Starting phenix.real_space_refine
on Fri Aug 22 22:26:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dzq_27805/08_2025/8dzq_27805.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dzq_27805/08_2025/8dzq_27805.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dzq_27805/08_2025/8dzq_27805.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dzq_27805/08_2025/8dzq_27805.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dzq_27805/08_2025/8dzq_27805.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dzq_27805/08_2025/8dzq_27805.map"
  }
  resolution = 2.82
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.021
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      58      5.16       5
     C    5337      2.51       5
     N    1397      2.21       5
     O    1550      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8342
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 2484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2484
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 127
          Unresolved non-hydrogen dihedrals: 79
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 5, 'GLN:plan1': 5, 'ARG:plan': 5, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 79
    Chain: "D"
      Number of atoms: 292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 292
          Classifications: {'peptide': 44}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 2, 'TRANS': 41}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 65
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 30
    Chain: "E"
      Number of atoms: 1770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1770
          Classifications: {'peptide': 230}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1648
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 4, 'TRANS': 211}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 64
          Unresolved non-hydrogen angles: 76
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "A"
      Number of atoms: 2117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2117
          Classifications: {'peptide': 274}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 8, 'TRANS': 265}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 79
          Unresolved non-hydrogen dihedrals: 58
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 47
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'U99': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.70, per 1000 atoms: 0.20
  Number of scatterers: 8342
  At special positions: 0
  Unit cell: (90.64, 121.44, 127.6, 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      58     16.00
     O    1550      8.00
     N    1397      7.00
     C    5337      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 210 " distance=2.03

  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: 0.52
  Conformation dependent library (CDL) restraints added in 318.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2060

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 13 sheets defined
      36.0% alpha, 23.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'C' and resid 5 through 25
    Processing helix  chain 'C' and resid 128 through 132
      removed outlier: 4.171A  pdb=" N   GLY C 131 " --> pdb=" O   THR C 128 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ASN C 132 " --> pdb=" O   ARG C 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 128 through 132'
    Processing helix  chain 'D' and resid 12 through 24
    Processing helix  chain 'D' and resid 29 through 44
      removed outlier: 3.610A  pdb=" N   ALA D  33 " --> pdb=" O   LYS D  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 48
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 4.158A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'B' and resid 6 through 31
    Processing helix  chain 'B' and resid 46 through 53
    Processing helix  chain 'B' and resid 212 through 217
      removed outlier: 3.538A  pdb=" N   CYS B 215 " --> pdb=" O   TRP B 212 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLU B 217 " --> pdb=" O   HIS B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 232
      removed outlier: 4.534A  pdb=" N   ASP B 232 " --> pdb=" O   SER B 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 229 through 232'
    Processing helix  chain 'B' and resid 245 through 249
    Processing helix  chain 'B' and resid 251 through 256
    Processing helix  chain 'B' and resid 271 through 277
    Processing helix  chain 'B' and resid 296 through 310
      removed outlier: 4.342A  pdb=" N   ALA B 302 " --> pdb=" O   GLU B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 351
      removed outlier: 4.165A  pdb=" N   VAL B 335 " --> pdb=" O   ASN B 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 87
    Processing helix  chain 'A' and resid 88 through 91
    Processing helix  chain 'A' and resid 92 through 110
    Processing helix  chain 'A' and resid 111 through 122
    Processing helix  chain 'A' and resid 127 through 162
    Processing helix  chain 'A' and resid 165 through 170
    Processing helix  chain 'A' and resid 171 through 197
      removed outlier: 3.869A  pdb=" N   VAL A 189 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 235
    Processing helix  chain 'A' and resid 235 through 255
      removed outlier: 4.289A  pdb=" N   SER A 255 " --> pdb=" O   LEU A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 299
      Proline residue:  A 289  - end of helix
    Processing helix  chain 'A' and resid 306 through 331
      removed outlier: 3.720A  pdb=" N   TYR A 312 " --> pdb=" O   ALA A 308 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   TYR A 313 " --> pdb=" O   LEU A 309 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   PHE A 314 " --> pdb=" O   SER A 310 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   SER A 323 " --> pdb=" O   GLY A 319 " (cutoff:3.500A)
      Proline residue:  A 327  - end of helix
    Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 51
      removed outlier: 6.786A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.763A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 105
      removed outlier: 4.194A  pdb=" N   GLY C 116 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   ILE C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 4.769A  pdb=" N   ARG C 137 " --> pdb=" O   ILE C 123 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 146 through 151
      removed outlier: 6.863A  pdb=" N   SER C 160 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   CYS C 149 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   VAL C 158 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 5.144A  pdb=" N   PHE C 151 " --> pdb=" O   GLN C 156 " (cutoff:3.500A)
      removed outlier: 7.458A  pdb=" N   GLN C 156 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 5.729A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 191 through 192
      removed outlier: 6.533A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.686A  pdb=" N   ASP C 254 " --> pdb=" O   GLU C 260 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   GLU C 260 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.650A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.311A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 128 through 129
    Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136
      removed outlier: 3.600A  pdb=" N   GLU E 234 " --> pdb=" O   VAL E 135 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   LEU E 162 " --> pdb=" O   TYR E 178 " (cutoff:3.500A)
      removed outlier: 5.087A  pdb=" N   TYR E 178 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 186 through 192
      removed outlier: 3.662A  pdb=" N   ALA B 221 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   ILE B 222 " --> pdb=" O   ILE B 266 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   PHE B 268 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   PHE B 224 " --> pdb=" O   PHE B 268 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   ASN B 270 " --> pdb=" O   PHE B 224 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   VAL B 226 " --> pdb=" O   ASN B 270 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 198 through 200

