Starting phenix.real_space_refine
on Tue Apr 29 15:21:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uh3_42245/04_2025/8uh3_42245.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uh3_42245/04_2025/8uh3_42245.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uh3_42245/04_2025/8uh3_42245.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uh3_42245/04_2025/8uh3_42245.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uh3_42245/04_2025/8uh3_42245.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uh3_42245/04_2025/8uh3_42245.cif"
  }
  resolution = 3.31
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.078
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      63      5.16       5
     C    5631      2.51       5
     N    1457      2.21       5
     O    1608      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8759
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 2558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2558
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 5, 'TRANS': 327}
    Chain: "A"
      Number of atoms: 1747
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1747
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "D"
      Number of atoms: 2168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 269, 2168
          Classifications: {'peptide': 269}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 260}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "E"
      Number of atoms: 1762
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1762
          Classifications: {'peptide': 229}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 391
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
    Chain: "D"
      Number of atoms: 132
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 132
          Unusual residues: {'CLR': 4, 'WOQ': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 5.36, per 1000 atoms: 0.61
  Number of scatterers: 8759
  At special positions: 0
  Unit cell: (91.46, 117.284, 123.74, 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      63     16.00
     O    1608      8.00
     N    1457      7.00
     C    5631      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  95 " - pdb=" SG  CYS D 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.28
  Conformation dependent library (CDL) restraints added in 973.7 milliseconds
  

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2058

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      39.2% alpha, 22.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'B' and resid 7 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'A' and resid 6 through 32
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 4.378A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 216
      No H-bonds generated for 'chain 'A' and resid 214 through 216'
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 3.983A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.828A  pdb=" N   PHE A 274 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 287
      removed outlier: 4.068A  pdb=" N   CYS A 286 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.742A  pdb=" N   GLU A 308 " --> pdb=" O   GLN A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 352
    Processing helix  chain 'D' and resid 20 through 50
    Processing helix  chain 'D' and resid 55 through 75
    Processing helix  chain 'D' and resid 75 through 86
      removed outlier: 3.509A  pdb=" N   VAL D  84 " --> pdb=" O   ILE D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 91 through 126
      removed outlier: 3.623A  pdb=" N   MET D 103 " --> pdb=" O   LEU D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 126 through 134
      removed outlier: 3.968A  pdb=" N   ARG D 132 " --> pdb=" O   ILE D 128 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 155
    Processing helix  chain 'D' and resid 155 through 161
      removed outlier: 3.730A  pdb=" N   PHE D 159 " --> pdb=" O   MET D 155 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 179 through 191
    Processing helix  chain 'D' and resid 191 through 210
      removed outlier: 3.785A  pdb=" N   LYS D 210 " --> pdb=" O   TYR D 206 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 211 through 213
      No H-bonds generated for 'chain 'D' and resid 211 through 213'
    Processing helix  chain 'D' and resid 286 through 316
      removed outlier: 3.610A  pdb=" N   TRP D 304 " --> pdb=" O   PHE D 300 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   LEU D 305 " --> pdb=" O   ILE D 301 " (cutoff:3.500A)
      Proline residue:  D 306  - end of helix
    Processing helix  chain 'D' and resid 322 through 346
      removed outlier: 3.788A  pdb=" N   GLY D 333 " --> pdb=" O   LEU D 329 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   TYR D 334 " --> pdb=" O   THR D 330 " (cutoff:3.500A)
      Proline residue:  D 341  - end of helix
    Processing helix  chain 'D' and resid 348 through 359
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 4.049A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.716A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 220 through 224
    Processing helix  chain 'G' and resid 14 through 23
    Processing helix  chain 'G' and resid 29 through 44
    Processing sheet with id=AA1, first strand: chain 'B' and resid 49 through 52
      removed outlier: 4.231A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.602A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.648A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.102A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.509A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.634A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 192
      removed outlier: 6.709A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.804A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.886A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.901A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.246A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.664A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.538A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.704A  pdb=" N   VAL E  97 " --> pdb=" O   HIS E  35 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 4.918A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148
      removed outlier: 3.589A  pdb=" N   GLY E 225 " --> pdb=" O   LEU E 245 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   LEU E 178 " --> pdb=" O   LEU E 187 " (cutoff:3.500A)
      removed outlier: 5.635A  pdb=" N   LEU E 187 " --> pdb=" O   LEU E 178 " (cutoff:3.500A)

    449 hydrogen bonds defined for protein.
