Starting phenix.real_space_refine
on Wed Mar 12 07:46:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5uz7_8623/03_2025/5uz7_8623.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5uz7_8623/03_2025/5uz7_8623.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5uz7_8623/03_2025/5uz7_8623.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5uz7_8623/03_2025/5uz7_8623.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5uz7_8623/03_2025/5uz7_8623.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5uz7_8623/03_2025/5uz7_8623.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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      53      5.16       5
     C    4877      2.51       5
     N    1334      2.21       5
     O    1379      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7643
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1566
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1566
          Classifications: {'peptide': 185}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 4, 'TRANS': 180}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 16
    Chain: "B"
      Number of atoms: 2579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2579
          Classifications: {'peptide': 340}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 30
    Chain: "G"
      Number of atoms: 420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 420
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "N"
      Number of atoms: 972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 972
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "R"
      Number of atoms: 2106
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2106
          Classifications: {'peptide': 266}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 7, 'TRANS': 258}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 118
          Unresolved non-hydrogen angles: 151
          Unresolved non-hydrogen dihedrals: 101
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 86
  Time building chain proxies: 5.56, per 1000 atoms: 0.73
  Number of scatterers: 7643
  At special positions: 0
  Unit cell: (130.38, 95.4, 98.58, 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      53     16.00
     O    1379      8.00
     N    1334      7.00
     C    4877      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R 219 " - pdb=" SG  CYS R 289 " 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: 1.68
  Conformation dependent library (CDL) restraints added in 998.9 milliseconds
  

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1834

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 10 sheets defined
      40.6% alpha, 18.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 39
      removed outlier: 3.736A  pdb=" N   GLU A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.537A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 353
      removed outlier: 3.893A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 391
      removed outlier: 3.807A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 25
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.866A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 13
    Processing helix  chain 'G' and resid 14 through 24
      removed outlier: 4.146A  pdb=" N   GLN G  18 " --> pdb=" O   LYS G  14 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.721A  pdb=" N   ALA G  35 " --> pdb=" O   SER G  31 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ASP G  36 " --> pdb=" O   LYS G  32 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.531A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 4.097A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 173
    Processing helix  chain 'R' and resid 178 through 205
      removed outlier: 3.653A  pdb=" N   LEU R 183 " --> pdb=" O   GLN R 179 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 215 through 250
    Processing helix  chain 'R' and resid 258 through 268
      removed outlier: 3.879A  pdb=" N   TYR R 262 " --> pdb=" O   ARG R 258 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 285
    Processing helix  chain 'R' and resid 298 through 326
      Proline residue:  R 304  - end of helix
    Processing helix  chain 'R' and resid 338 through 349
    Processing helix  chain 'R' and resid 350 through 353
    Processing helix  chain 'R' and resid 354 through 359
    Processing helix  chain 'R' and resid 367 through 382
    Processing helix  chain 'R' and resid 382 through 393
    Processing helix  chain 'R' and resid 395 through 418
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214
      removed outlier: 3.565A  pdb=" N   HIS A 220 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 10.073A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.372A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.851A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   THR B 329 " --> pdb=" O   LYS B 337 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62
      removed outlier: 6.582A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.710A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151
      removed outlier: 3.646A  pdb=" N   CYS B 166 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 190 through 192
      removed outlier: 4.081A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234
      removed outlier: 3.873A  pdb=" N   LEU B 252 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278
      removed outlier: 3.775A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 7.045A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    398 hydrogen bonds defined for protein.