    441 hydrogen bonds defined for protein.
    1233 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.14

  Time building geometry restraints manager: 0.67 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: 1566
        1.33 -     1.45: 2172
        1.45 -     1.57: 4689
        1.57 -     1.70: 0
        1.70 -     1.82: 83
  Bond restraints: 8510
  Sorted by residual:
  bond pdb=" N   LEU E 166 "
       pdb=" CA  LEU E 166 "
    ideal  model  delta    sigma   weight residual
    1.455  1.477 -0.022 1.25e-02 6.40e+03 3.01e+00
  bond pdb=" CG1 ILE B 342 "
       pdb=" CD1 ILE B 342 "
    ideal  model  delta    sigma   weight residual
    1.513  1.464  0.049 3.90e-02 6.57e+02 1.60e+00
  bond pdb=" CA  ILE C  37 "
       pdb=" C   ILE C  37 "
    ideal  model  delta    sigma   weight residual
    1.518  1.533 -0.014 1.13e-02 7.83e+03 1.58e+00
  bond pdb=" CG  LEU B  38 "
       pdb=" CD2 LEU B  38 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.58e+00
  bond pdb=" CG1 ILE A 178 "
       pdb=" CD1 ILE A 178 "
    ideal  model  delta    sigma   weight residual
    1.513  1.465  0.048 3.90e-02 6.57e+02 1.53e+00
  ... (remaining 8505 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 11163
        1.80 -     3.60: 333
        3.60 -     5.40: 47
        5.40 -     7.21: 14
        7.21 -     9.01: 8
  Bond angle restraints: 11565
  Sorted by residual:
  angle pdb=" N   VAL B 202 "
        pdb=" CA  VAL B 202 "
        pdb=" C   VAL B 202 "
      ideal   model   delta    sigma   weight residual
     111.88  106.75    5.13 1.06e+00 8.90e-01 2.34e+01
  angle pdb=" C   ASN B 295 "
        pdb=" N   THR B 296 "
        pdb=" CA  THR B 296 "
      ideal   model   delta    sigma   weight residual
     121.54  130.43   -8.89 1.91e+00 2.74e-01 2.17e+01
  angle pdb=" N   ARG C  68 "
        pdb=" CA  ARG C  68 "
        pdb=" C   ARG C  68 "
      ideal   model   delta    sigma   weight residual
     114.56  109.40    5.16 1.27e+00 6.20e-01 1.65e+01
  angle pdb=" C   ASN A 122 "
        pdb=" N   SER A 123 "
        pdb=" CA  SER A 123 "
      ideal   model   delta    sigma   weight residual
     121.54  114.59    6.95 1.91e+00 2.74e-01 1.32e+01
  angle pdb=" N   ILE C  37 "
        pdb=" CA  ILE C  37 "
        pdb=" C   ILE C  37 "
      ideal   model   delta    sigma   weight residual
     112.98  108.49    4.49 1.25e+00 6.40e-01 1.29e+01
  ... (remaining 11560 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.01: 4573
       17.01 -    34.02: 405
       34.02 -    51.03: 60
       51.03 -    68.04: 9
       68.04 -    85.04: 7
  Dihedral angle restraints: 5054
    sinusoidal: 1868
      harmonic: 3186
  Sorted by residual:
  dihedral pdb=" CB  CYS A 131 "
           pdb=" SG  CYS A 131 "
           pdb=" SG  CYS A 210 "
           pdb=" CB  CYS A 210 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -165.52   79.52     1      1.00e+01 1.00e-02 7.85e+01
  dihedral pdb=" CA  LEU B 199 "
           pdb=" C   LEU B 199 "
           pdb=" N   PHE B 200 "
           pdb=" CA  PHE B 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.03  -24.97     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  LYS C  78 "
           pdb=" C   LYS C  78 "
           pdb=" N   LEU C  79 "
           pdb=" CA  LEU C  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.51   19.49     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 5051 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1156
       0.068 -    0.136: 197
       0.136 -    0.203: 6
       0.203 -    0.271: 1
       0.271 -    0.339: 2
  Chirality restraints: 1362
  Sorted by residual:
  chirality pdb=" CG  LEU B 269 "
            pdb=" CB  LEU B 269 "
            pdb=" CD1 LEU B 269 "
            pdb=" CD2 LEU B 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.25   -0.34 2.00e-01 2.50e+01 2.87e+00
  chirality pdb=" C22 U99 A 401 "
            pdb=" C20 U99 A 401 "
            pdb=" C23 U99 A 401 "
            pdb=" C8  U99 A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.23   -1.93   -0.29 2.00e-01 2.50e+01 2.14e+00
  chirality pdb=" CB  VAL B 202 "
            pdb=" CA  VAL B 202 "
            pdb=" CG1 VAL B 202 "
            pdb=" CG2 VAL B 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.32e+00
  ... (remaining 1359 not shown)

