Starting phenix.real_space_refine
on Sun May 11 16:00:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i95_35257/05_2025/8i95_35257.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i95_35257/05_2025/8i95_35257.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i95_35257/05_2025/8i95_35257.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i95_35257/05_2025/8i95_35257.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i95_35257/05_2025/8i95_35257.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i95_35257/05_2025/8i95_35257.cif"
  }
  resolution = 2.88
  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=   0.032
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      52      5.16       5
     C    5205      2.51       5
     N    1403      2.21       5
     O    1493      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8153
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1550
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1550
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 4, 'TRANS': 203}
          Chain breaks: 2
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 100
          Unresolved non-hydrogen angles: 123
          Unresolved non-hydrogen dihedrals: 80
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 57
    Chain: "B"
      Number of atoms: 2416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2416
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 57}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 185
          Unresolved non-hydrogen angles: 230
          Unresolved non-hydrogen dihedrals: 140
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 10}
          Unresolved non-hydrogen planarities: 103
    Chain: "G"
      Number of atoms: 400
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 400
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "H"
      Number of atoms: 1658
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1658
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 117
          Unresolved non-hydrogen angles: 140
          Unresolved non-hydrogen dihedrals: 94
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 53
    Chain: "C"
      Number of atoms: 2057
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2057
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 14, 'TRANS': 265}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 158
          Unresolved non-hydrogen angles: 197
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 82
    Chain: "D"
      Number of atoms: 55
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 55
          Classifications: {'peptide': 7}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 4}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "D"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 17
          Classifications: {'peptide': 2}
          Modifications used: {'COO': 1, 'PEPT-D': 1}
          Link IDs: {'TRANS': 1}
  Time building chain proxies: 5.75, per 1000 atoms: 0.71
  Number of scatterers: 8153
  At special positions: 0
  Unit cell: (85.56, 119.6, 123.28, 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      52     16.00
     O    1493      8.00
     N    1403      7.00
     C    5205      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 229 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C  95 " - pdb=" SG  CYS C 172 " 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
  Links applied
    TRANS
      " DAL D   9 " - " LEU D   8 "
  Time building additional restraints: 2.08
  Conformation dependent library (CDL) restraints added in 955.9 milliseconds
  

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DAL D   9 "
  Number of C-beta restraints generated:  2086