    1149 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: 2.07

  Time building geometry restraints manager: 2.06 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: 2427
        1.34 -     1.46: 1850
        1.46 -     1.58: 3453
        1.58 -     1.70: 0
        1.70 -     1.82: 76
  Bond restraints: 7806
  Sorted by residual:
  bond pdb=" C   VAL R 349 "
       pdb=" N   PRO R 350 "
    ideal  model  delta    sigma   weight residual
    1.334  1.434 -0.100 2.34e-02 1.83e+03 1.82e+01
  bond pdb=" CB  VAL N  48 "
       pdb=" CG2 VAL N  48 "
    ideal  model  delta    sigma   weight residual
    1.521  1.444  0.077 3.30e-02 9.18e+02 5.44e+00
  bond pdb=" CG  LEU B  14 "
       pdb=" CD2 LEU B  14 "
    ideal  model  delta    sigma   weight residual
    1.521  1.460  0.061 3.30e-02 9.18e+02 3.45e+00
  bond pdb=" CB  PRO R 350 "
       pdb=" CG  PRO R 350 "
    ideal  model  delta    sigma   weight residual
    1.492  1.403  0.089 5.00e-02 4.00e+02 3.18e+00
  bond pdb=" CB  CYS B 204 "
       pdb=" SG  CYS B 204 "
    ideal  model  delta    sigma   weight residual
    1.808  1.752  0.056 3.30e-02 9.18e+02 2.90e+00
  ... (remaining 7801 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.12: 10313
        3.12 -     6.25: 220
        6.25 -     9.37: 30
        9.37 -    12.50: 12
       12.50 -    15.62: 3
  Bond angle restraints: 10578
  Sorted by residual:
  angle pdb=" C   ILE R 248 "
        pdb=" N   VAL R 249 "
        pdb=" CA  VAL R 249 "
      ideal   model   delta    sigma   weight residual
     121.71  113.62    8.09 1.20e+00 6.94e-01 4.54e+01
  angle pdb=" CA  LEU B  79 "
        pdb=" CB  LEU B  79 "
        pdb=" CG  LEU B  79 "
      ideal   model   delta    sigma   weight residual
     116.30  131.92  -15.62 3.50e+00 8.16e-02 1.99e+01
  angle pdb=" CA  LEU R 142 "
        pdb=" CB  LEU R 142 "
        pdb=" CG  LEU R 142 "
      ideal   model   delta    sigma   weight residual
     116.30  131.60  -15.30 3.50e+00 8.16e-02 1.91e+01
  angle pdb=" CA  GLU A 392 "
        pdb=" CB  GLU A 392 "
        pdb=" CG  GLU A 392 "
      ideal   model   delta    sigma   weight residual
     114.10  122.40   -8.30 2.00e+00 2.50e-01 1.72e+01
  angle pdb=" C   THR N 113 "
        pdb=" N   THR N 114 "
        pdb=" CA  THR N 114 "
      ideal   model   delta    sigma   weight residual
     122.61  128.81   -6.20 1.56e+00 4.11e-01 1.58e+01
  ... (remaining 10573 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.98: 4286
       15.98 -    31.95: 263
       31.95 -    47.93: 40
       47.93 -    63.90: 7
       63.90 -    79.88: 5
  Dihedral angle restraints: 4601
    sinusoidal: 1769
      harmonic: 2832
  Sorted by residual:
  dihedral pdb=" CA  THR N 113 "
           pdb=" C   THR N 113 "
           pdb=" N   THR N 114 "
           pdb=" CA  THR N 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.99   29.01     0      5.00e+00 4.00e-02 3.37e+01
  dihedral pdb=" CA  THR B 165 "
           pdb=" C   THR B 165 "
           pdb=" N   CYS B 166 "
           pdb=" CA  CYS B 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.16   24.84     0      5.00e+00 4.00e-02 2.47e+01
  dihedral pdb=" CA  LYS R 326 "
           pdb=" C   LYS R 326 "
           pdb=" N   MET R 327 "
           pdb=" CA  MET R 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.89   22.11     0      5.00e+00 4.00e-02 1.96e+01
  ... (remaining 4598 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 804
       0.057 -    0.114: 299
       0.114 -    0.171: 74
       0.171 -    0.228: 13
       0.228 -    0.285: 4
  Chirality restraints: 1194
  Sorted by residual:
  chirality pdb=" CB  VAL A 241 "
            pdb=" CA  VAL A 241 "
            pdb=" CG1 VAL A 241 "
            pdb=" CG2 VAL A 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.28 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CG  LEU R 238 "
            pdb=" CB  LEU R 238 "
            pdb=" CD1 LEU R 238 "
            pdb=" CD2 LEU R 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.32   -0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" CB  VAL N 110 "
            pdb=" CA  VAL N 110 "
            pdb=" CG1 VAL N 110 "
            pdb=" CG2 VAL N 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.43e+00
