Starting phenix.real_space_refine
on Thu Mar 13 01:43:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y12_33554/03_2025/7y12_33554.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y12_33554/03_2025/7y12_33554.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y12_33554/03_2025/7y12_33554.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y12_33554/03_2025/7y12_33554.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y12_33554/03_2025/7y12_33554.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y12_33554/03_2025/7y12_33554.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
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      69      5.16       5
     C    5431      2.51       5
     N    1454      2.21       5
     O    1547      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8501
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1654
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 1, 'TRANS': 216}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 104
          Unresolved non-hydrogen angles: 123
          Unresolved non-hydrogen dihedrals: 85
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 66
    Chain: "B"
      Number of atoms: 2553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2553
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 35
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 46
    Chain: "C"
      Number of atoms: 435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 435
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "R"
      Number of atoms: 2053
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2053
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 10, 'TRANS': 253}
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 40
    Chain: "S"
      Number of atoms: 1746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1746
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "R"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 6
          Unusual residues: {'BAL': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 54
          Unusual residues: {'PLM': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.90, per 1000 atoms: 0.69
  Number of scatterers: 8501
  At special positions: 0
  Unit cell: (122.85, 84.375, 124.2, 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      69     16.00
     O    1547      8.00
     N    1454      7.00
     C    5431      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 164 " - pdb=" SG  CYS R 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.42
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  BAL R1001 "
  Number of C-beta restraints generated:  2082

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      37.6% alpha, 22.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 51
    Processing helix  chain 'A' and resid 202 through 205
      removed outlier: 4.038A  pdb=" N   ARG A 205 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 202 through 205'
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.158A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.503A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.537A  pdb=" N   PHE A 274 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.686A  pdb=" N   CYS A 286 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 352
      removed outlier: 3.583A  pdb=" N   PHE A 334 " --> pdb=" O   LYS A 330 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE A 336 " --> pdb=" O   VAL A 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 280 through 282
      No H-bonds generated for 'chain 'B' and resid 280 through 282'
    Processing helix  chain 'C' and resid 9 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'R' and resid 23 through 52
    Processing helix  chain 'R' and resid 62 through 88
    Processing helix  chain 'R' and resid 92 through 129
      removed outlier: 3.949A  pdb=" N   LYS R  96 " --> pdb=" O   ASN R  92 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   VAL R  97 " --> pdb=" O   THR R  93 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   VAL R 127 " --> pdb=" O   ARG R 123 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 129 through 136
    Processing helix  chain 'R' and resid 140 through 165
    Processing helix  chain 'R' and resid 171 through 189
    Processing helix  chain 'R' and resid 189 through 209
      removed outlier: 3.564A  pdb=" N   SER R 209 " --> pdb=" O   VAL R 205 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 216 through 234
    Processing helix  chain 'R' and resid 234 through 244
      removed outlier: 3.983A  pdb=" N   SER R 238 " --> pdb=" O   SER R 234 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 245 through 247
      No H-bonds generated for 'chain 'R' and resid 245 through 247'
    Processing helix  chain 'R' and resid 253 through 277
      Proline residue:  R 273  - end of helix
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.925A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.408A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.651A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.802A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.987A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151
      removed outlier: 3.690A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.921A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.701A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.507A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.551A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.596A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   SER S  21 " --> pdb=" O   SER S   7 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.929A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.929A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AB4, first strand: chain 'S' and resid 135 through 136
      removed outlier: 6.915A  pdb=" N   VAL S 135 " --> pdb=" O   GLU S 234 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'S' and resid 182 through 183
      removed outlier: 6.752A  pdb=" N   ASN S 182 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
      removed outlier: 5.269A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)

    434 hydrogen bonds defined for protein.