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      37.6% alpha, 23.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 32
      removed outlier: 3.796A  pdb=" N   LYS A  32 " --> pdb=" O   ILE A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 51
    Processing helix  chain 'A' and resid 208 through 217
      removed outlier: 3.560A  pdb=" N   LYS A 211 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   ILE A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 256
    Processing helix  chain 'A' and resid 257 through 261
      removed outlier: 4.130A  pdb=" N   ILE A 261 " --> pdb=" O   LYS A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 282
    Processing helix  chain 'A' and resid 296 through 310
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 8 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.549A  pdb=" N   ASP H  90 " --> pdb=" O   ARG H  87 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 87 through 91'
    Processing helix  chain 'H' and resid 220 through 224
      removed outlier: 3.757A  pdb=" N   VAL H 224 " --> pdb=" O   ALA H 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 50
      removed outlier: 3.555A  pdb=" N   SER C  26 " --> pdb=" O   PRO C  22 " (cutoff:3.500A)
      Proline residue:  C  39  - end of helix
      removed outlier: 3.576A  pdb=" N   VAL C  44 " --> pdb=" O   GLY C  40 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 74
      removed outlier: 4.104A  pdb=" N   TRP C  60 " --> pdb=" O   VAL C  56 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   PHE C  61 " --> pdb=" O   ASN C  57 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 84
      removed outlier: 3.824A  pdb=" N   SER C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 126
      Proline residue:  C  99  - end of helix
      removed outlier: 5.197A  pdb=" N   VAL C 103 " --> pdb=" O   PRO C  99 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL C 110 " --> pdb=" O   MET C 106 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL C 124 " --> pdb=" O   ARG C 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 128 through 133
      removed outlier: 3.562A  pdb=" N   ASN C 132 " --> pdb=" O   ILE C 128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 135 through 154
    Processing helix  chain 'C' and resid 154 through 160
      removed outlier: 3.766A  pdb=" N   TYR C 160 " --> pdb=" O   PRO C 156 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 333 through 363
      removed outlier: 5.256A  pdb=" N   LEU C 347 " --> pdb=" O   VAL C 343 " (cutoff:3.500A)
      Proline residue:  C 348  - end of helix
    Processing helix  chain 'C' and resid 373 through 403
      Proline residue:  C 392  - end of helix
      removed outlier: 3.953A  pdb=" N   LEU C 401 " --> pdb=" O   GLY C 397 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU C 402 " --> pdb=" O   VAL C 398 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 407 through 431
      removed outlier: 6.367A  pdb=" N   LEU C 413 " --> pdb=" O   LEU C 409 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   HIS C 418 " --> pdb=" O   MET C 414 " (cutoff:3.500A)
      removed outlier: 4.959A  pdb=" N   VAL C 419 " --> pdb=" O   SER C 415 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   SER C 428 " --> pdb=" O   ALA C 424 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   CYS C 429 " --> pdb=" O   SER C 425 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 432 through 434
      No H-bonds generated for 'chain 'C' and resid 432 through 434'
    Processing helix  chain 'C' and resid 435 through 438
      removed outlier: 3.820A  pdb=" N   LEU C 438 " --> pdb=" O   TYR C 435 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 435 through 438'
    Processing helix  chain 'C' and resid 439 through 451
      removed outlier: 3.827A  pdb=" N   GLN C 451 " --> pdb=" O   ARG C 447 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191
      removed outlier: 6.164A  pdb=" N   VAL A  34 " --> pdb=" O   ARG A 198 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   PHE A 200 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ALA A 221 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.813A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.878A  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: 6.923A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.546A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.127A  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: 3.569A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.727A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.514A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.648A  pdb=" N   ARG H  18 " --> pdb=" O   MET H  83 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 58 through 60
      removed outlier: 6.527A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   PHE H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 60
      removed outlier: 6.527A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 149
      removed outlier: 3.623A  pdb=" N   VAL H 149 " --> pdb=" O   GLU H 246 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   LEU H 178 " --> pdb=" O   LEU H 187 " (cutoff:3.500A)
      removed outlier: 5.609A  pdb=" N   LEU H 187 " --> pdb=" O   LEU H 178 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 162 through 166
      removed outlier: 3.969A  pdb=" N   PHE C 164 " --> pdb=" O   ARG C 171 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ARG C 171 " --> pdb=" O   PHE C 164 " (cutoff:3.500A)

    435 hydrogen bonds defined for protein.
    1236 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: 2.48