    1290 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: 2.58

  Time building geometry restraints manager: 2.66 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2747
        1.34 -     1.46: 2120
        1.46 -     1.58: 3993
        1.58 -     1.70: 0
        1.70 -     1.82: 91
  Bond restraints: 8951
  Sorted by residual:
  bond pdb=" CA  ALA B  11 "
       pdb=" C   ALA B  11 "
    ideal  model  delta    sigma   weight residual
    1.524  1.495  0.029 1.27e-02 6.20e+03 5.11e+00
  bond pdb=" CA  ALA B  11 "
       pdb=" CB  ALA B  11 "
    ideal  model  delta    sigma   weight residual
    1.529  1.497  0.032 1.55e-02 4.16e+03 4.18e+00
  bond pdb=" C   ALA B  11 "
       pdb=" N   GLU B  12 "
    ideal  model  delta    sigma   weight residual
    1.335  1.311  0.024 1.30e-02 5.92e+03 3.45e+00
  bond pdb=" C   ALA B  11 "
       pdb=" O   ALA B  11 "
    ideal  model  delta    sigma   weight residual
    1.236  1.219  0.017 1.15e-02 7.56e+03 2.19e+00
  bond pdb=" C3  WOQ D 405 "
       pdb=" C4  WOQ D 405 "
    ideal  model  delta    sigma   weight residual
    1.347  1.321  0.026 2.00e-02 2.50e+03 1.74e+00
  ... (remaining 8946 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 11827
        1.52 -     3.03: 260
        3.03 -     4.55: 41
        4.55 -     6.07: 14
        6.07 -     7.58: 3
  Bond angle restraints: 12145
  Sorted by residual:
  angle pdb=" N   ARG B 197 "
        pdb=" CA  ARG B 197 "
        pdb=" C   ARG B 197 "
      ideal   model   delta    sigma   weight residual
     114.56  109.80    4.76 1.27e+00 6.20e-01 1.40e+01
  angle pdb=" N   ALA B  11 "
        pdb=" CA  ALA B  11 "
        pdb=" C   ALA B  11 "
      ideal   model   delta    sigma   weight residual
     111.07  107.90    3.17 1.07e+00 8.73e-01 8.78e+00
  angle pdb=" N   PRO D 156 "
        pdb=" CA  PRO D 156 "
        pdb=" C   PRO D 156 "
      ideal   model   delta    sigma   weight residual
     110.70  114.26   -3.56 1.22e+00 6.72e-01 8.51e+00
  angle pdb=" CA  ARG B 197 "
        pdb=" C   ARG B 197 "
        pdb=" N   LEU B 198 "
      ideal   model   delta    sigma   weight residual
     119.26  116.34    2.92 1.14e+00 7.69e-01 6.57e+00
  angle pdb=" CB  MET A 247 "
        pdb=" CG  MET A 247 "
        pdb=" SD  MET A 247 "
      ideal   model   delta    sigma   weight residual
     112.70  120.28   -7.58 3.00e+00 1.11e-01 6.39e+00
  ... (remaining 12140 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.79: 5207
       23.79 -    47.58: 269
       47.58 -    71.38: 21
       71.38 -    95.17: 12
       95.17 -   118.96: 4
  Dihedral angle restraints: 5513
    sinusoidal: 2323
      harmonic: 3190
  Sorted by residual:
  dihedral pdb=" C10 CLR D 402 "
           pdb=" C1  CLR D 402 "
           pdb=" C2  CLR D 402 "
           pdb=" C3  CLR D 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.83   62.13 -118.96     1      3.00e+01 1.11e-03 1.58e+01
  dihedral pdb=" C1  CLR D 402 "
           pdb=" C2  CLR D 402 "
           pdb=" C3  CLR D 402 "
           pdb=" O1  CLR D 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.04   70.31  109.73     1      3.00e+01 1.11e-03 1.43e+01
  dihedral pdb=" C1  CLR D 402 "
           pdb=" C2  CLR D 402 "
           pdb=" C3  CLR D 402 "
           pdb=" C4  CLR D 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
      57.41  -50.54  107.95     1      3.00e+01 1.11e-03 1.40e+01
  ... (remaining 5510 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 997
       0.041 -    0.081: 302
       0.081 -    0.122: 86
       0.122 -    0.162: 9
       0.162 -    0.203: 2
  Chirality restraints: 1396
  Sorted by residual:
  chirality pdb=" CB  THR D 148 "
            pdb=" CA  THR D 148 "
            pdb=" OG1 THR D 148 "
            pdb=" CG2 THR D 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CG  LEU A 268 "
            pdb=" CB  LEU A 268 "
            pdb=" CD1 LEU A 268 "
            pdb=" CD2 LEU A 268 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 8.04e-01
  chirality pdb=" CA  ILE B 232 "
            pdb=" N   ILE B 232 "
            pdb=" C   ILE B 232 "
            pdb=" CB  ILE B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.26e-01
  ... (remaining 1393 not shown)

  Planarity restraints: 1488
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO D 156 "   -0.049 5.00e-02 4.00e+02   7.39e-02 8.73e+00
        pdb=" N   PRO D 157 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO D 157 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO D 157 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C12 WOQ D 405 "    0.025 2.00e-02 2.50e+03   1.40e-02 3.91e+00
        pdb=" C13 WOQ D 405 "   -0.012 2.00e-02 2.50e+03
        pdb=" C14 WOQ D 405 "   -0.017 2.00e-02 2.50e+03
        pdb=" C15 WOQ D 405 "   -0.003 2.00e-02 2.50e+03
        pdb=" C16 WOQ D 405 "    0.014 2.00e-02 2.50e+03
        pdb=" C17 WOQ D 405 "    0.010 2.00e-02 2.50e+03
        pdb=" C18 WOQ D 405 "   -0.005 2.00e-02 2.50e+03
        pdb=" C3  WOQ D 405 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP E 201 "    0.007 2.00e-02 2.50e+03   1.42e-02 2.00e+00
        pdb=" CG  ASP E 201 "   -0.024 2.00e-02 2.50e+03
        pdb=" OD1 ASP E 201 "    0.009 2.00e-02 2.50e+03