  ... (remaining 1191 not shown)

  Planarity restraints: 1340
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 303 "   -0.054 5.00e-02 4.00e+02   8.22e-02 1.08e+01
        pdb=" N   PRO R 304 "    0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO R 304 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO R 304 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 138 "    0.053 5.00e-02 4.00e+02   8.02e-02 1.03e+01
        pdb=" N   PRO R 139 "   -0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO R 139 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO R 139 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 332 "    0.017 2.00e-02 2.50e+03   1.81e-02 8.19e+00
        pdb=" CG  TRP B 332 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 332 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 332 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 332 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 332 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 332 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 332 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 332 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 332 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1337 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1941
        2.79 -     3.32: 6949
        3.32 -     3.85: 12554
        3.85 -     4.37: 14079
        4.37 -     4.90: 24743
  Nonbonded interactions: 60266
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" OG  SER B 160 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OE1 GLN A 384 "
            pdb=" NZ  LYS R 326 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" O   CYS B 204 "
            pdb=" OH  TYR N 117 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" O   CYS N  22 "
            pdb=" OG1 THR N  78 "
     model   vdw
     2.322 3.040
  ... (remaining 60261 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.640
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
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      :  0.008   0.100   7806  Z= 0.489
  Angle     :  1.174  15.623  10578  Z= 0.611
  Chirality :  0.063   0.285   1194
  Planarity :  0.008   0.082   1340
  Dihedral  : 11.044  79.876   2758
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  6.34 %
    Favored  : 93.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.30 (0.24), residues: 948
  helix: -1.12 (0.23), residues: 363
  sheet: -0.53 (0.33), residues: 220
  loop : -2.49 (0.26), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.005   TRP B 332 
 HIS   0.019   0.003   HIS B 183 
 PHE   0.037   0.003   PHE B 151 
 TYR   0.043   0.004   TYR R 372 
 ARG   0.009   0.001   ARG N 118 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 344
  time to evaluate  : 0.857 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8476 (mtt180) cc_final: 0.8114 (mtt-85)
REVERT: A   24 LYS cc_start: 0.8910 (mttt) cc_final: 0.8636 (mtmt)
REVERT: A   29 GLN cc_start: 0.8961 (tt0) cc_final: 0.8616 (tm-30)
REVERT: A   32 LYS cc_start: 0.9471 (mttt) cc_final: 0.9014 (mmtt)
REVERT: A  222 PHE cc_start: 0.8040 (t80) cc_final: 0.7659 (t80)
REVERT: A  272 LEU cc_start: 0.9161 (tp) cc_final: 0.8806 (tp)
REVERT: A  281 TRP cc_start: 0.8071 (m100) cc_final: 0.7864 (m100)
REVERT: A  340 PHE cc_start: 0.8411 (t80) cc_final: 0.8063 (t80)
REVERT: B  127 LYS cc_start: 0.8563 (ptmm) cc_final: 0.8027 (ptmm)
REVERT: B  145 TYR cc_start: 0.8989 (p90) cc_final: 0.8755 (p90)
REVERT: B  188 MET cc_start: 0.8522 (mmm) cc_final: 0.8232 (mmt)
REVERT: B  325 MET cc_start: 0.8471 (tpp) cc_final: 0.7820 (tpt)
REVERT: G   18 GLN cc_start: 0.7087 (mm-40) cc_final: 0.6790 (mm-40)
REVERT: R  262 TYR cc_start: 0.8175 (m-80) cc_final: 0.7953 (m-80)
REVERT: R  328 ARG cc_start: 0.7640 (tpm170) cc_final: 0.7416 (mtp85)
REVERT: R  342 VAL cc_start: 0.8536 (p) cc_final: 0.8209 (p)
REVERT: R  352 LEU cc_start: 0.7715 (pt) cc_final: 0.7379 (pt)
  outliers start: 3
  outliers final: 0
  residues processed: 347
  average time/residue: 0.2173
  time to fit residues: 97.0504
Evaluate side-chains
  230 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 80 optimal weight:    9.9990
   chunk 72 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0370