  Time building geometry restraints manager: 2.39 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: 1623
        1.33 -     1.45: 2170
        1.45 -     1.58: 4468
        1.58 -     1.70: 1
        1.70 -     1.83: 67
  Bond restraints: 8329
  Sorted by residual:
  bond pdb=" CA  THR C 331 "
       pdb=" CB  THR C 331 "
    ideal  model  delta    sigma   weight residual
    1.540  1.642 -0.102 2.70e-02 1.37e+03 1.44e+01
  bond pdb=" C   PRO C 156 "
       pdb=" O   PRO C 156 "
    ideal  model  delta    sigma   weight residual
    1.237  1.203  0.034 1.32e-02 5.74e+03 6.79e+00
  bond pdb=" N   ILE C 155 "
       pdb=" CA  ILE C 155 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.23e-02 6.61e+03 6.67e+00
  bond pdb=" CA  THR C 331 "
       pdb=" C   THR C 331 "
    ideal  model  delta    sigma   weight residual
    1.525  1.576 -0.051 2.10e-02 2.27e+03 5.96e+00
  bond pdb=" N   PRO C 156 "
       pdb=" CA  PRO C 156 "
    ideal  model  delta    sigma   weight residual
    1.471  1.443  0.028 1.32e-02 5.74e+03 4.49e+00
  ... (remaining 8324 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 11121
        1.69 -     3.38: 171
        3.38 -     5.08: 47
        5.08 -     6.77: 13
        6.77 -     8.46: 4
  Bond angle restraints: 11356
  Sorted by residual:
  angle pdb=" CA  THR C 331 "
        pdb=" C   THR C 331 "
        pdb=" N   PRO C 332 "
      ideal   model   delta    sigma   weight residual
     116.90  124.88   -7.98 1.50e+00 4.44e-01 2.83e+01
  angle pdb=" C   PRO C 156 "
        pdb=" N   VAL C 157 "
        pdb=" CA  VAL C 157 "
      ideal   model   delta    sigma   weight residual
     121.77  114.35    7.42 1.44e+00 4.82e-01 2.65e+01
  angle pdb=" C   CYS C 154 "
        pdb=" N   ILE C 155 "
        pdb=" CA  ILE C 155 "
      ideal   model   delta    sigma   weight residual
     122.13  115.07    7.06 1.85e+00 2.92e-01 1.46e+01
  angle pdb=" N   PRO C 156 "
        pdb=" CA  PRO C 156 "
        pdb=" C   PRO C 156 "
      ideal   model   delta    sigma   weight residual
     113.84  109.29    4.55 1.30e+00 5.92e-01 1.22e+01
  angle pdb=" C   ARG D  10 "
        pdb=" CA  ARG D  10 "
        pdb=" CB  ARG D  10 "
      ideal   model   delta    sigma   weight residual
     110.10  116.53   -6.43 1.90e+00 2.77e-01 1.15e+01
  ... (remaining 11351 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 4377
       17.53 -    35.05: 382
       35.05 -    52.58: 75
       52.58 -    70.11: 8
       70.11 -    87.63: 8
  Dihedral angle restraints: 4850
    sinusoidal: 1619
      harmonic: 3231
  Sorted by residual:
  dihedral pdb=" CB  CYS H 159 "
           pdb=" SG  CYS H 159 "
           pdb=" SG  CYS H 229 "
           pdb=" CB  CYS H 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.84   55.16     1      1.00e+01 1.00e-02 4.12e+01
  dihedral pdb=" CB  CYS C  95 "
           pdb=" SG  CYS C  95 "
           pdb=" SG  CYS C 172 "
           pdb=" CB  CYS C 172 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -121.90   35.90     1      1.00e+01 1.00e-02 1.82e+01
  dihedral pdb=" CA  PRO C  99 "
           pdb=" C   PRO C  99 "
           pdb=" N   SER C 100 "
           pdb=" CA  SER C 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.15   18.85     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 4847 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1079
       0.052 -    0.104: 206
       0.104 -    0.156: 42
       0.156 -    0.207: 1
       0.207 -    0.259: 1
  Chirality restraints: 1329
  Sorted by residual:
  chirality pdb=" CA  DAL D   9 "
            pdb=" N   DAL D   9 "
            pdb=" C   DAL D   9 "
            pdb=" CB  DAL D   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.23   -0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CA  THR C 391 "
            pdb=" N   THR C 391 "
            pdb=" C   THR C 391 "
            pdb=" CB  THR C 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.16 2.00e-01 2.50e+01 6.19e-01
  chirality pdb=" CB  ILE C 155 "
            pdb=" CA  ILE C 155 "
            pdb=" CG1 ILE C 155 "
            pdb=" CG2 ILE C 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.16e-01
  ... (remaining 1326 not shown)

  Planarity restraints: 1449
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C  21 "   -0.063 5.00e-02 4.00e+02   9.39e-02 1.41e+01
        pdb=" N   PRO C  22 "    0.162 5.00e-02 4.00e+02
        pdb=" CA  PRO C  22 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO C  22 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 347 "   -0.039 5.00e-02 4.00e+02   5.92e-02 5.61e+00
        pdb=" N   PRO C 348 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO C 348 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO C 348 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 258 "   -0.010 2.00e-02 2.50e+03   1.89e-02 3.58e+00
        pdb=" C   ASP B 258 "    0.033 2.00e-02 2.50e+03
        pdb=" O   ASP B 258 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLN B 259 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1446 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 565
        2.74 -     3.28: 8023
        3.28 -     3.82: 13786
        3.82 -     4.36: 16328
        4.36 -     4.90: 29141
  Nonbonded interactions: 67843
  Sorted by model distance:
  nonbonded pdb=" O   LEU C 387 "
            pdb=" OG1 THR C 391 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" NZ  LYS C  96 "
            pdb=" O   ARG C 161 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" OG1 THR B 321 "
            pdb=" OD1 ASP B 323 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.272 3.040
  ... (remaining 67838 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:             4.270
  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:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.980
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
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   0.102   8333  Z= 0.171
  Angle     :  0.617   8.794  11365  Z= 0.327
  Chirality :  0.043   0.259   1329
  Planarity :  0.005   0.094   1448
  Dihedral  : 14.095  87.632   2752
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 14.01 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.26), residues: 1098
  helix:  1.29 (0.28), residues: 380
  sheet: -0.22 (0.29), residues: 304
  loop : -0.77 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.012   0.001   PHE C 107 
 TYR   0.021   0.002   TYR B 105 
 ARG   0.008   0.000   ARG B 214 