        pdb=" OD2 ASP E 201 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1485 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 625
        2.74 -     3.28: 8857
        3.28 -     3.82: 14771
        3.82 -     4.36: 17754
        4.36 -     4.90: 30945
  Nonbonded interactions: 72952
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 354 "
            pdb=" OH  TYR D 213 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OD1 ASP D 119 "
            pdb=" OH  TYR D 130 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" O   ALA A  41 "
            pdb=" NZ  LYS A  46 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" NH1 ARG E 202 "
            pdb=" OE1 GLU E 220 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.244 3.040
  ... (remaining 72947 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.900
  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:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     22.450
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8955  Z= 0.153
  Angle     :  0.571   7.585  12153  Z= 0.307
  Chirality :  0.042   0.203   1396
  Planarity :  0.004   0.074   1488
  Dihedral  : 14.491 118.960   3443
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.64 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.42 (0.26), residues: 1078
  helix:  1.25 (0.27), residues: 392
  sheet: -0.40 (0.32), residues: 248
  loop : -0.03 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  82 
 HIS   0.002   0.001   HIS B 142 
 PHE   0.013   0.001   PHE D 307 
 TYR   0.016   0.001   TYR E 190 
 ARG   0.006   0.001   ARG B  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06299 (  449)
  hydrogen bonds       : angle       5.10722 ( 1290)
  SS BOND              : bond        0.00494 (    4)
  SS BOND              : angle       1.35576 (    8)
  covalent geometry    : bond        0.00322 ( 8951)
  covalent geometry    : angle       0.57008 (12145)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 199
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
REVERT: B  145 TYR cc_start: 0.9099 (p90) cc_final: 0.8605 (p90)
REVERT: B  189 SER cc_start: 0.8543 (p) cc_final: 0.8311 (p)
REVERT: B  291 ASP cc_start: 0.7488 (t70) cc_final: 0.7276 (t0)
REVERT: A   24 ARG cc_start: 0.6786 (ttp-110) cc_final: 0.6572 (ttp-170)
REVERT: G   20 LYS cc_start: 0.8423 (ptpp) cc_final: 0.7755 (mtmm)
  outliers start: 1
  outliers final: 1
  residues processed: 200
  average time/residue: 0.2592
  time to fit residues: 67.3395
Evaluate side-chains
  171 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 170
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   13 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 81 optimal weight:    7.9990
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   chunk 54 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 32 optimal weight:    0.3980
   chunk 50 optimal weight:    0.0970
   chunk 62 optimal weight:    4.9990
   chunk 97 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
A 256 ASN
** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  13 GLN
E 169 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.170548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.129466 restraints weight = 11025.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.49
r_work: 0.3292 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.1063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8955  Z= 0.127
  Angle     :  0.528   6.998  12153  Z= 0.277
  Chirality :  0.041   0.143   1396
  Planarity :  0.004   0.080   1488
  Dihedral  :  8.251  93.598   1472
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  9.85 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.51 (0.26), residues: 1078
  helix:  1.28 (0.26), residues: 396
  sheet: -0.38 (0.32), residues: 254
  loop :  0.08 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS D 112 
 PHE   0.010   0.001   PHE A 189 
 TYR   0.016   0.001   TYR E 190 
 ARG   0.004   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03303 (  449)
  hydrogen bonds       : angle       4.82719 ( 1290)
  SS BOND              : bond        0.00495 (    4)
  SS BOND              : angle       1.17949 (    8)
  covalent geometry    : bond        0.00286 ( 8951)
  covalent geometry    : angle       0.52712 (12145)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 184
  time to evaluate  : 1.013 
Fit side-chains
REVERT: B  163 ASP cc_start: 0.8271 (t0) cc_final: 0.7730 (t0)
REVERT: B  189 SER cc_start: 0.8862 (p) cc_final: 0.8657 (p)
REVERT: B  214 ARG cc_start: 0.8311 (mmp80) cc_final: 0.8096 (mmt180)
REVERT: B  291 ASP cc_start: 0.8251 (t70) cc_final: 0.7798 (t0)
REVERT: A   24 ARG cc_start: 0.6930 (ttp-110) cc_final: 0.6705 (ttp-170)
REVERT: A   53 MET cc_start: 0.6293 (mpp) cc_final: 0.6076 (mpp)
REVERT: A  333 GLN cc_start: 0.8272 (tm-30) cc_final: 0.8003 (tm-30)
REVERT: A  337 ASP cc_start: 0.8662 (m-30) cc_final: 0.8373 (m-30)
REVERT: D   27 MET cc_start: 0.7904 (ptp) cc_final: 0.7159 (ttt)
REVERT: D  215 LYS cc_start: 0.6413 (mmtm) cc_final: 0.5636 (mttp)
  outliers start: 16
  outliers final: 12
  residues processed: 189
  average time/residue: 0.3379
  time to fit residues: 82.8347