   chunk 48 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   overall best weight:    0.7660

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 377 ASN
A 390 GLN
B  36 ASN
B 259 GLN
B 340 ASN
G  24 ASN
G  44 HIS
R 186 ASN
R 194 ASN
R 233 ASN
** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.132930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.108854 restraints weight = 13332.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.111728 restraints weight = 7931.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.113673 restraints weight = 5494.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7806  Z= 0.217
  Angle     :  0.720   9.757  10578  Z= 0.371
  Chirality :  0.044   0.164   1194
  Planarity :  0.005   0.064   1340
  Dihedral  :  5.285  23.793   1054
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  1.86 %
    Favored  : 97.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.26), residues: 948
  helix:  0.38 (0.25), residues: 364
  sheet: -0.44 (0.34), residues: 225
  loop : -2.01 (0.29), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  82 
 HIS   0.007   0.001   HIS R 377 
 PHE   0.026   0.002   PHE R 314 
 TYR   0.021   0.002   TYR A 360 
 ARG   0.005   0.001   ARG R 281 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 306
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.8672 (tttt) cc_final: 0.8374 (tppt)
REVERT: A   35 GLN cc_start: 0.8413 (pt0) cc_final: 0.7808 (pp30)
REVERT: A  342 ARG cc_start: 0.7179 (ttt180) cc_final: 0.6832 (ptm-80)
REVERT: A  357 HIS cc_start: 0.7742 (p-80) cc_final: 0.7103 (p-80)
REVERT: A  389 ARG cc_start: 0.8090 (ttm110) cc_final: 0.7639 (ttm110)
REVERT: B   13 GLN cc_start: 0.8044 (pp30) cc_final: 0.7792 (pp30)
REVERT: B   55 LEU cc_start: 0.8956 (mp) cc_final: 0.8731 (mp)
REVERT: B   75 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7833 (tm-30)
REVERT: B  127 LYS cc_start: 0.7944 (ptmm) cc_final: 0.7467 (ptmm)
REVERT: B  226 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7562 (mm-30)
REVERT: B  254 ASP cc_start: 0.8025 (t70) cc_final: 0.7770 (t70)
REVERT: N    5 GLN cc_start: 0.7255 (tp-100) cc_final: 0.6984 (tm-30)
REVERT: R  197 ILE cc_start: 0.9038 (tt) cc_final: 0.8662 (tt)
REVERT: R  204 GLU cc_start: 0.7721 (tt0) cc_final: 0.7404 (mt-10)
REVERT: R  273 PRO cc_start: 0.9241 (Cg_exo) cc_final: 0.9033 (Cg_endo)
REVERT: R  406 TRP cc_start: 0.7926 (t60) cc_final: 0.6771 (t60)
  outliers start: 2
  outliers final: 1
  residues processed: 307
  average time/residue: 0.2134
  time to fit residues: 85.0149
Evaluate side-chains
  233 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 232
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 61 optimal weight:    8.9990
   chunk 92 optimal weight:    8.9990
   chunk 21 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 377 ASN
B 142 HIS
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 194 ASN
** R 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.126374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.102313 restraints weight = 14188.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.105090 restraints weight = 8597.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.106942 restraints weight = 6033.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.3572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7806  Z= 0.315
  Angle     :  0.728  11.436  10578  Z= 0.375
  Chirality :  0.046   0.155   1194
  Planarity :  0.005   0.058   1340
  Dihedral  :  5.120  22.740   1054
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.85 %
    Favored  : 96.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.97 (0.26), residues: 948
  helix:  0.71 (0.26), residues: 367
  sheet: -0.80 (0.34), residues: 233
  loop : -1.94 (0.29), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  82 
 HIS   0.009   0.002   HIS B 183 
 PHE   0.025   0.002   PHE R 314 
 TYR   0.018   0.002   TYR N  32 
 ARG   0.006   0.001   ARG B 197 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 268
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 GLN cc_start: 0.8353 (mt0) cc_final: 0.8036 (mt0)
REVERT: A   28 LYS cc_start: 0.8651 (tttt) cc_final: 0.8410 (tppt)
REVERT: A   35 GLN cc_start: 0.8265 (pt0) cc_final: 0.7919 (pp30)
REVERT: A  389 ARG cc_start: 0.8076 (ttm110) cc_final: 0.7762 (ttm110)