Details of bonding type rmsd
  link_TRANS           : bond        0.01061 (    1)
  link_TRANS           : angle       2.86819 (    3)
  hydrogen bonds       : bond        0.16975 (  424)
  hydrogen bonds       : angle       6.95701 ( 1236)
  SS BOND              : bond        0.01081 (    3)
  SS BOND              : angle       4.76495 (    6)
  covalent geometry    : bond        0.00365 ( 8329)
  covalent geometry    : angle       0.60598 (11356)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.873 
Fit side-chains
  outliers start: 9
  outliers final: 8
  residues processed: 108
  average time/residue: 1.0098
  time to fit residues: 117.2901
Evaluate side-chains
  108 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  331 THR
Chi-restraints excluded: chain C residue  347 LEU
Chi-restraints excluded: chain D residue   10 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 55 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 85 optimal weight:    0.0670
   chunk 33 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   overall best weight:    0.6518

-------------------------------------------------------------------------------
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 = 0.3895 r_free = 0.3895 target = 0.168963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.128050 restraints weight = 8829.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.79
r_work: 0.3287 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.0760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8333  Z= 0.178
  Angle     :  0.580   8.364  11365  Z= 0.309
  Chirality :  0.044   0.203   1329
  Planarity :  0.004   0.061   1448
  Dihedral  :  5.371  47.507   1204
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.27 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.12 (0.26), residues: 1098
  helix:  1.33 (0.28), residues: 387
  sheet: -0.26 (0.29), residues: 288
  loop : -0.75 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  47 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.011   0.001   PHE C 107 
 TYR   0.017   0.002   TYR H 190 
 ARG   0.003   0.000   ARG A 198 

Details of bonding type rmsd
  link_TRANS           : bond        0.00479 (    1)
  link_TRANS           : angle       1.64358 (    3)
  hydrogen bonds       : bond        0.04658 (  424)
  hydrogen bonds       : angle       5.28902 ( 1236)
  SS BOND              : bond        0.00455 (    3)
  SS BOND              : angle       1.99420 (    6)
  covalent geometry    : bond        0.00402 ( 8329)
  covalent geometry    : angle       0.57796 (11356)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A  254 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7788 (tp)
REVERT: B  325 MET cc_start: 0.8723 (tpp) cc_final: 0.8278 (mmt)
REVERT: H   82 GLN cc_start: 0.8241 (tp40) cc_final: 0.7476 (tp40)
REVERT: H  140 MET cc_start: 0.8464 (mtp) cc_final: 0.8128 (mtp)
REVERT: H  213 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8202 (t)
REVERT: C  367 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.6960 (ttt-90)
  outliers start: 19
  outliers final: 11
  residues processed: 118
  average time/residue: 0.9715
  time to fit residues: 123.4577
Evaluate side-chains
  115 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  331 THR
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  337 THR
Chi-restraints excluded: chain C residue  367 ARG
Chi-restraints excluded: chain C residue  399 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 102 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 101 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
H 113 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.167623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.126435 restraints weight = 9028.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 1.81
r_work: 0.3278 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.0992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8333  Z= 0.176
  Angle     :  0.567   8.257  11365  Z= 0.299
  Chirality :  0.043   0.204   1329
  Planarity :  0.004   0.056   1448
  Dihedral  :  4.783  40.590   1193
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 15.16 %
    Favored  : 81.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.26), residues: 1098
  helix:  1.36 (0.28), residues: 387
  sheet: -0.30 (0.29), residues: 286
  loop : -0.79 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.011   0.001   PHE C 107 
 TYR   0.015   0.002   TYR H 190 
 ARG   0.004   0.000   ARG A 198 