    1230 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: 2.74

  Time building geometry restraints manager: 2.82 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2292
        1.33 -     1.45: 1585
        1.45 -     1.57: 4699
        1.57 -     1.69: 0
        1.69 -     1.81: 100
  Bond restraints: 8676
  Sorted by residual:
  bond pdb=" C   BAL R1001 "
       pdb=" OXT BAL R1001 "
    ideal  model  delta    sigma   weight residual
    1.247  1.306 -0.059 2.00e-02 2.50e+03 8.61e+00
  bond pdb=" C1  PLM R1004 "
       pdb=" C2  PLM R1004 "
    ideal  model  delta    sigma   weight residual
    1.542  1.508  0.034 2.00e-02 2.50e+03 2.85e+00
  bond pdb=" C1  PLM R1003 "
       pdb=" C2  PLM R1003 "
    ideal  model  delta    sigma   weight residual
    1.542  1.511  0.031 2.00e-02 2.50e+03 2.36e+00
  bond pdb=" C1  PLM R1002 "
       pdb=" C2  PLM R1002 "
    ideal  model  delta    sigma   weight residual
    1.542  1.512  0.030 2.00e-02 2.50e+03 2.27e+00
  bond pdb=" C   LEU R 235 "
       pdb=" N   PRO R 236 "
    ideal  model  delta    sigma   weight residual
    1.334  1.367 -0.033 2.34e-02 1.83e+03 2.00e+00
  ... (remaining 8671 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.21: 11614
        2.21 -     4.41: 122
        4.41 -     6.62: 14
        6.62 -     8.83: 5
        8.83 -    11.04: 1
  Bond angle restraints: 11756
  Sorted by residual:
  angle pdb=" CA  BAL R1001 "
        pdb=" C   BAL R1001 "
        pdb=" OXT BAL R1001 "
      ideal   model   delta    sigma   weight residual
     120.80  113.33    7.47 1.70e+00 3.46e-01 1.93e+01
  angle pdb=" CB  MET R  42 "
        pdb=" CG  MET R  42 "
        pdb=" SD  MET R  42 "
      ideal   model   delta    sigma   weight residual
     112.70  123.74  -11.04 3.00e+00 1.11e-01 1.35e+01
  angle pdb=" CA  MET R  42 "
        pdb=" CB  MET R  42 "
        pdb=" CG  MET R  42 "
      ideal   model   delta    sigma   weight residual
     114.10  120.87   -6.77 2.00e+00 2.50e-01 1.15e+01
  angle pdb=" N   BAL R1001 "
        pdb=" CB  BAL R1001 "
        pdb=" CA  BAL R1001 "
      ideal   model   delta    sigma   weight residual
     110.40  114.96   -4.56 1.50e+00 4.44e-01 9.25e+00
  angle pdb=" N   MET R  42 "
        pdb=" CA  MET R  42 "
        pdb=" CB  MET R  42 "
      ideal   model   delta    sigma   weight residual
     110.30  114.67   -4.37 1.54e+00 4.22e-01 8.03e+00
  ... (remaining 11751 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 4517
       17.97 -    35.93: 479
       35.93 -    53.90: 110
       53.90 -    71.86: 13
       71.86 -    89.83: 12
  Dihedral angle restraints: 5131
    sinusoidal: 1912
      harmonic: 3219
  Sorted by residual:
  dihedral pdb=" CB  CYS S 147 "
           pdb=" SG  CYS S 147 "
           pdb=" SG  CYS S 217 "
           pdb=" CB  CYS S 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   63.90   29.10     1      1.00e+01 1.00e-02 1.21e+01
  dihedral pdb=" CA  ASP B 303 "
           pdb=" CB  ASP B 303 "
           pdb=" CG  ASP B 303 "
           pdb=" OD1 ASP B 303 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.66   58.66     1      2.00e+01 2.50e-03 1.15e+01
  dihedral pdb=" CA  LEU B  51 "
           pdb=" C   LEU B  51 "
           pdb=" N   ARG B  52 "
           pdb=" CA  ARG B  52 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.02  -15.98     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 5128 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 808
       0.028 -    0.056: 355
       0.056 -    0.085: 112
       0.085 -    0.113: 67
       0.113 -    0.141: 15
  Chirality restraints: 1357
  Sorted by residual:
  chirality pdb=" CA  ILE S 177 "
            pdb=" N   ILE S 177 "
            pdb=" C   ILE S 177 "
            pdb=" CB  ILE S 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.97e-01
  chirality pdb=" CA  TRP R 144 "
            pdb=" N   TRP R 144 "
            pdb=" C   TRP R 144 "
            pdb=" CB  TRP R 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.68e-01
  chirality pdb=" CA  ILE B 232 "
            pdb=" N   ILE B 232 "
            pdb=" C   ILE B 232 "
            pdb=" CB  ILE B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.17e-01
  ... (remaining 1354 not shown)

  Planarity restraints: 1468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 105 "    0.010 2.00e-02 2.50e+03   9.66e-03 1.87e+00
        pdb=" CG  TYR B 105 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 105 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 105 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 105 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 105 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 105 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 105 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.022 5.00e-02 4.00e+02   3.35e-02 1.79e+00
        pdb=" N   PRO B 236 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR R 240 "   -0.006 2.00e-02 2.50e+03   1.30e-02 1.69e+00
        pdb=" C   TYR R 240 "    0.023 2.00e-02 2.50e+03
        pdb=" O   TYR R 240 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   TRP R 241 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1465 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 124
        2.65 -     3.21: 7641
        3.21 -     3.77: 13387
        3.77 -     4.34: 18365
        4.34 -     4.90: 30773
  Nonbonded interactions: 70290
  Sorted by model distance:
  nonbonded pdb=" OH  TYR R 109 "
            pdb=" O   SER R 234 "
     model   vdw