  Planarity restraints: 1445
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG C 137 "   -0.012 2.00e-02 2.50e+03   2.47e-02 6.10e+00
        pdb=" C   ARG C 137 "    0.043 2.00e-02 2.50e+03
        pdb=" O   ARG C 137 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   GLU C 138 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE E 165 "   -0.012 2.00e-02 2.50e+03   2.35e-02 5.52e+00
        pdb=" C   PHE E 165 "    0.041 2.00e-02 2.50e+03
        pdb=" O   PHE E 165 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LEU E 166 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 246 "    0.010 2.00e-02 2.50e+03   1.95e-02 3.81e+00
        pdb=" C   ALA B 246 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ALA B 246 "    0.013 2.00e-02 2.50e+03
        pdb=" N   SER B 247 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1442 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 1635
        2.78 -     3.31: 7688
        3.31 -     3.84: 13707
        3.84 -     4.37: 15878
        4.37 -     4.90: 28121
  Nonbonded interactions: 67029
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 245 "
            pdb=" OD1 ASP C 247 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   GLY E   8 "
            pdb=" OG1 THR E 115 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OG1 THR C  86 "
            pdb=" OD1 ASN C  88 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" OD2 ASP C 186 "
            pdb=" OG  SER B 207 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   ALA C 231 "
            pdb=" OG1 THR C 243 "
     model   vdw
     2.309 3.040
  ... (remaining 67024 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=1.00 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:             1.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.350
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:7.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6748
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8512  Z= 0.183
  Angle     :  0.750   9.007  11569  Z= 0.396
  Chirality :  0.049   0.339   1362
  Planarity :  0.004   0.043   1445
  Dihedral  : 13.130  85.045   2988
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.23 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.25), residues: 1072
  helix:  1.13 (0.27), residues: 355
  sheet: -0.04 (0.30), residues: 276
  loop : -1.68 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 219 
 TYR   0.023   0.002   TYR A 140 
 PHE   0.019   0.002   PHE C 278 
 TRP   0.024   0.002   TRP E 164 
 HIS   0.017   0.002   HIS E 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 8510)
  covalent geometry    : angle       0.74976 (11565)
  SS BOND              : bond        0.00511 (    2)
  SS BOND              : angle       1.25708 (    4)
  hydrogen bonds       : bond        0.12438 (  441)
  hydrogen bonds       : angle       6.24164 ( 1233)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 165
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: E   95 TYR cc_start: 0.6503 (m-10) cc_final: 0.6295 (m-10)
REVERT: A  228 ILE cc_start: 0.7726 (mm) cc_final: 0.7472 (mm)
  outliers start: 2
  outliers final: 0
  residues processed: 166
  average time/residue: 0.3322
  time to fit residues: 60.1299
Evaluate side-chains
  150 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0270
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
C 155 ASN
C 230 ASN
C 293 ASN
E 219 GLN
B 233 GLN
A 122 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.158072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.140390 restraints weight = 11608.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 1.98
r_work: 0.3788 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3645 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
moved from start:          0.0936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8512  Z= 0.143
  Angle     :  0.590   7.333  11569  Z= 0.313
  Chirality :  0.043   0.171   1362
  Planarity :  0.004   0.034   1445
  Dihedral  :  4.600  42.321   1239
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 11.34 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.26), residues: 1072