Details of bonding type rmsd
  link_TRANS           : bond        0.00288 (    1)
  link_TRANS           : angle       1.47697 (    3)
  hydrogen bonds       : bond        0.04259 (  424)
  hydrogen bonds       : angle       5.07414 ( 1236)
  SS BOND              : bond        0.00389 (    3)
  SS BOND              : angle       1.56493 (    6)
  covalent geometry    : bond        0.00406 ( 8329)
  covalent geometry    : angle       0.56563 (11356)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.831 
Fit side-chains
REVERT: A  254 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.7914 (tp)
REVERT: H  213 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8363 (t)
REVERT: C  367 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.6974 (ttt-90)
  outliers start: 25
  outliers final: 13
  residues processed: 121
  average time/residue: 0.9259
  time to fit residues: 121.0541
Evaluate side-chains
  117 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  367 ARG
Chi-restraints excluded: chain D residue    4 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 107 optimal weight:    0.0270
   chunk 55 optimal weight:    0.6980
   chunk 105 optimal weight:    0.7980
   chunk 106 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 259 GLN
H 113 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.169764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.128548 restraints weight = 8896.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.84
r_work: 0.3273 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3148 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.1158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8333  Z= 0.141
  Angle     :  0.539   7.559  11365  Z= 0.283
  Chirality :  0.042   0.207   1329
  Planarity :  0.004   0.052   1448
  Dihedral  :  4.584  35.248   1192
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 16.31 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.15 (0.26), residues: 1098
  helix:  1.48 (0.28), residues: 385
  sheet: -0.38 (0.29), residues: 288
  loop : -0.75 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.011   0.001   PHE B 241 
 TYR   0.015   0.001   TYR H 190 
 ARG   0.002   0.000   ARG C 367 

Details of bonding type rmsd
  link_TRANS           : bond        0.00298 (    1)
  link_TRANS           : angle       1.53403 (    3)
  hydrogen bonds       : bond        0.03850 (  424)
  hydrogen bonds       : angle       4.88707 ( 1236)
  SS BOND              : bond        0.00392 (    3)
  SS BOND              : angle       1.35761 (    6)
  covalent geometry    : bond        0.00317 ( 8329)
  covalent geometry    : angle       0.53765 (11356)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.831 
Fit side-chains
REVERT: A  254 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8006 (tp)
REVERT: H  213 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8376 (t)
REVERT: C  367 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6896 (ttt-90)
  outliers start: 23
  outliers final: 9
  residues processed: 121
  average time/residue: 0.9338
  time to fit residues: 121.9947
Evaluate side-chains
  118 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  367 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0070
   chunk 8 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0870
   chunk 107 optimal weight:    0.0060
   overall best weight:    0.2992

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 259 GLN
B 340 ASN
H 113 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.171324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.130651 restraints weight = 8835.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.81
r_work: 0.3304 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.1359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8333  Z= 0.116
  Angle     :  0.521   6.796  11365  Z= 0.271
  Chirality :  0.042   0.196   1329
  Planarity :  0.004   0.049   1448
  Dihedral  :  4.416  34.171   1192
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 17.58 %
    Favored  : 79.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.24 (0.26), residues: 1098
  helix:  1.60 (0.28), residues: 385
  sheet: -0.37 (0.29), residues: 283
  loop : -0.71 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 211 
 HIS   0.002   0.001   HIS H 232 
 PHE   0.010   0.001   PHE C 107 
 TYR   0.015   0.001   TYR H 190 
 ARG   0.002   0.000   ARG D  10 

Details of bonding type rmsd
  link_TRANS           : bond        0.00304 (    1)
  link_TRANS           : angle       1.45943 (    3)
  hydrogen bonds       : bond        0.03574 (  424)
  hydrogen bonds       : angle       4.70597 ( 1236)
  SS BOND              : bond        0.00324 (    3)
  SS BOND              : angle       1.28849 (    6)
  covalent geometry    : bond        0.00252 ( 8329)
  covalent geometry    : angle       0.51981 (11356)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.855 
Fit side-chains
REVERT: B  139 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8074 (mt)
REVERT: B  325 MET cc_start: 0.8690 (tpp) cc_final: 0.8165 (mmt)
REVERT: H  213 THR cc_start: 0.8621 (m) cc_final: 0.8351 (t)
REVERT: C  367 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6896 (ttt-90)
  outliers start: 24
  outliers final: 10
  residues processed: 127
  average time/residue: 0.8477
  time to fit residues: 116.7393
Evaluate side-chains
  118 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  367 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   chunk 99 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.168312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.127208 restraints weight = 8915.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 1.80
r_work: 0.3243 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.1308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   8333  Z= 0.195
  Angle     :  0.579   7.967  11365  Z= 0.301
  Chirality :  0.044   0.208   1329
  Planarity :  0.004   0.050   1448
  Dihedral  :  4.501  28.006   1190
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 18.22 %
    Favored  : 78.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.09 (0.26), residues: 1098
  helix:  1.49 (0.28), residues: 383
  sheet: -0.45 (0.29), residues: 288
  loop : -0.81 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.013   0.001   PHE C 107 
 TYR   0.021   0.002   TYR B  59 
 ARG   0.003   0.000   ARG H 160 