REVERT: B  127 LYS cc_start: 0.8071 (ptmm) cc_final: 0.7520 (ptmm)
REVERT: B  156 GLN cc_start: 0.8107 (pt0) cc_final: 0.7899 (pt0)
REVERT: B  254 ASP cc_start: 0.8096 (t70) cc_final: 0.7864 (t70)
REVERT: G   46 LYS cc_start: 0.8649 (pttt) cc_final: 0.8443 (ptmt)
REVERT: R  197 ILE cc_start: 0.8972 (tt) cc_final: 0.8651 (tt)
REVERT: R  204 GLU cc_start: 0.7712 (tt0) cc_final: 0.7337 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 269
  average time/residue: 0.2010
  time to fit residues: 70.9952
Evaluate side-chains
  224 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 66 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 70 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 233 ASN
R 302 HIS
** R 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 408 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.121038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.096959 restraints weight = 14204.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.099416 restraints weight = 8736.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.101107 restraints weight = 6257.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.4096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.058   7806  Z= 0.517
  Angle     :  0.855  11.629  10578  Z= 0.448
  Chirality :  0.051   0.203   1194
  Planarity :  0.006   0.060   1340
  Dihedral  :  5.606  25.464   1054
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.25), residues: 948
  helix:  0.52 (0.25), residues: 367
  sheet: -0.96 (0.35), residues: 221
  loop : -2.12 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP B 339 
 HIS   0.010   0.002   HIS B 183 
 PHE   0.024   0.003   PHE R 314 
 TYR   0.019   0.002   TYR A 360 
 ARG   0.012   0.001   ARG A  20 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 GLN cc_start: 0.8224 (mt0) cc_final: 0.7955 (mt0)
REVERT: A   35 GLN cc_start: 0.8398 (pt0) cc_final: 0.7942 (pp30)
REVERT: A  342 ARG cc_start: 0.7303 (ttt180) cc_final: 0.7090 (ptm-80)
REVERT: A  389 ARG cc_start: 0.8034 (ttm110) cc_final: 0.7678 (ttm110)
REVERT: B   55 LEU cc_start: 0.8847 (mp) cc_final: 0.8589 (mt)
REVERT: B  127 LYS cc_start: 0.8069 (ptmm) cc_final: 0.7555 (ptmm)
REVERT: B  254 ASP cc_start: 0.8233 (t70) cc_final: 0.7812 (t0)
REVERT: B  339 TRP cc_start: 0.8080 (m-10) cc_final: 0.7688 (m-10)
REVERT: R  187 MET cc_start: 0.8044 (mmm) cc_final: 0.7643 (tpt)
REVERT: R  197 ILE cc_start: 0.9012 (tt) cc_final: 0.8692 (tt)
REVERT: R  204 GLU cc_start: 0.7796 (tt0) cc_final: 0.7364 (mt-10)
REVERT: R  223 HIS cc_start: 0.7926 (t70) cc_final: 0.7607 (t70)
REVERT: R  262 TYR cc_start: 0.8346 (m-80) cc_final: 0.8010 (m-80)
REVERT: R  366 LYS cc_start: 0.7632 (tttt) cc_final: 0.7409 (tttp)
  outliers start: 0
  outliers final: 0
  residues processed: 264
  average time/residue: 0.2075
  time to fit residues: 71.3602
Evaluate side-chains
  210 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 15 optimal weight:    8.9990
   chunk 1 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 69 optimal weight:   10.0000
   chunk 2 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 218 ASN
A 236 GLN
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
N  82 GLN
** R 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 408 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.127171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.102510 restraints weight = 13951.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.105282 restraints weight = 8395.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.107125 restraints weight = 5909.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.4287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7806  Z= 0.232
  Angle     :  0.726  10.208  10578  Z= 0.367
  Chirality :  0.045   0.173   1194
  Planarity :  0.005   0.067   1340
  Dihedral  :  5.176  22.902   1054
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.93 (0.26), residues: 948
  helix:  0.90 (0.25), residues: 366
  sheet: -0.91 (0.35), residues: 222
  loop : -1.99 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP R 413 
 HIS   0.005   0.001   HIS R 377 
 PHE   0.026   0.002   PHE R 314 
 TYR   0.021   0.002   TYR A 360 