  helix:  1.83 (0.28), residues: 349
  sheet: -0.06 (0.30), residues: 280
  loop : -1.60 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 219 
 TYR   0.018   0.002   TYR A 140 
 PHE   0.020   0.002   PHE B 200 
 TRP   0.017   0.002   TRP C 169 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8510)
  covalent geometry    : angle       0.58933 (11565)
  SS BOND              : bond        0.00367 (    2)
  SS BOND              : angle       0.99497 (    4)
  hydrogen bonds       : bond        0.04224 (  441)
  hydrogen bonds       : angle       5.19405 ( 1233)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 156
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: C  217 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7151 (pmt)
REVERT: B  199 LEU cc_start: 0.8305 (mt) cc_final: 0.8082 (mp)
REVERT: B  309 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6779 (mp0)
REVERT: A  228 ILE cc_start: 0.7831 (mm) cc_final: 0.7597 (mm)
REVERT: A  332 PHE cc_start: 0.7952 (m-10) cc_final: 0.7682 (m-80)
  outliers start: 15
  outliers final: 1
  residues processed: 159
  average time/residue: 0.3458
  time to fit residues: 59.8225
Evaluate side-chains
  147 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 145
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain B residue  296 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 105 optimal weight:    0.5980
   chunk 57 optimal weight:    0.4980
   chunk 69 optimal weight:    0.9990
   chunk 49 optimal weight:    0.2980
   chunk 89 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
C 155 ASN
C 293 ASN
E 219 GLN
A 122 ASN
A 322 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.157265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.139786 restraints weight = 11565.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 1.94
r_work: 0.3783 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3641 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.1175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8512  Z= 0.146
  Angle     :  0.587   8.254  11569  Z= 0.306
  Chirality :  0.043   0.140   1362
  Planarity :  0.004   0.031   1445
  Dihedral  :  4.415  35.290   1239
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 14.55 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.26), residues: 1072
  helix:  1.98 (0.28), residues: 349
  sheet:  0.08 (0.31), residues: 282
  loop : -1.61 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 137 
 TYR   0.017   0.002   TYR A 140 
 PHE   0.018   0.002   PHE C 253 
 TRP   0.019   0.002   TRP C 169 
 HIS   0.004   0.001   HIS B 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8510)
  covalent geometry    : angle       0.58695 (11565)
  SS BOND              : bond        0.00351 (    2)
  SS BOND              : angle       0.90026 (    4)
  hydrogen bonds       : bond        0.04110 (  441)
  hydrogen bonds       : angle       5.02635 ( 1233)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 147
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
REVERT: C  217 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7140 (pmt)
REVERT: E  201 THR cc_start: 0.7235 (p) cc_final: 0.7029 (t)
REVERT: E  208 GLU cc_start: 0.7718 (mp0) cc_final: 0.7212 (mp0)
REVERT: B  309 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6706 (mp0)
REVERT: A  169 PHE cc_start: 0.6722 (m-10) cc_final: 0.6444 (m-10)
REVERT: A  228 ILE cc_start: 0.7907 (mm) cc_final: 0.7683 (OUTLIER)
REVERT: A  332 PHE cc_start: 0.7941 (m-10) cc_final: 0.7692 (m-80)
  outliers start: 18
  outliers final: 6
  residues processed: 152
  average time/residue: 0.3662
  time to fit residues: 60.0299
Evaluate side-chains
  155 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 148
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue  120 SER
Chi-restraints excluded: chain E residue  163 TYR
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 86 optimal weight:    0.1980
   chunk 68 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0010
   chunk 52 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    0.7388