Details of bonding type rmsd
  link_TRANS           : bond        0.00227 (    1)
  link_TRANS           : angle       1.32185 (    3)
  hydrogen bonds       : bond        0.03978 (  424)
  hydrogen bonds       : angle       4.85845 ( 1236)
  SS BOND              : bond        0.00387 (    3)
  SS BOND              : angle       1.55614 (    6)
  covalent geometry    : bond        0.00459 ( 8329)
  covalent geometry    : angle       0.57816 (11356)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.850 
Fit side-chains
REVERT: A  254 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8004 (tp)
REVERT: B   13 GLN cc_start: 0.7448 (tt0) cc_final: 0.6898 (tm-30)
REVERT: B  214 ARG cc_start: 0.7536 (mmt180) cc_final: 0.7216 (mmp-170)
REVERT: H  213 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8369 (t)
REVERT: C  367 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.6967 (ttt-90)
  outliers start: 25
  outliers final: 13
  residues processed: 124
  average time/residue: 0.8912
  time to fit residues: 119.6867
Evaluate side-chains
  123 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  367 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 67 optimal weight:    0.1980
   chunk 101 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   chunk 105 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0870
   chunk 28 optimal weight:    0.0970
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.3756

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.169552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.128210 restraints weight = 8948.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 1.84
r_work: 0.3280 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
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   0.037   8333  Z= 0.125
  Angle     :  0.531   7.788  11365  Z= 0.275
  Chirality :  0.042   0.192   1329
  Planarity :  0.004   0.048   1448
  Dihedral  :  4.312  25.574   1190
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 18.85 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.17 (0.26), residues: 1098
  helix:  1.58 (0.28), residues: 386
  sheet: -0.47 (0.29), residues: 282
  loop : -0.75 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.012   0.001   PHE B 335 
 TYR   0.017   0.001   TYR B  59 
 ARG   0.002   0.000   ARG C 367 

Details of bonding type rmsd
  link_TRANS           : bond        0.00247 (    1)
  link_TRANS           : angle       1.27120 (    3)
  hydrogen bonds       : bond        0.03543 (  424)
  hydrogen bonds       : angle       4.70020 ( 1236)
  SS BOND              : bond        0.00358 (    3)
  SS BOND              : angle       1.38562 (    6)
  covalent geometry    : bond        0.00279 ( 8329)
  covalent geometry    : angle       0.52979 (11356)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.854 
Fit side-chains
REVERT: B   13 GLN cc_start: 0.7394 (tt0) cc_final: 0.6842 (tm-30)
REVERT: B   46 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7366 (mmm160)
REVERT: B  139 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8120 (mt)
REVERT: B  212 ASP cc_start: 0.8303 (p0) cc_final: 0.8101 (p0)
REVERT: B  214 ARG cc_start: 0.7626 (mmt180) cc_final: 0.7275 (mmp-170)
REVERT: H   82 GLN cc_start: 0.8348 (tp40) cc_final: 0.8020 (tp40)
REVERT: H  213 THR cc_start: 0.8636 (m) cc_final: 0.8371 (t)
REVERT: H  219 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7053 (tt)
REVERT: C   36 LEU cc_start: 0.7893 (mp) cc_final: 0.7352 (tp)
REVERT: C  367 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.6812 (ttt-90)
  outliers start: 21
  outliers final: 12
  residues processed: 125
  average time/residue: 0.9114
  time to fit residues: 122.9379
Evaluate side-chains
  125 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  219 LEU
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  367 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 32 optimal weight:    0.2980
   chunk 2 optimal weight:    0.0980
   chunk 23 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 102 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0670
   chunk 68 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.4118

