54 ASP cc_start: 0.8455 (p0) cc_final: 0.7468 (p0)
REVERT: B   83 ASP cc_start: 0.8262 (t0) cc_final: 0.7840 (t0)
REVERT: B  148 ASP cc_start: 0.7542 (m-30) cc_final: 0.7298 (m-30)
REVERT: B  354 ASP cc_start: 0.9098 (m-30) cc_final: 0.8289 (t0)
REVERT: A   54 HIS cc_start: 0.7206 (m90) cc_final: 0.6609 (m170)
REVERT: A  173 CYS cc_start: 0.9326 (m) cc_final: 0.9084 (m)
REVERT: A  241 CYS cc_start: 0.8321 (p) cc_final: 0.7416 (m)
REVERT: A  291 MET cc_start: 0.8502 (tpp) cc_final: 0.7233 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.2126
  time to fit residues: 54.6708
Evaluate side-chains
  125 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 20 optimal weight:    8.9990
   chunk 61 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0570
   chunk 89 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 73 optimal weight:    0.0670
   chunk 6 optimal weight:    6.9990
   chunk 47 optimal weight:    0.0030
   chunk 22 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.2250

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

Flipped N/Q/H residues before XYZ refinement:
** E1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 160 GLN ** 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 109 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.080753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.068651 restraints weight = 61071.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.070554 restraints weight = 39772.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.071900 restraints weight = 28743.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3529
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3529 r_free = 0.3529    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 = 0.3529 r_free = 0.3529    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3529
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7289
moved from start:          0.5612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10658  Z= 0.205
  Angle     :  0.766  11.977  14519  Z= 0.392
  Chirality :  0.049   0.267   1686
  Planarity :  0.004   0.051   1879
  Dihedral  :  6.747  35.259   1491
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 17.74
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 15.31 %
    Favored  : 84.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  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: -3.45 (0.20), residues: 1385
  helix: -0.09 (0.32), residues: 244
  sheet: -2.49 (0.38), residues: 163
  loop : -3.09 (0.18), residues: 978

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 183 
 HIS   0.008   0.001   HIS B  71 
 PHE   0.026   0.002   PHE B  58 
 TYR   0.029   0.002   TYR A 260 
 ARG   0.005   0.000   ARG E 980 

********************** 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
  191 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 1.349 
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  815 ASP cc_start: 0.9021 (t70) cc_final: 0.8369 (t70)
REVERT: E  819 GLU cc_start: 0.9321 (mm-30) cc_final: 0.8926 (mm-30)
REVERT: E  825 PHE cc_start: 0.6878 (m-10) cc_final: 0.6341 (m-10)
REVERT: E  934 ASN cc_start: 0.8935 (t0) cc_final: 0.8477 (p0)
REVERT: K  117 TYR cc_start: 0.5839 (m-10) cc_final: 0.5438 (m-10)
REVERT: K  135 TRP cc_start: 0.8375 (t60) cc_final: 0.7972 (t60)
REVERT: K  436 TYR cc_start: 0.8523 (m-80) cc_final: 0.8294 (m-10)
REVERT: K  483 LYS cc_start: 0.8988 (mptt) cc_final: 0.8330 (mttm)
REVERT: M  135 LEU cc_start: 0.8560 (pt) cc_final: 0.8353 (pt)
REVERT: M  139 ARG cc_start: 0.8960 (mmp-170) cc_final: 0.8596 (mmt180)
REVERT: M  156 TYR cc_start: 0.8564 (t80) cc_final: 0.8221 (t80)
REVERT: F  269 TYR cc_start: 0.7725 (p90) cc_final: 0.7436 (p90)
REVERT: F  291 LYS cc_start: 0.7583 (pttp) cc_final: 0.7211 (pttm)
REVERT: B   54 ASP cc_start: 0.8491 (p0) cc_final: 0.7520 (p0)
REVERT: B   83 ASP cc_start: 0.8090 (t0) cc_final: 0.7694 (t0)
REVERT: B  148 ASP cc_start: 0.7516 (m-30) cc_final: 0.7264 (m-30)
REVERT: B  199 HIS cc_start: 0.7394 (t70) cc_final: 0.6964 (t70)
REVERT: B  325 MET cc_start: 0.8702 (mmp) cc_final: 0.7277 (ppp)
REVERT: B  354 ASP cc_start: 0.9047 (m-30) cc_final: 0.8207 (t0)
REVERT: A   54 HIS cc_start: 0.7116 (m90) cc_final: 0.6542 (m170)
REVERT: A   68 GLN cc_start: 0.8516 (tt0) cc_final: 0.8227 (tm-30)
REVERT: A  233 GLU cc_start: 0.8504 (tp30) cc_final: 0.8198 (tp30)
REVERT: A  241 CYS cc_start: 0.8287 (p) cc_final: 0.7353 (m)
REVERT: A  291 MET cc_start: 0.8430 (tpp) cc_final: 0.7110 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.2100
  time to fit residues: 58.9471
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  : 1.165 
-------------------------------------------------------------------------------
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:    0.0000
   chunk 111 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 60 optimal weight:   10.0000
   chunk 114 optimal weight:    7.9990
   chunk 116 optimal weight:    0.0370
   chunk 34 optimal weight:    0.8980
   chunk 136 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.5062

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

Flipped N/Q/H residues before XYZ refinement:
** E1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 160 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 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 ASN
A  95 HIS
A 109 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 = 0.3779 r_free = 0.3779 target = 0.082930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.071311 restraints weight = 61974.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.073135 restraints weight = 40868.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.074425 restraints weight = 29589.219|
|-----------------------------------------------------------------------------|
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: 0.7210
moved from start:          0.5924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10658  Z= 0.191
  Angle     :  0.749  11.573  14519  Z= 0.380
  Chirality :  0.048   0.273   1686
  Planarity :  0.004   0.047   1879
  Dihedral  :  6.401  35.737   1491
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 16.14
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 14.22 %
    Favored  : 85.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  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: -3.34 (0.20), residues: 1385
  helix:  0.13 (0.33), residues: 240
  sheet: -2.27 (0.39), residues: 152
  loop : -3.07 (0.17), residues: 993

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 320 
 HIS   0.012   0.001   HIS B  71 
 PHE   0.025   0.002   PHE B  58 
 TYR   0.028   0.001   TYR F 213 
 ARG   0.005   0.000   ARG E 983 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3595.19 seconds
wall clock time: 65 minutes 23.63 seconds (3923.63 seconds total)