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

Flipped N/Q/H residues before XYZ refinement:
C 155 ASN
C 268 ASN
E 219 GLN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN
A 322 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.156058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.138555 restraints weight = 11714.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3864 rms_B_bonded: 1.95
r_work: 0.3766 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3621 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.1350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8512  Z= 0.170
  Angle     :  0.598   8.355  11569  Z= 0.312
  Chirality :  0.043   0.142   1362
  Planarity :  0.004   0.035   1445
  Dihedral  :  4.467  35.448   1239
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.27 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.05 (0.27), residues: 1072
  helix:  1.85 (0.28), residues: 356
  sheet:  0.12 (0.31), residues: 281
  loop : -1.62 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 137 
 TYR   0.018   0.002   TYR A 140 
 PHE   0.020   0.002   PHE C 253 
 TRP   0.017   0.002   TRP C 169 
 HIS   0.006   0.001   HIS B 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 8510)
  covalent geometry    : angle       0.59793 (11565)
  SS BOND              : bond        0.00371 (    2)
  SS BOND              : angle       1.08232 (    4)
  hydrogen bonds       : bond        0.04213 (  441)
  hydrogen bonds       : angle       5.00534 ( 1233)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 152
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: C  217 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7202 (pmt)
REVERT: E  180 MET cc_start: 0.5662 (ttp) cc_final: 0.5277 (ttp)
REVERT: E  201 THR cc_start: 0.7232 (p) cc_final: 0.7025 (t)
REVERT: E  208 GLU cc_start: 0.7762 (mp0) cc_final: 0.7256 (mp0)
REVERT: B  309 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6748 (mp0)
REVERT: A  107 LEU cc_start: 0.8119 (mt) cc_final: 0.7851 (mp)
REVERT: A  169 PHE cc_start: 0.6724 (m-10) cc_final: 0.6430 (m-10)
REVERT: A  332 PHE cc_start: 0.7925 (m-10) cc_final: 0.7683 (m-80)
  outliers start: 23
  outliers final: 8
  residues processed: 164
  average time/residue: 0.3342
  time to fit residues: 59.5011
Evaluate side-chains
  156 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 146
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue  163 TYR
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  256 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.0770
   chunk 89 optimal weight:    0.7980
   chunk 99 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0970
   chunk 58 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.4736

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

Flipped N/Q/H residues before XYZ refinement:
C 155 ASN
C 268 ASN
E 219 GLN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN
A 322 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.157192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.139896 restraints weight = 11732.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 1.91
r_work: 0.3786 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3645 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7194
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8512  Z= 0.132
  Angle     :  0.572   8.637  11569  Z= 0.298
  Chirality :  0.042   0.150   1362
  Planarity :  0.003   0.032   1445
  Dihedral  :  4.328  33.922   1239
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.75 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.27), residues: 1072
  helix:  1.93 (0.28), residues: 358
  sheet:  0.11 (0.31), residues: 281
  loop : -1.54 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 137 
 TYR   0.019   0.002   TYR A 140 
 PHE   0.014   0.001   PHE C 253 
 TRP   0.017   0.002   TRP C 169 
 HIS   0.004   0.001   HIS B 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8510)
  covalent geometry    : angle       0.57133 (11565)
  SS BOND              : bond        0.00301 (    2)
  SS BOND              : angle       0.96774 (    4)
  hydrogen bonds       : bond        0.03917 (  441)
  hydrogen bonds       : angle       4.90470 ( 1233)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 156
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: C   61 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7573 (ppp)
REVERT: E  180 MET cc_start: 0.5550 (ttp) cc_final: 0.5221 (ttp)
REVERT: E  201 THR cc_start: 0.7247 (p) cc_final: 0.7037 (t)
REVERT: E  208 GLU cc_start: 0.7751 (mp0) cc_final: 0.7276 (mp0)
REVERT: B  309 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6632 (mp0)
REVERT: A  107 LEU cc_start: 0.8126 (mt) cc_final: 0.7872 (mp)
REVERT: A  112 MET cc_start: 0.3443 (mmt) cc_final: 0.2611 (mmp)
REVERT: A  169 PHE cc_start: 0.6686 (m-10) cc_final: 0.6415 (m-10)
REVERT: A  332 PHE cc_start: 0.7913 (m-10) cc_final: 0.7708 (m-80)
  outliers start: 24
  outliers final: 9
  residues processed: 168
  average time/residue: 0.3154
  time to fit residues: 57.7089
Evaluate side-chains
  159 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 148
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain B residue    6 SER
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  256 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 86 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0670
   chunk 29 optimal weight:    1.9990
   chunk 44 optimal weight:    0.2980
   chunk 5 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0770
   chunk 55 optimal weight:    1.9990
   chunk 4 optimal weight:    0.3980
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.2876