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.170975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.128846 restraints weight = 8943.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 1.81
r_work: 0.3301 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8333  Z= 0.130
  Angle     :  0.535   8.274  11365  Z= 0.276
  Chirality :  0.042   0.181   1329
  Planarity :  0.004   0.047   1448
  Dihedral  :  4.284  24.747   1190
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 18.34 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.18 (0.26), residues: 1098
  helix:  1.61 (0.28), residues: 385
  sheet: -0.48 (0.29), residues: 282
  loop : -0.74 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.012   0.001   PHE B 335 
 TYR   0.019   0.001   TYR B  59 
 ARG   0.002   0.000   ARG C 161 

Details of bonding type rmsd
  link_TRANS           : bond        0.00210 (    1)
  link_TRANS           : angle       1.18607 (    3)
  hydrogen bonds       : bond        0.03517 (  424)
  hydrogen bonds       : angle       4.65247 ( 1236)
  SS BOND              : bond        0.00358 (    3)
  SS BOND              : angle       1.47198 (    6)
  covalent geometry    : bond        0.00293 ( 8329)
  covalent geometry    : angle       0.53377 (11356)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.932 
Fit side-chains
REVERT: B   13 GLN cc_start: 0.7412 (tt0) cc_final: 0.6860 (tm-30)
REVERT: B   46 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7338 (mmm160)
REVERT: B  139 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8112 (mt)
REVERT: B  160 SER cc_start: 0.8911 (OUTLIER) cc_final: 0.8698 (p)
REVERT: B  212 ASP cc_start: 0.8276 (p0) cc_final: 0.8059 (p0)
REVERT: B  215 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7815 (mm-30)
REVERT: H   82 GLN cc_start: 0.8351 (tp40) cc_final: 0.8019 (tp40)
REVERT: H  213 THR cc_start: 0.8633 (m) cc_final: 0.8373 (t)
REVERT: C   36 LEU cc_start: 0.7868 (mp) cc_final: 0.7326 (tp)
REVERT: C  367 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7029 (ttt-90)
  outliers start: 25
  outliers final: 15
  residues processed: 127
  average time/residue: 0.9818
  time to fit residues: 134.4738
Evaluate side-chains
  127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  367 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 94 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 4 optimal weight:    5.9990
   chunk 72 optimal weight:    0.2980
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.169279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.128694 restraints weight = 9054.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.86
r_work: 0.3256 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8333  Z= 0.164
  Angle     :  0.560   8.137  11365  Z= 0.289
  Chirality :  0.043   0.176   1329
  Planarity :  0.004   0.047   1448
  Dihedral  :  4.424  26.426   1190
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 19.11 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.12 (0.26), residues: 1098
  helix:  1.58 (0.28), residues: 384
  sheet: -0.50 (0.29), residues: 281
  loop : -0.81 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.014   0.001   PHE B 335 
 TYR   0.014   0.001   TYR H 190 
 ARG   0.004   0.000   ARG C 362 

Details of bonding type rmsd
  link_TRANS           : bond        0.00159 (    1)
  link_TRANS           : angle       1.12104 (    3)
  hydrogen bonds       : bond        0.03732 (  424)
  hydrogen bonds       : angle       4.75659 ( 1236)
  SS BOND              : bond        0.00408 (    3)
  SS BOND              : angle       1.59517 (    6)
  covalent geometry    : bond        0.00381 ( 8329)
  covalent geometry    : angle       0.55872 (11356)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.932 
Fit side-chains
REVERT: B   46 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7340 (mmm160)
REVERT: B  139 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8156 (mt)
REVERT: B  160 SER cc_start: 0.8942 (OUTLIER) cc_final: 0.8707 (p)
REVERT: B  215 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7854 (mm-30)
REVERT: H   82 GLN cc_start: 0.8298 (tp40) cc_final: 0.7937 (tp40)
REVERT: H  213 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8368 (t)
REVERT: C   36 LEU cc_start: 0.7906 (mp) cc_final: 0.7416 (tt)
REVERT: C  163 ILE cc_start: 0.7682 (mt) cc_final: 0.7114 (tp)
REVERT: C  367 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.6830 (ttt-90)
  outliers start: 25
  outliers final: 15
  residues processed: 125
  average time/residue: 0.9158
  time to fit residues: 123.7828
Evaluate side-chains
  130 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  367 ARG
Chi-restraints excluded: chain C residue  437 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 106 optimal weight:    0.6980
   chunk 61 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9980
   chunk 88 optimal weight:    9.9990
   chunk 57 optimal weight:    0.1980
   chunk 81 optimal weight:    0.2980
   chunk 27 optimal weight:    3.9990
   chunk 43 optimal weight:    0.3980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.169268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.127795 restraints weight = 8873.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.86
r_work: 0.3279 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.1542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8333  Z= 0.135
  Angle     :  0.545   7.756  11365  Z= 0.282
  Chirality :  0.042   0.161   1329
  Planarity :  0.004   0.047   1448
  Dihedral  :  4.338  25.353   1190
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 19.62 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.19 (0.26), residues: 1098
  helix:  1.65 (0.28), residues: 385
  sheet: -0.50 (0.29), residues: 281
  loop : -0.75 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 211 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.013   0.001   PHE B 335 
 TYR   0.014   0.001   TYR H 190 
 ARG   0.004   0.000   ARG C 161 