Evaluate side-chains
  179 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 167
  time to evaluate  : 1.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain D residue   69 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  319 TYR
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue  169 ASN
Chi-restraints excluded: chain G residue   13 ARG
Chi-restraints excluded: chain G residue   36 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 69 optimal weight:    7.9990
   chunk 12 optimal weight:    0.8980
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 85 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 86 optimal weight:    3.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
A 195 HIS
** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.164681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.114937 restraints weight = 11239.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 2.45
r_work: 0.3210 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.1367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   8955  Z= 0.255
  Angle     :  0.610   7.235  12153  Z= 0.319
  Chirality :  0.044   0.151   1396
  Planarity :  0.004   0.079   1488
  Dihedral  :  8.453  95.348   1472
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 13.35 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.23 (0.26), residues: 1078
  helix:  1.22 (0.26), residues: 388
  sheet: -0.77 (0.31), residues: 270
  loop : -0.02 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.005   0.001   HIS E 167 
 PHE   0.016   0.002   PHE D 347 
 TYR   0.020   0.002   TYR E 175 
 ARG   0.005   0.001   ARG E 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03711 (  449)
  hydrogen bonds       : angle       5.06756 ( 1290)
  SS BOND              : bond        0.00799 (    4)
  SS BOND              : angle       1.89427 (    8)
  covalent geometry    : bond        0.00601 ( 8951)
  covalent geometry    : angle       0.60860 (12145)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 178
  time to evaluate  : 1.386 
Fit side-chains
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.9009 (m-80) cc_final: 0.8587 (m-80)
REVERT: B  105 TYR cc_start: 0.9276 (t80) cc_final: 0.8980 (t80)
REVERT: B  291 ASP cc_start: 0.8498 (t70) cc_final: 0.7992 (t0)
REVERT: A   24 ARG cc_start: 0.7129 (ttp-110) cc_final: 0.6920 (ttp-170)
REVERT: A  333 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8244 (tm-30)
REVERT: D   23 MET cc_start: 0.8461 (mtt) cc_final: 0.7717 (mmp)
REVERT: D   27 MET cc_start: 0.7887 (ptp) cc_final: 0.7202 (ttt)
REVERT: D  134 ARG cc_start: 0.8145 (ttp-170) cc_final: 0.7914 (ttp-170)
  outliers start: 23
  outliers final: 17
  residues processed: 187
  average time/residue: 0.2791
  time to fit residues: 68.2637
Evaluate side-chains
  185 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 168
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain D residue   69 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  196 THR
Chi-restraints excluded: chain D residue  319 TYR
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain G residue   13 ARG
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   36 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 104 optimal weight:    0.9990
   chunk 93 optimal weight:    9.9990
   chunk 43 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 73 optimal weight:    0.0970
   chunk 32 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 95 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 167 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.168022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.126111 restraints weight = 11055.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 2.55
r_work: 0.3244 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8955  Z= 0.136
  Angle     :  0.532   6.834  12153  Z= 0.278
  Chirality :  0.041   0.179   1396
  Planarity :  0.004   0.076   1488
  Dihedral  :  8.277  96.641   1472
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 15.68 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.43 (0.26), residues: 1078
  helix:  1.36 (0.27), residues: 388
  sheet: -0.59 (0.32), residues: 255
  loop :  0.02 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.002   0.001   HIS B  91 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.016   0.001   TYR E 190 
 ARG   0.006   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03349 (  449)
  hydrogen bonds       : angle       4.85948 ( 1290)
  SS BOND              : bond        0.00547 (    4)
  SS BOND              : angle       1.28541 (    8)
  covalent geometry    : bond        0.00310 ( 8951)
  covalent geometry    : angle       0.53141 (12145)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 181
  time to evaluate  : 1.512 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.8798 (m-80) cc_final: 0.8429 (m-80)
REVERT: B  163 ASP cc_start: 0.8174 (t0) cc_final: 0.7531 (t0)
REVERT: B  291 ASP cc_start: 0.8303 (t70) cc_final: 0.7774 (t0)
REVERT: A  308 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7408 (mp0)
REVERT: A  333 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8115 (tm-30)
REVERT: D   23 MET cc_start: 0.8414 (mtt) cc_final: 0.7689 (mmp)