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

Flipped N/Q/H residues before XYZ refinement:
C 155 ASN
C 268 ASN
E 219 GLN
B 189 HIS
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN
A 336 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.158688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.141334 restraints weight = 11604.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 1.95
r_work: 0.3801 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3660 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8512  Z= 0.110
  Angle     :  0.551   8.798  11569  Z= 0.287
  Chirality :  0.042   0.153   1362
  Planarity :  0.003   0.031   1445
  Dihedral  :  4.155  35.886   1239
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.90 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.27), residues: 1072
  helix:  2.16 (0.28), residues: 357
  sheet:  0.13 (0.31), residues: 280
  loop : -1.57 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 137 
 TYR   0.020   0.001   TYR A 140 
 PHE   0.011   0.001   PHE C 199 
 TRP   0.015   0.001   TRP C 169 
 HIS   0.005   0.001   HIS E 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 8510)
  covalent geometry    : angle       0.55106 (11565)
  SS BOND              : bond        0.00311 (    2)
  SS BOND              : angle       0.59185 (    4)
  hydrogen bonds       : bond        0.03607 (  441)
  hydrogen bonds       : angle       4.77353 ( 1233)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 158
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: C   61 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7541 (ppp)
REVERT: C  217 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7246 (pmt)
REVERT: E  201 THR cc_start: 0.7251 (p) cc_final: 0.7047 (t)
REVERT: E  208 GLU cc_start: 0.7739 (mp0) cc_final: 0.7240 (mp0)
REVERT: B  309 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6517 (mp0)
REVERT: A  107 LEU cc_start: 0.7994 (mt) cc_final: 0.7709 (mp)
REVERT: A  249 MET cc_start: 0.7783 (ttt) cc_final: 0.7203 (ttt)
REVERT: A  332 PHE cc_start: 0.7919 (m-10) cc_final: 0.7714 (m-80)
  outliers start: 25
  outliers final: 8
  residues processed: 173
  average time/residue: 0.3195
  time to fit residues: 60.2070
Evaluate side-chains
  162 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  177 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain A residue  180 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 64 optimal weight:    0.8980
   chunk 90 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 78 optimal weight:    0.2980
   chunk 85 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 103 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
C 155 ASN
C 220 GLN
E 219 GLN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.157272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.140054 restraints weight = 11663.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 1.89
r_work: 0.3788 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3647 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8512  Z= 0.147
  Angle     :  0.584   8.945  11569  Z= 0.303
  Chirality :  0.043   0.162   1362
  Planarity :  0.004   0.045   1445
  Dihedral  :  4.219  32.982   1239
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 20.39 %
    Favored  : 76.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.27), residues: 1072
  helix:  2.10 (0.28), residues: 358
  sheet:  0.06 (0.31), residues: 288
  loop : -1.56 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 137 
 TYR   0.019   0.002   TYR A 140 
 PHE   0.016   0.002   PHE C 253 
 TRP   0.014   0.002   TRP C 169 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8510)
  covalent geometry    : angle       0.58405 (11565)
  SS BOND              : bond        0.00331 (    2)
  SS BOND              : angle       0.76390 (    4)
  hydrogen bonds       : bond        0.03887 (  441)
  hydrogen bonds       : angle       4.81326 ( 1233)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 152
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: C   61 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7562 (ppp)
REVERT: C  217 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7248 (pmt)
REVERT: E  201 THR cc_start: 0.7232 (p) cc_final: 0.7022 (t)
REVERT: E  208 GLU cc_start: 0.7729 (mp0) cc_final: 0.7246 (mp0)
REVERT: B  309 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6748 (mp0)
REVERT: A  107 LEU cc_start: 0.8069 (mt) cc_final: 0.7789 (mp)
REVERT: A  121 MET cc_start: 0.5515 (mpm) cc_final: 0.5079 (mpm)
REVERT: A  249 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7272 (ttt)
  outliers start: 27
  outliers final: 11
  residues processed: 167
  average time/residue: 0.3462
  time to fit residues: 62.6481
Evaluate side-chains
  158 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  279 SER
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  177 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  256 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0000
   chunk 104 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 106 optimal weight:    0.5980
   chunk 68 optimal weight:    0.8980
   chunk 72 optimal weight:    0.7980
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
C 155 ASN
C 220 GLN
E 219 GLN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.157299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.140127 restraints weight = 11515.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 1.88
r_work: 0.3788 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3646 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.1674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8512  Z= 0.142
  Angle     :  0.587   9.040  11569  Z= 0.306
  Chirality :  0.043   0.160   1362
  Planarity :  0.004   0.037   1445
  Dihedral  :  4.249  31.314   1239
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 20.50 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.26), residues: 1072
  helix:  1.95 (0.28), residues: 364
  sheet:  0.05 (0.31), residues: 281
  loop : -1.61 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  68 
 TYR   0.019   0.002   TYR A 140 
 PHE   0.015   0.001   PHE C 253 
 TRP   0.016   0.002   TRP C 169 
 HIS   0.003   0.001   HIS B 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 8510)
  covalent geometry    : angle       0.58672 (11565)
  SS BOND              : bond        0.00264 (    2)
  SS BOND              : angle       0.99183 (    4)
  hydrogen bonds       : bond        0.03888 (  441)
  hydrogen bonds       : angle       4.82484 ( 1233)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 141
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: C   61 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7578 (ppp)
REVERT: C  217 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7228 (pmt)
REVERT: E  201 THR cc_start: 0.7238 (p) cc_final: 0.7031 (t)
REVERT: E  208 GLU cc_start: 0.7725 (mp0) cc_final: 0.7249 (mp0)
REVERT: B  309 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6719 (mp0)
REVERT: A   81 MET cc_start: 0.6594 (mmt) cc_final: 0.6388 (mmt)
REVERT: A  107 LEU cc_start: 0.8069 (mt) cc_final: 0.7748 (mp)
REVERT: A  112 MET cc_start: 0.3692 (mmt) cc_final: 0.2344 (mmp)
REVERT: A  121 MET cc_start: 0.5557 (mpm) cc_final: 0.5103 (mpm)
REVERT: A  249 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7205 (ttt)
REVERT: A  332 PHE cc_start: 0.7961 (m-80) cc_final: 0.7738 (m-80)
  outliers start: 30
  outliers final: 15
  residues processed: 161
  average time/residue: 0.3432
  time to fit residues: 59.9529
Evaluate side-chains
  156 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  163 TYR
Chi-restraints excluded: chain E residue  177 ILE
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain A residue  153 SER
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  256 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 72 optimal weight:    0.0060
   chunk 4 optimal weight:    0.0050
   chunk 91 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 95 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.5410