     2.086 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   MET B 188 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" NE2 GLN B 220 "
            pdb=" OD1 ASP B 258 "
     model   vdw
     2.187 3.120
  nonbonded pdb=" OD1 ASN A 241 "
            pdb=" OH  TYR A 287 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   THR R 191 "
            pdb=" OG1 THR R 195 "
     model   vdw
     2.262 3.040
  ... (remaining 70285 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.870
  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:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     24.650
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8676  Z= 0.223
  Angle     :  0.581  11.036  11756  Z= 0.295
  Chirality :  0.040   0.141   1357
  Planarity :  0.003   0.033   1468
  Dihedral  : 15.813  89.828   3043
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  : 15.96 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.27), residues: 1093
  helix:  2.18 (0.28), residues: 361
  sheet: -0.05 (0.32), residues: 271
  loop : -0.27 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 144 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.019   0.001   PHE R  75 
 TYR   0.024   0.002   TYR B 105 
 ARG   0.004   0.000   ARG B 214 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 144
  time to evaluate  : 0.926 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 145
  average time/residue: 0.2072
  time to fit residues: 41.3935
Evaluate side-chains
  144 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 142
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  262 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 81 optimal weight:    0.0000
   chunk 45 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 55 optimal weight:    7.9990
   chunk 43 optimal weight:    0.7980
   chunk 84 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 98 optimal weight:   20.0000
   overall best weight:    0.5584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.172407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.138130 restraints weight = 10345.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 2.05
r_work: 0.3437 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.0862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8676  Z= 0.155
  Angle     :  0.501   5.625  11756  Z= 0.272
  Chirality :  0.040   0.155   1357
  Planarity :  0.003   0.033   1468
  Dihedral  :  5.543  50.898   1242
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 15.51 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.27), residues: 1093
  helix:  2.35 (0.28), residues: 380
  sheet: -0.00 (0.32), residues: 266
  loop : -0.17 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 144 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.012   0.001   PHE R  75 
 TYR   0.012   0.001   TYR B 105 
 ARG   0.003   0.000   ARG S 148 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 155
  time to evaluate  : 0.989 
Fit side-chains
REVERT: A  328 ASP cc_start: 0.6516 (m-30) cc_final: 0.6288 (m-30)
REVERT: A  333 GLN cc_start: 0.7134 (tm-30) cc_final: 0.6913 (mt0)
  outliers start: 15
  outliers final: 9
  residues processed: 161
  average time/residue: 0.2015
  time to fit residues: 45.1517
Evaluate side-chains
  151 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 142
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue  148 LEU
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   83 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 104 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 101 optimal weight:    0.2980
   chunk 38 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0970
   chunk 95 optimal weight:    2.9990
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.171566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.136927 restraints weight = 10551.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 2.09
r_work: 0.3427 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3306 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.1058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8676  Z= 0.172
  Angle     :  0.495   6.701  11756  Z= 0.267
  Chirality :  0.040   0.152   1357
  Planarity :  0.003   0.032   1468
  Dihedral  :  5.293  51.486   1239
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.40 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.26), residues: 1093
  helix:  2.41 (0.27), residues: 380
  sheet: -0.02 (0.32), residues: 263
  loop : -0.24 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 144 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.016   0.001   PHE R  75 
 TYR   0.014   0.001   TYR B 105 
 ARG   0.002   0.000   ARG B 214 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 0.884 
Fit side-chains
REVERT: A    5 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7259 (mp)
REVERT: A  328 ASP cc_start: 0.6574 (m-30) cc_final: 0.6226 (m-30)
REVERT: A  333 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6978 (mt0)
REVERT: R   95 ASP cc_start: 0.5853 (OUTLIER) cc_final: 0.5647 (t70)
  outliers start: 23
  outliers final: 15
  residues processed: 161
  average time/residue: 0.1922
  time to fit residues: 43.1347
Evaluate side-chains
  159 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   95 ASP
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0470
   chunk 66 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 103 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   overall best weight:    1.1482