REVERT: D   27 MET cc_start: 0.7979 (ptp) cc_final: 0.7263 (ttt)
  outliers start: 23
  outliers final: 17
  residues processed: 191
  average time/residue: 0.2679
  time to fit residues: 66.7938
Evaluate side-chains
  192 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 174
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain D residue   69 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  176 GLN
Chi-restraints excluded: chain D residue  179 HIS
Chi-restraints excluded: chain D residue  319 TYR
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  169 ASN
Chi-restraints excluded: chain G residue   13 ARG
Chi-restraints excluded: chain G residue   36 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 84 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 80 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0870
   chunk 86 optimal weight:    0.7980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 169 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.168459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.126895 restraints weight = 11129.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 2.56
r_work: 0.3242 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8955  Z= 0.132
  Angle     :  0.528   6.773  12153  Z= 0.275
  Chirality :  0.041   0.146   1396
  Planarity :  0.004   0.075   1488
  Dihedral  :  8.238  97.571   1472
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 16.63 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.49 (0.26), residues: 1078
  helix:  1.36 (0.27), residues: 388
  sheet: -0.46 (0.33), residues: 252
  loop :  0.03 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D  88 
 HIS   0.002   0.001   HIS B  91 
 PHE   0.015   0.001   PHE A 354 
 TYR   0.014   0.001   TYR E 190 
 ARG   0.005   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03288 (  449)
  hydrogen bonds       : angle       4.80004 ( 1290)
  SS BOND              : bond        0.00517 (    4)
  SS BOND              : angle       1.24055 (    8)
  covalent geometry    : bond        0.00301 ( 8951)
  covalent geometry    : angle       0.52721 (12145)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 183
  time to evaluate  : 0.990 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.8821 (m-80) cc_final: 0.8439 (m-80)
REVERT: B  291 ASP cc_start: 0.8283 (t70) cc_final: 0.7755 (t0)
REVERT: A  333 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8025 (tm-30)
REVERT: D   23 MET cc_start: 0.8281 (mtt) cc_final: 0.7677 (mmp)
REVERT: D   27 MET cc_start: 0.7939 (ptp) cc_final: 0.7193 (ttp)
REVERT: D   74 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7376 (tt)
REVERT: D   88 TRP cc_start: 0.6326 (t-100) cc_final: 0.5841 (t-100)
REVERT: D  122 TRP cc_start: 0.7952 (m100) cc_final: 0.7750 (m-10)
REVERT: D  134 ARG cc_start: 0.7953 (ttp-170) cc_final: 0.7654 (ttm170)
REVERT: D  215 LYS cc_start: 0.6477 (mmtm) cc_final: 0.5812 (mttp)
  outliers start: 24
  outliers final: 17
  residues processed: 195
  average time/residue: 0.2624
  time to fit residues: 66.9922
Evaluate side-chains
  189 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 171
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain D residue   69 LEU
Chi-restraints excluded: chain D residue   74 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  179 HIS
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  169 ASN
Chi-restraints excluded: chain G residue   13 ARG
Chi-restraints excluded: chain G residue   36 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 106 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 73 optimal weight:    5.9990
   chunk 54 optimal weight:    9.9990
   chunk 70 optimal weight:    0.5980
   chunk 60 optimal weight:    4.9990
   chunk 76 optimal weight:    6.9990
   overall best weight:    1.6184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.164577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.115065 restraints weight = 11034.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 2.41
r_work: 0.3215 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   8955  Z= 0.240
  Angle     :  0.617   7.576  12153  Z= 0.321
  Chirality :  0.044   0.152   1396
  Planarity :  0.004   0.075   1488
  Dihedral  :  8.462  98.063   1472
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 17.27 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: 1078
  helix:  1.19 (0.26), residues: 396
  sheet: -0.77 (0.31), residues: 269
  loop : -0.04 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.014   0.002   PHE E  29 
 TYR   0.022   0.002   TYR D 130 
 ARG   0.005   0.001   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03670 (  449)
  hydrogen bonds       : angle       5.02833 ( 1290)
  SS BOND              : bond        0.00735 (    4)
  SS BOND              : angle       1.82928 (    8)
  covalent geometry    : bond        0.00568 ( 8951)
  covalent geometry    : angle       0.61533 (12145)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 178
  time to evaluate  : 0.949 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.9078 (m-80) cc_final: 0.8697 (m-80)
REVERT: B  163 ASP cc_start: 0.8420 (t0) cc_final: 0.7828 (t0)