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

Flipped N/Q/H residues before XYZ refinement:
C 155 ASN
E 219 GLN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.157273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.140126 restraints weight = 11529.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 1.88
r_work: 0.3790 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3649 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8512  Z= 0.143
  Angle     :  0.591   9.179  11569  Z= 0.308
  Chirality :  0.043   0.170   1362
  Planarity :  0.004   0.034   1445
  Dihedral  :  4.258  31.949   1239
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 21.08 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.26), residues: 1072
  helix:  1.94 (0.28), residues: 364
  sheet:  0.05 (0.31), residues: 281
  loop : -1.63 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 137 
 TYR   0.020   0.002   TYR A 140 
 PHE   0.015   0.001   PHE C 253 
 TRP   0.015   0.002   TRP C 169 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8510)
  covalent geometry    : angle       0.59121 (11565)
  SS BOND              : bond        0.00302 (    2)
  SS BOND              : angle       0.83739 (    4)
  hydrogen bonds       : bond        0.03901 (  441)
  hydrogen bonds       : angle       4.84484 ( 1233)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 147
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
REVERT: C   61 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7559 (ppp)
REVERT: C  217 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7207 (pmt)
REVERT: E  201 THR cc_start: 0.7228 (p) cc_final: 0.7022 (t)
REVERT: E  208 GLU cc_start: 0.7711 (mp0) cc_final: 0.7238 (mp0)
REVERT: B  309 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6772 (mp0)
REVERT: A  107 LEU cc_start: 0.8064 (mt) cc_final: 0.7752 (mp)
REVERT: A  112 MET cc_start: 0.3670 (mmt) cc_final: 0.2587 (mmp)
REVERT: A  249 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7208 (ttt)
REVERT: A  332 PHE cc_start: 0.8000 (m-80) cc_final: 0.7792 (m-80)
  outliers start: 27
  outliers final: 20
  residues processed: 163
  average time/residue: 0.3222
  time to fit residues: 57.0189
Evaluate side-chains
  169 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  268 ASN
Chi-restraints excluded: chain C residue  325 MET
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  163 TYR
Chi-restraints excluded: chain E residue  177 ILE
Chi-restraints excluded: chain B residue    6 SER
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  153 SER
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  256 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 67 optimal weight:    4.9990
   chunk 77 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 55 optimal weight:    0.0010
   overall best weight:    0.6386