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

Flipped N/Q/H residues before XYZ refinement:
C  18 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.169997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.135350 restraints weight = 10454.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 2.07
r_work: 0.3403 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3282 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.1095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8676  Z= 0.209
  Angle     :  0.530   8.994  11756  Z= 0.280
  Chirality :  0.041   0.154   1357
  Planarity :  0.003   0.033   1468
  Dihedral  :  5.479  55.200   1239
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 17.19 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.26), residues: 1093
  helix:  2.32 (0.27), residues: 380
  sheet: -0.11 (0.32), residues: 263
  loop : -0.32 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 144 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.021   0.001   PHE R  75 
 TYR   0.014   0.002   TYR B 105 
 ARG   0.003   0.000   ARG S 148 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 150
  time to evaluate  : 0.913 
Fit side-chains
REVERT: A    5 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7281 (mp)
REVERT: A  328 ASP cc_start: 0.6695 (m-30) cc_final: 0.6377 (m-30)
REVERT: B  105 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7729 (t80)
REVERT: R   42 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5937 (pmm)
REVERT: R   95 ASP cc_start: 0.5976 (OUTLIER) cc_final: 0.5706 (t70)
REVERT: S   46 GLU cc_start: 0.7435 (pt0) cc_final: 0.7148 (pt0)
REVERT: S  113 GLN cc_start: 0.6817 (mm-40) cc_final: 0.6533 (mm-40)
  outliers start: 31
  outliers final: 19
  residues processed: 170
  average time/residue: 0.1910
  time to fit residues: 45.6471
Evaluate side-chains
  166 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   42 MET
Chi-restraints excluded: chain R residue   56 MET
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   95 ASP
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 105 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9980
   chunk 76 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 92 optimal weight:    5.9990
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.8980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.170841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.136039 restraints weight = 10460.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 2.09
r_work: 0.3414 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3295 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8676  Z= 0.179
  Angle     :  0.507   8.360  11756  Z= 0.268
  Chirality :  0.040   0.152   1357
  Planarity :  0.003   0.033   1468
  Dihedral  :  5.269  56.208   1239
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 18.09 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.26), residues: 1093
  helix:  2.44 (0.27), residues: 375
  sheet: -0.10 (0.32), residues: 263
  loop : -0.36 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 144 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.017   0.001   PHE R  75 
 TYR   0.013   0.002   TYR B 105 
 ARG   0.002   0.000   ARG B 214 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 149
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7254 (mp)
REVERT: A  328 ASP cc_start: 0.6684 (m-30) cc_final: 0.6356 (m-30)
REVERT: A  333 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6964 (mt0)
REVERT: B  105 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7703 (t80)
REVERT: R   95 ASP cc_start: 0.5912 (OUTLIER) cc_final: 0.5667 (t70)
REVERT: S   46 GLU cc_start: 0.7400 (pt0) cc_final: 0.7151 (pt0)
REVERT: S  113 GLN cc_start: 0.6808 (mm-40) cc_final: 0.6586 (mm-40)
  outliers start: 32
  outliers final: 21
  residues processed: 169
  average time/residue: 0.1854
  time to fit residues: 43.9662
Evaluate side-chains
  167 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 142
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   22 GLU
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   95 ASP
Chi-restraints excluded: chain R residue  148 LEU
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 107 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   chunk 57 optimal weight:    0.7980
   chunk 100 optimal weight:    5.9990
   chunk 86 optimal weight:    9.9990
   chunk 65 optimal weight:    6.9990
   chunk 88 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   overall best weight:    1.8786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.166993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.132469 restraints weight = 10421.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 2.04
r_work: 0.3366 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3246 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.1272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   8676  Z= 0.308
  Angle     :  0.594   8.003  11756  Z= 0.316
  Chirality :  0.044   0.167   1357
  Planarity :  0.004   0.033   1468
  Dihedral  :  6.149  56.454   1239
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 17.98 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.26), residues: 1093
  helix:  2.09 (0.27), residues: 369
  sheet: -0.14 (0.32), residues: 257
  loop : -0.59 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 144 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.025   0.002   PHE R  75 
 TYR   0.020   0.002   TYR B 105 
 ARG   0.003   0.000   ARG B 214 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 148