REVERT: B  291 ASP cc_start: 0.8548 (t70) cc_final: 0.8063 (t0)
REVERT: A  256 ASN cc_start: 0.7844 (m-40) cc_final: 0.7578 (m-40)
REVERT: A  333 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8208 (tm-30)
REVERT: D   23 MET cc_start: 0.8282 (mtt) cc_final: 0.7659 (mmp)
REVERT: D   27 MET cc_start: 0.7905 (ptp) cc_final: 0.7167 (ttp)
REVERT: D   74 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7554 (tt)
REVERT: D  132 ARG cc_start: 0.8671 (ptm-80) cc_final: 0.7877 (ptp-110)
REVERT: D  134 ARG cc_start: 0.7949 (ttp-170) cc_final: 0.7602 (ttm170)
  outliers start: 28
  outliers final: 22
  residues processed: 192
  average time/residue: 0.3389
  time to fit residues: 85.6816
Evaluate side-chains
  194 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 171
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain D residue   69 LEU
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain D residue   74 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  105 CYS
Chi-restraints excluded: chain D residue  179 HIS
Chi-restraints excluded: chain D residue  319 TYR
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  169 ASN
Chi-restraints excluded: chain G residue   13 ARG
Chi-restraints excluded: chain G residue   36 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 100 optimal weight:    7.9990
   chunk 103 optimal weight:    0.5980
   chunk 87 optimal weight:    0.7980
   chunk 56 optimal weight:    6.9990
   chunk 11 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9980
   chunk 106 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 105 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
E 169 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.169473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.119018 restraints weight = 11164.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 2.52
r_work: 0.3216 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8955  Z= 0.144
  Angle     :  0.556   6.929  12153  Z= 0.290
  Chirality :  0.042   0.220   1396
  Planarity :  0.004   0.076   1488
  Dihedral  :  8.279  97.774   1472
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 18.22 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.35 (0.26), residues: 1078
  helix:  1.33 (0.27), residues: 388
  sheet: -0.55 (0.33), residues: 252
  loop : -0.13 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D  88 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.013   0.001   PHE D 347 
 TYR   0.033   0.001   TYR D 130 
 ARG   0.006   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03371 (  449)
  hydrogen bonds       : angle       4.89154 ( 1290)
  SS BOND              : bond        0.00512 (    4)
  SS BOND              : angle       1.29062 (    8)
  covalent geometry    : bond        0.00331 ( 8951)
  covalent geometry    : angle       0.55559 (12145)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 178
  time to evaluate  : 1.149 
Fit side-chains
REVERT: B   32 GLN cc_start: 0.8789 (pt0) cc_final: 0.8457 (pt0)
REVERT: B   59 TYR cc_start: 0.8867 (m-80) cc_final: 0.8481 (m-80)
REVERT: B  163 ASP cc_start: 0.8149 (t0) cc_final: 0.7440 (t0)
REVERT: B  291 ASP cc_start: 0.8304 (t70) cc_final: 0.7785 (t0)
REVERT: A  256 ASN cc_start: 0.7832 (m-40) cc_final: 0.7591 (m-40)
REVERT: A  333 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8056 (tm-30)
REVERT: D   23 MET cc_start: 0.8293 (mtt) cc_final: 0.7651 (mmp)
REVERT: D   27 MET cc_start: 0.7925 (ptp) cc_final: 0.7242 (ttp)
REVERT: D   74 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7401 (tt)
REVERT: D   76 MET cc_start: 0.8358 (mtt) cc_final: 0.8154 (mtp)
REVERT: D   88 TRP cc_start: 0.6410 (t-100) cc_final: 0.5796 (t-100)
REVERT: D  132 ARG cc_start: 0.8627 (ptm-80) cc_final: 0.7843 (ptp-110)
REVERT: D  215 LYS cc_start: 0.6254 (mmtm) cc_final: 0.5733 (mttp)
  outliers start: 29
  outliers final: 23
  residues processed: 193
  average time/residue: 0.3224
  time to fit residues: 82.2319
Evaluate side-chains
  195 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 171
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain D residue   69 LEU
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain D residue   74 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  155 MET
Chi-restraints excluded: chain D residue  179 HIS
Chi-restraints excluded: chain D residue  319 TYR
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  169 ASN
Chi-restraints excluded: chain G residue   13 ARG
Chi-restraints excluded: chain G residue   36 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0000
   chunk 96 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 104 optimal weight:    0.5980
   chunk 57 optimal weight:    7.9990
   chunk 26 optimal weight:    0.8980
   chunk 82 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
E 169 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.168387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.126821 restraints weight = 11174.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 2.54
r_work: 0.3243 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8955  Z= 0.133
  Angle     :  0.560   7.262  12153  Z= 0.292
  Chirality :  0.042   0.194   1396
  Planarity :  0.004   0.075   1488