Details of bonding type rmsd
  link_TRANS           : bond        0.00128 (    1)
  link_TRANS           : angle       1.03005 (    3)
  hydrogen bonds       : bond        0.03546 (  424)
  hydrogen bonds       : angle       4.68713 ( 1236)
  SS BOND              : bond        0.00375 (    3)
  SS BOND              : angle       1.57601 (    6)
  covalent geometry    : bond        0.00307 ( 8329)
  covalent geometry    : angle       0.54361 (11356)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.824 
Fit side-chains
REVERT: B   46 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7261 (mmm160)
REVERT: B  139 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8091 (mt)
REVERT: B  160 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8675 (p)
REVERT: B  214 ARG cc_start: 0.7434 (mmt180) cc_final: 0.7213 (mmp-170)
REVERT: H   82 GLN cc_start: 0.8282 (tp40) cc_final: 0.7907 (tp40)
REVERT: H  213 THR cc_start: 0.8603 (m) cc_final: 0.8336 (t)
REVERT: C   36 LEU cc_start: 0.7903 (mp) cc_final: 0.7434 (tt)
REVERT: C  362 ARG cc_start: 0.6953 (tpt170) cc_final: 0.6226 (tpt90)
REVERT: C  367 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.6950 (ttt-90)
  outliers start: 20
  outliers final: 14
  residues processed: 120
  average time/residue: 0.9540
  time to fit residues: 123.6040
Evaluate side-chains
  125 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  367 ARG
Chi-restraints excluded: chain C residue  437 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 0 optimal weight:    0.5980
   chunk 63 optimal weight:    0.0670
   chunk 92 optimal weight:    0.0470
   chunk 54 optimal weight:    0.6980
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.4016

-------------------------------------------------------------------------------
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 = 0.3917 r_free = 0.3917 target = 0.171069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.130602 restraints weight = 8942.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 1.82
r_work: 0.3292 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.1602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8333  Z= 0.129
  Angle     :  0.532   7.560  11365  Z= 0.277
  Chirality :  0.042   0.142   1329
  Planarity :  0.004   0.046   1448
  Dihedral  :  4.282  24.824   1190
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 19.62 %
    Favored  : 77.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.22 (0.26), residues: 1098
  helix:  1.70 (0.28), residues: 386
  sheet: -0.54 (0.29), residues: 285
  loop : -0.73 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 211 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.011   0.001   PHE B 241 
 TYR   0.015   0.001   TYR H 190 
 ARG   0.003   0.000   ARG C 362 

Details of bonding type rmsd
  link_TRANS           : bond        0.00098 (    1)
  link_TRANS           : angle       0.92005 (    3)
  hydrogen bonds       : bond        0.03475 (  424)
  hydrogen bonds       : angle       4.62751 ( 1236)
  SS BOND              : bond        0.00373 (    3)
  SS BOND              : angle       1.51574 (    6)
  covalent geometry    : bond        0.00291 ( 8329)
  covalent geometry    : angle       0.53072 (11356)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6236.18 seconds
wall clock time: 108 minutes 19.27 seconds (6499.27 seconds total)