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7363 (mp)
REVERT: A  328 ASP cc_start: 0.6839 (m-30) cc_final: 0.6531 (m-30)
REVERT: A  333 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6851 (mt0)
REVERT: B  105 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.8007 (t80)
REVERT: B  134 ARG cc_start: 0.7179 (ttp80) cc_final: 0.6703 (ttp-110)
REVERT: R   95 ASP cc_start: 0.6053 (OUTLIER) cc_final: 0.5745 (t70)
REVERT: S   46 GLU cc_start: 0.7387 (pt0) cc_final: 0.7145 (pt0)
  outliers start: 36
  outliers final: 26
  residues processed: 172
  average time/residue: 0.1928
  time to fit residues: 46.4736
Evaluate side-chains
  174 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 144
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   22 GLU
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   95 ASP
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  239 ILE
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 76 optimal weight:    0.8980
   chunk 94 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 59 optimal weight:    7.9990
   chunk 92 optimal weight:    2.9990
   chunk 100 optimal weight:    0.5980
   chunk 69 optimal weight:    0.6980
   chunk 88 optimal weight:    2.9990
   overall best weight:    1.2384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.168566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.134022 restraints weight = 10494.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 2.07
r_work: 0.3387 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3267 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.1300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8676  Z= 0.225
  Angle     :  0.542   6.984  11756  Z= 0.288
  Chirality :  0.042   0.158   1357
  Planarity :  0.003   0.034   1468
  Dihedral  :  5.777  56.733   1239
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 18.65 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.26), residues: 1093
  helix:  2.10 (0.27), residues: 376
  sheet: -0.18 (0.32), residues: 265
  loop : -0.49 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 144 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.019   0.002   PHE R  75 
 TYR   0.015   0.002   TYR B 105 
 ARG   0.003   0.000   ARG S 148 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 148
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7346 (mp)
REVERT: A  328 ASP cc_start: 0.6700 (m-30) cc_final: 0.6376 (m-30)
REVERT: A  333 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.7027 (mt0)
REVERT: B  105 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7807 (t80)
REVERT: B  134 ARG cc_start: 0.7184 (ttp80) cc_final: 0.6721 (ttp-110)
REVERT: B  340 ASN cc_start: 0.8038 (t0) cc_final: 0.7797 (t0)
REVERT: R   95 ASP cc_start: 0.6001 (OUTLIER) cc_final: 0.5734 (t70)
REVERT: S   46 GLU cc_start: 0.7383 (pt0) cc_final: 0.7146 (pt0)
  outliers start: 38
  outliers final: 26
  residues processed: 175
  average time/residue: 0.1969
  time to fit residues: 48.2447
Evaluate side-chains
  174 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 144
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   22 GLU
Chi-restraints excluded: chain R residue   42 MET
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   95 ASP
Chi-restraints excluded: chain R residue  127 VAL
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain R residue  285 HIS
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 50 optimal weight:    0.3980
   chunk 69 optimal weight:    0.4980
   chunk 59 optimal weight:    6.9990
   chunk 92 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 94 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 98 optimal weight:   30.0000
   overall best weight:    1.0982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.169112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.134494 restraints weight = 10638.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 2.09
r_work: 0.3395 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8676  Z= 0.207
  Angle     :  0.533   6.698  11756  Z= 0.283
  Chirality :  0.041   0.157   1357
  Planarity :  0.003   0.034   1468
  Dihedral  :  5.609  56.802   1239
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 19.21 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.26), residues: 1093
  helix:  2.16 (0.27), residues: 376
  sheet: -0.18 (0.32), residues: 263
  loop : -0.52 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 144 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.019   0.002   PHE R  75 
 TYR   0.015   0.002   TYR B 105 
 ARG   0.002   0.000   ARG S 148 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 145
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7331 (mp)
REVERT: B  105 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7788 (t80)
REVERT: B  134 ARG cc_start: 0.7186 (ttp80) cc_final: 0.6731 (ttp-110)
REVERT: R   95 ASP cc_start: 0.5950 (OUTLIER) cc_final: 0.5680 (t70)
REVERT: S   46 GLU cc_start: 0.7311 (pt0) cc_final: 0.7110 (pt0)
REVERT: S  113 GLN cc_start: 0.6901 (mm-40) cc_final: 0.6573 (mm-40)
  outliers start: 33
  outliers final: 26
  residues processed: 168
  average time/residue: 0.1929
  time to fit residues: 45.3711
Evaluate side-chains
  171 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 142
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   22 GLU
Chi-restraints excluded: chain R residue   42 MET
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   95 ASP