  Dihedral  :  8.249  97.931   1472
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 18.64 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.41 (0.26), residues: 1078
  helix:  1.33 (0.27), residues: 388
  sheet: -0.49 (0.33), residues: 251
  loop : -0.06 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 160 
 HIS   0.003   0.001   HIS E 167 
 PHE   0.017   0.001   PHE E  32 
 TYR   0.037   0.001   TYR D 130 
 ARG   0.007   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03309 (  449)
  hydrogen bonds       : angle       4.88386 ( 1290)
  SS BOND              : bond        0.00482 (    4)
  SS BOND              : angle       1.21878 (    8)
  covalent geometry    : bond        0.00307 ( 8951)
  covalent geometry    : angle       0.55898 (12145)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 182
  time to evaluate  : 0.909 
Fit side-chains
REVERT: B   32 GLN cc_start: 0.8764 (pt0) cc_final: 0.8419 (pt0)
REVERT: B   59 TYR cc_start: 0.8797 (m-80) cc_final: 0.8454 (m-80)
REVERT: B  163 ASP cc_start: 0.8169 (t0) cc_final: 0.7468 (t0)
REVERT: B  291 ASP cc_start: 0.8290 (t70) cc_final: 0.7769 (t0)
REVERT: A  256 ASN cc_start: 0.7848 (OUTLIER) cc_final: 0.7592 (m-40)
REVERT: A  308 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7563 (mp0)
REVERT: A  333 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8059 (tm-30)
REVERT: D   23 MET cc_start: 0.8240 (mtt) cc_final: 0.7622 (mmp)
REVERT: D   27 MET cc_start: 0.7996 (ptp) cc_final: 0.7215 (ttp)
REVERT: D   74 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7370 (tt)
REVERT: D   76 MET cc_start: 0.8238 (mtt) cc_final: 0.8037 (mtp)
REVERT: D   88 TRP cc_start: 0.6300 (t-100) cc_final: 0.5754 (t-100)
REVERT: D  132 ARG cc_start: 0.8569 (ptm-80) cc_final: 0.7811 (ptp-110)
REVERT: D  215 LYS cc_start: 0.6414 (mmtm) cc_final: 0.5765 (mttp)
  outliers start: 29
  outliers final: 23
  residues processed: 197
  average time/residue: 0.2477
  time to fit residues: 63.9958
Evaluate side-chains
  202 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 176
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain D residue   69 LEU
Chi-restraints excluded: chain D residue   74 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  155 MET
Chi-restraints excluded: chain D residue  179 HIS
Chi-restraints excluded: chain D residue  319 TYR
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain G residue   13 ARG
Chi-restraints excluded: chain G residue   36 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 81 optimal weight:    7.9990
   chunk 71 optimal weight:    0.8980
   chunk 18 optimal weight:    0.3980
   chunk 88 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   chunk 30 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 78 optimal weight:    0.0770
   chunk 48 optimal weight:    0.0010
   overall best weight:    0.4344

-------------------------------------------------------------------------------
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 = 0.3997 r_free = 0.3997 target = 0.171908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.130041 restraints weight = 11291.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.61
r_work: 0.3269 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8955  Z= 0.117
  Angle     :  0.551   7.473  12153  Z= 0.286
  Chirality :  0.042   0.182   1396
  Planarity :  0.004   0.074   1488
  Dihedral  :  8.185  97.904   1472
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 18.54 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.46 (0.26), residues: 1078
  helix:  1.29 (0.27), residues: 396
  sheet: -0.39 (0.33), residues: 250
  loop : -0.03 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 211 
 HIS   0.002   0.001   HIS B  91 
 PHE   0.013   0.001   PHE E  32 
 TYR   0.031   0.001   TYR D 130 
 ARG   0.007   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03194 (  449)
  hydrogen bonds       : angle       4.82975 ( 1290)
  SS BOND              : bond        0.00418 (    4)
  SS BOND              : angle       1.07438 (    8)
  covalent geometry    : bond        0.00264 ( 8951)
  covalent geometry    : angle       0.55079 (12145)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 178
  time to evaluate  : 0.991 
Fit side-chains
REVERT: B   32 GLN cc_start: 0.8739 (pt0) cc_final: 0.8384 (pt0)
REVERT: B   59 TYR cc_start: 0.8756 (m-80) cc_final: 0.8414 (m-80)
REVERT: B  291 ASP cc_start: 0.8268 (t70) cc_final: 0.7742 (t0)
REVERT: A  256 ASN cc_start: 0.7769 (OUTLIER) cc_final: 0.7499 (m-40)
REVERT: A  308 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7613 (mp0)
REVERT: A  333 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8026 (tm-30)
REVERT: D   23 MET cc_start: 0.8248 (mtt) cc_final: 0.7641 (mmp)
REVERT: D   27 MET cc_start: 0.7981 (ptp) cc_final: 0.7234 (ttp)
REVERT: D   74 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7260 (tt)
REVERT: D   88 TRP cc_start: 0.6426 (t-100) cc_final: 0.5806 (t-100)
REVERT: D  129 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7598 (mp0)
REVERT: D  215 LYS cc_start: 0.6325 (mmtm) cc_final: 0.5694 (mttp)
REVERT: G   14 LYS cc_start: 0.8653 (mmmt) cc_final: 0.8407 (mmtp)
  outliers start: 26
  outliers final: 20