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

Flipped N/Q/H residues before XYZ refinement:
C 155 ASN
C 220 GLN
E 219 GLN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.156614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.139401 restraints weight = 11552.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3875 rms_B_bonded: 1.88
r_work: 0.3780 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3639 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.1759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   8512  Z= 0.158
  Angle     :  0.608   9.279  11569  Z= 0.316
  Chirality :  0.043   0.177   1362
  Planarity :  0.004   0.038   1445
  Dihedral  :  4.329  30.253   1239
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 20.73 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.26), residues: 1072
  helix:  1.89 (0.28), residues: 364
  sheet:  0.05 (0.31), residues: 280
  loop : -1.63 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 137 
 TYR   0.019   0.002   TYR A 140 
 PHE   0.018   0.002   PHE C 253 
 TRP   0.015   0.002   TRP C 169 
 HIS   0.003   0.001   HIS E 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 8510)
  covalent geometry    : angle       0.60826 (11565)
  SS BOND              : bond        0.00325 (    2)
  SS BOND              : angle       0.92335 (    4)
  hydrogen bonds       : bond        0.04041 (  441)
  hydrogen bonds       : angle       4.88755 ( 1233)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 146
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: C   61 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7602 (ppp)
REVERT: C  217 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7181 (pmt)
REVERT: E  180 MET cc_start: 0.5639 (ttp) cc_final: 0.5286 (ttp)
REVERT: E  201 THR cc_start: 0.7218 (p) cc_final: 0.7017 (t)
REVERT: E  208 GLU cc_start: 0.7732 (mp0) cc_final: 0.7253 (mp0)
REVERT: B  309 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6823 (mp0)
REVERT: A  107 LEU cc_start: 0.8073 (mt) cc_final: 0.7785 (mp)
REVERT: A  112 MET cc_start: 0.3685 (mmt) cc_final: 0.2759 (mmp)
REVERT: A  121 MET cc_start: 0.5569 (mpm) cc_final: 0.5160 (mpm)
REVERT: A  249 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7191 (ttt)
  outliers start: 29
  outliers final: 19
  residues processed: 165
  average time/residue: 0.3200
  time to fit residues: 57.3206
Evaluate side-chains
  169 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  268 ASN
Chi-restraints excluded: chain C residue  279 SER
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  163 TYR
Chi-restraints excluded: chain E residue  177 ILE
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  153 SER
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  256 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 97 optimal weight:    0.8980
   chunk 79 optimal weight:    0.8980
   chunk 100 optimal weight:    0.8980
   chunk 82 optimal weight:    0.5980
   chunk 77 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 84 optimal weight:    6.9990
   chunk 31 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0980
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C 155 ASN
C 220 GLN
E 219 GLN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.156628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.139406 restraints weight = 11472.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3874 rms_B_bonded: 1.88
r_work: 0.3778 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3637 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   8512  Z= 0.158
  Angle     :  0.608   9.323  11569  Z= 0.317
  Chirality :  0.043   0.167   1362
  Planarity :  0.004   0.038   1445
  Dihedral  :  4.346  29.641   1239
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 20.73 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.26), residues: 1072
  helix:  1.87 (0.27), residues: 364
  sheet:  0.11 (0.31), residues: 277
  loop : -1.66 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 137 
 TYR   0.020   0.002   TYR A 140 
 PHE   0.017   0.002   PHE C 253 
 TRP   0.015   0.002   TRP C 169 
 HIS   0.003   0.001   HIS B 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 8510)
  covalent geometry    : angle       0.60820 (11565)
  SS BOND              : bond        0.00335 (    2)
  SS BOND              : angle       0.89261 (    4)
  hydrogen bonds       : bond        0.04039 (  441)
  hydrogen bonds       : angle       4.90307 ( 1233)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2529.74 seconds
wall clock time: 43 minutes 55.42 seconds (2635.42 seconds total)