Chi-restraints excluded: chain R residue  127 VAL
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain R residue  285 HIS
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 77 optimal weight:    0.7980
   chunk 46 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 90 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 41 optimal weight:    0.4980
   chunk 105 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.171475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.136994 restraints weight = 10535.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 2.09
r_work: 0.3419 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.1436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8676  Z= 0.160
  Angle     :  0.507   7.954  11756  Z= 0.267
  Chirality :  0.040   0.153   1357
  Planarity :  0.003   0.034   1468
  Dihedral  :  5.241  56.012   1239
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 18.99 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.26), residues: 1093
  helix:  2.36 (0.27), residues: 377
  sheet: -0.12 (0.32), residues: 263
  loop : -0.47 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP R 144 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.017   0.001   PHE R  75 
 TYR   0.011   0.001   TYR B 105 
 ARG   0.002   0.000   ARG B 214 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 144
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7294 (mp)
REVERT: R   95 ASP cc_start: 0.5843 (OUTLIER) cc_final: 0.5635 (t70)
REVERT: R  156 MET cc_start: 0.7882 (mmm) cc_final: 0.7650 (mmt)
REVERT: S  113 GLN cc_start: 0.6863 (mm-40) cc_final: 0.6570 (mm-40)
  outliers start: 35
  outliers final: 25
  residues processed: 170
  average time/residue: 0.1927
  time to fit residues: 46.3701
Evaluate side-chains
  165 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 138
  time to evaluate  : 1.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   22 GLU
Chi-restraints excluded: chain R residue   42 MET
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   95 ASP
Chi-restraints excluded: chain R residue  127 VAL
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain R residue  285 HIS
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 99 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 107 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 98 optimal weight:   30.0000
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.9382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.170558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.135860 restraints weight = 10415.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.09
r_work: 0.3411 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.1441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8676  Z= 0.188
  Angle     :  0.533   8.578  11756  Z= 0.278
  Chirality :  0.041   0.154   1357
  Planarity :  0.003   0.034   1468
  Dihedral  :  5.338  57.166   1239
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 19.78 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.26), residues: 1093
  helix:  2.36 (0.27), residues: 377
  sheet: -0.11 (0.32), residues: 263
  loop : -0.49 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP R 144 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.018   0.001   PHE R  75 
 TYR   0.013   0.002   TYR B 105 
 ARG   0.002   0.000   ARG S  38 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 143
  time to evaluate  : 1.295 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7273 (mp)
REVERT: R   95 ASP cc_start: 0.5874 (OUTLIER) cc_final: 0.5651 (t70)
REVERT: R  156 MET cc_start: 0.7872 (mmm) cc_final: 0.7644 (mmt)
REVERT: S  113 GLN cc_start: 0.6873 (mm-40) cc_final: 0.6583 (mm-40)
  outliers start: 32
  outliers final: 29
  residues processed: 169
  average time/residue: 0.2050
  time to fit residues: 48.5768
Evaluate side-chains
  172 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 141
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   22 GLU
Chi-restraints excluded: chain R residue   42 MET
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   95 ASP
Chi-restraints excluded: chain R residue  127 VAL
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain R residue  285 HIS
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain S residue  201 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 105 optimal weight:    6.9990
   chunk 97 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 95 optimal weight:    0.7980
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.170783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.136058 restraints weight = 10639.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 2.11
r_work: 0.3412 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3294 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8676  Z= 0.178
  Angle     :  0.523   8.478  11756  Z= 0.274
  Chirality :  0.040   0.154   1357
  Planarity :  0.003   0.034   1468
  Dihedral  :  5.281  57.283   1239
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 19.78 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.26), residues: 1093
  helix:  2.39 (0.27), residues: 377
  sheet: -0.10 (0.32), residues: 263
  loop : -0.48 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP R 144 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.018   0.001   PHE R  75 
 TYR   0.013   0.002   TYR B 105 
 ARG   0.005   0.000   ARG S  38 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4924.28 seconds
wall clock time: 87 minutes 15.16 seconds (5235.16 seconds total)