  residues processed: 191
  average time/residue: 0.3458
  time to fit residues: 87.2802
Evaluate side-chains
  199 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 176
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain D residue   69 LEU
Chi-restraints excluded: chain D residue   74 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  155 MET
Chi-restraints excluded: chain D residue  179 HIS
Chi-restraints excluded: chain D residue  319 TYR
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain G residue   13 ARG
Chi-restraints excluded: chain G residue   36 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 87 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 92 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3983 r_free = 0.3983 target = 0.170513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.128083 restraints weight = 11279.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.69
r_work: 0.3237 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8955  Z= 0.147
  Angle     :  0.590   7.927  12153  Z= 0.302
  Chirality :  0.043   0.208   1396
  Planarity :  0.004   0.074   1488
  Dihedral  :  8.232  97.496   1472
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 18.64 %
    Favored  : 78.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.45 (0.26), residues: 1078
  helix:  1.27 (0.27), residues: 397
  sheet: -0.46 (0.33), residues: 252
  loop :  0.02 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D 160 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.018   0.001   PHE A 354 
 TYR   0.030   0.001   TYR D 130 
 ARG   0.007   0.001   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03272 (  449)
  hydrogen bonds       : angle       4.84691 ( 1290)
  SS BOND              : bond        0.00486 (    4)
  SS BOND              : angle       1.28112 (    8)
  covalent geometry    : bond        0.00344 ( 8951)
  covalent geometry    : angle       0.58972 (12145)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 173
  time to evaluate  : 0.915 
Fit side-chains
REVERT: B   32 GLN cc_start: 0.8752 (pt0) cc_final: 0.8387 (pt0)
REVERT: B   59 TYR cc_start: 0.8804 (m-80) cc_final: 0.8446 (m-80)
REVERT: B  189 SER cc_start: 0.8848 (p) cc_final: 0.8643 (p)
REVERT: B  291 ASP cc_start: 0.8301 (t70) cc_final: 0.7784 (t0)
REVERT: A  256 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7485 (m-40)
REVERT: A  308 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7574 (mp0)
REVERT: A  333 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8008 (tm-30)
REVERT: D   23 MET cc_start: 0.8261 (mtt) cc_final: 0.7655 (mmp)
REVERT: D   27 MET cc_start: 0.7987 (ptp) cc_final: 0.7263 (ttp)
REVERT: D   74 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7224 (tt)
REVERT: D  129 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7595 (mp0)
REVERT: D  132 ARG cc_start: 0.8594 (ptm-80) cc_final: 0.7767 (ptp-110)
REVERT: D  188 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7783 (mm)
REVERT: G   14 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8237 (tptm)
  outliers start: 26
  outliers final: 21
  residues processed: 185
  average time/residue: 0.2594
  time to fit residues: 62.4281
Evaluate side-chains
  197 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 172
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain D residue   69 LEU
Chi-restraints excluded: chain D residue   74 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  179 HIS
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  319 TYR
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   13 GLN
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain G residue   13 ARG
Chi-restraints excluded: chain G residue   36 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   chunk 81 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0980
   chunk 0 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 169 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.170261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.128231 restraints weight = 11300.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 2.59
r_work: 0.3246 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8955  Z= 0.146
  Angle     :  0.588   8.208  12153  Z= 0.301
  Chirality :  0.044   0.200   1396
  Planarity :  0.004   0.074   1488
  Dihedral  :  8.249  96.708   1472
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.86 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.43 (0.26), residues: 1078
  helix:  1.28 (0.27), residues: 396
  sheet: -0.44 (0.33), residues: 252
  loop : -0.02 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D 160 
 HIS   0.002   0.001   HIS B  91 
 PHE   0.017   0.001   PHE D 347 
 TYR   0.029   0.001   TYR D 130 
 ARG   0.007   0.001   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03295 (  449)
  hydrogen bonds       : angle       4.86063 ( 1290)
  SS BOND              : bond        0.00489 (    4)
  SS BOND              : angle       1.27099 (    8)
  covalent geometry    : bond        0.00340 ( 8951)
  covalent geometry    : angle       0.58761 (12145)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5324.10 seconds
wall clock time: 96 minutes 1.55 seconds (5761.55 seconds total)