 ARG   0.005   0.001   ARG B 150 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 GLN cc_start: 0.8079 (mt0) cc_final: 0.7838 (mt0)
REVERT: A   21 GLU cc_start: 0.6162 (tm-30) cc_final: 0.5861 (tm-30)
REVERT: A   35 GLN cc_start: 0.8441 (pt0) cc_final: 0.7913 (pp30)
REVERT: A  378 ASP cc_start: 0.8362 (t0) cc_final: 0.8077 (t70)
REVERT: A  389 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7636 (ttm110)
REVERT: B   55 LEU cc_start: 0.8893 (mp) cc_final: 0.8552 (mt)
REVERT: B   57 LYS cc_start: 0.9202 (ptpp) cc_final: 0.8991 (ptpp)
REVERT: B  127 LYS cc_start: 0.8124 (ptmm) cc_final: 0.7812 (ptmm)
REVERT: B  254 ASP cc_start: 0.8132 (t70) cc_final: 0.7857 (t0)
REVERT: N   78 THR cc_start: 0.8320 (p) cc_final: 0.7834 (p)
REVERT: R  187 MET cc_start: 0.8030 (mmm) cc_final: 0.7677 (tpt)
REVERT: R  197 ILE cc_start: 0.8946 (tt) cc_final: 0.8632 (tt)
REVERT: R  204 GLU cc_start: 0.7795 (tt0) cc_final: 0.7332 (mt-10)
REVERT: R  223 HIS cc_start: 0.7988 (t70) cc_final: 0.7627 (t70)
REVERT: R  262 TYR cc_start: 0.8446 (m-80) cc_final: 0.8066 (m-80)
REVERT: R  348 LEU cc_start: 0.9084 (tt) cc_final: 0.8758 (pp)
REVERT: R  404 ARG cc_start: 0.7868 (ptm-80) cc_final: 0.7611 (ptm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 270
  average time/residue: 0.2191
  time to fit residues: 77.0653
Evaluate side-chains
  218 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 41 optimal weight:    0.3980
   chunk 56 optimal weight:    0.0570
   chunk 43 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9990
   chunk 68 optimal weight:    0.5980
   chunk 78 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   overall best weight:    0.5900

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

Flipped N/Q/H residues before XYZ refinement:
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN
B 340 ASN
R 227 GLN
** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.126594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.102892 restraints weight = 13898.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.105765 restraints weight = 7846.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.107705 restraints weight = 5332.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.4533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7806  Z= 0.187
  Angle     :  0.688  11.345  10578  Z= 0.346
  Chirality :  0.044   0.198   1194
  Planarity :  0.005   0.054   1340
  Dihedral  :  4.844  19.347   1054
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.71 (0.26), residues: 948
  helix:  1.15 (0.25), residues: 366
  sheet: -0.89 (0.35), residues: 223
  loop : -1.89 (0.29), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 413 
 HIS   0.005   0.001   HIS R 377 
 PHE   0.017   0.001   PHE R 235 
 TYR   0.016   0.001   TYR R 263 
 ARG   0.005   0.001   ARG R 281 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 271
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.8538 (pt0) cc_final: 0.7904 (pp30)
REVERT: A  218 ASN cc_start: 0.8165 (m110) cc_final: 0.7928 (m110)
REVERT: A  339 TYR cc_start: 0.7588 (m-80) cc_final: 0.7267 (m-80)
REVERT: A  389 ARG cc_start: 0.8112 (ttm110) cc_final: 0.7773 (ttm110)
REVERT: B   55 LEU cc_start: 0.9058 (mp) cc_final: 0.8811 (mp)
REVERT: B  127 LYS cc_start: 0.8331 (ptmm) cc_final: 0.8056 (ptmm)
REVERT: B  335 PHE cc_start: 0.7705 (m-80) cc_final: 0.7420 (m-80)
REVERT: G   22 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7885 (tm-30)
REVERT: R  187 MET cc_start: 0.8295 (mmm) cc_final: 0.7805 (tpt)
REVERT: R  197 ILE cc_start: 0.8798 (tt) cc_final: 0.8427 (tt)
REVERT: R  204 GLU cc_start: 0.7672 (tt0) cc_final: 0.7226 (mt-10)
REVERT: R  223 HIS cc_start: 0.8096 (t70) cc_final: 0.7638 (t70)
REVERT: R  262 TYR cc_start: 0.8435 (m-80) cc_final: 0.8082 (m-80)
REVERT: R  348 LEU cc_start: 0.9074 (tt) cc_final: 0.8842 (pp)
REVERT: R  376 MET cc_start: 0.8493 (tpp) cc_final: 0.8210 (tpp)
REVERT: R  406 TRP cc_start: 0.7743 (t60) cc_final: 0.7427 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 271
  average time/residue: 0.2014
  time to fit residues: 71.9540
Evaluate side-chains
  230 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 10 optimal weight:    0.0570
   chunk 57 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0770
   chunk 42 optimal weight:    0.4980
   chunk 12 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.4656

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

Flipped N/Q/H residues before XYZ refinement:
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 377 ASN
A 390 GLN
B  13 GLN
B 340 ASN
R 227 GLN
** R 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 383 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.128353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.104774 restraints weight = 13783.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.107708 restraints weight = 7765.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.109635 restraints weight = 5216.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.4716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7806  Z= 0.183
  Angle     :  0.684  12.249  10578  Z= 0.339
  Chirality :  0.043   0.200   1194
  Planarity :  0.004   0.048   1340
  Dihedral  :  4.667  19.064   1054
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.24 %
    Favored  : 98.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.60 (0.26), residues: 948
  helix:  1.20 (0.25), residues: 367
  sheet: -0.65 (0.36), residues: 215
  loop : -1.90 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 413 
 HIS   0.005   0.001   HIS R 381 
 PHE   0.026   0.001   PHE R 314 
 TYR   0.013   0.002   TYR R 263 
 ARG   0.009   0.001   ARG A  20 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 274
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 ASP cc_start: 0.8587 (t0) cc_final: 0.8306 (t0)
REVERT: A   25 LYS cc_start: 0.8114 (tptp) cc_final: 0.7816 (tptp)
REVERT: A   32 LYS cc_start: 0.9108 (ptpp) cc_final: 0.8769 (ptpp)
REVERT: A   35 GLN cc_start: 0.8509 (pt0) cc_final: 0.7894 (pp30)
REVERT: A  278 ASN cc_start: 0.9280 (m110) cc_final: 0.8815 (m-40)
REVERT: A  389 ARG cc_start: 0.8057 (ttm110) cc_final: 0.7765 (ttm110)
REVERT: B   55 LEU cc_start: 0.9064 (mp) cc_final: 0.8834 (mp)
REVERT: B   75 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7685 (tm-30)
REVERT: B  127 LYS cc_start: 0.8332 (ptmm) cc_final: 0.8067 (ptmm)
REVERT: B  260 GLU cc_start: 0.7981 (mp0) cc_final: 0.7669 (mp0)
REVERT: B  335 PHE cc_start: 0.7708 (m-80) cc_final: 0.7421 (m-80)
REVERT: G   14 LYS cc_start: 0.8812 (mptt) cc_final: 0.8297 (mmtt)
REVERT: G   22 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7894 (tm-30)
REVERT: N   78 THR cc_start: 0.8203 (p) cc_final: 0.7487 (p)
REVERT: R  179 GLN cc_start: 0.8603 (tp40) cc_final: 0.7397 (pm20)
REVERT: R  187 MET cc_start: 0.7958 (mmm) cc_final: 0.7348 (tpt)
REVERT: R  197 ILE cc_start: 0.8757 (tt) cc_final: 0.8440 (tt)
REVERT: R  204 GLU cc_start: 0.7667 (tt0) cc_final: 0.7190 (mt-10)
REVERT: R  223 HIS cc_start: 0.8062 (t70) cc_final: 0.7586 (t70)
REVERT: R  229 MET cc_start: 0.8857 (tpp) cc_final: 0.7801 (tpp)
REVERT: R  262 TYR cc_start: 0.8286 (m-80) cc_final: 0.7963 (m-80)
REVERT: R  340 LYS cc_start: 0.8283 (pttt) cc_final: 0.7663 (pptt)
REVERT: R  366 LYS cc_start: 0.7584 (tppt) cc_final: 0.6938 (ttpp)
REVERT: R  406 TRP cc_start: 0.7849 (t60) cc_final: 0.7475 (t60)
  outliers start: 1
  outliers final: 0
  residues processed: 274
  average time/residue: 0.1998
  time to fit residues: 72.4531
Evaluate side-chains
  236 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 36 optimal weight:    6.9990
   chunk 73 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0770
   chunk 32 optimal weight:    6.9990
   chunk 80 optimal weight:    8.9990
   chunk 68 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 377 ASN
A 390 GLN
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
R 227 GLN
** R 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 383 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.128699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.105007 restraints weight = 13894.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.107819 restraints weight = 7971.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.109864 restraints weight = 5456.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.4818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7806  Z= 0.183
  Angle     :  0.674  12.754  10578  Z= 0.336
  Chirality :  0.043   0.188   1194
  Planarity :  0.004   0.046   1340
  Dihedral  :  4.584  18.166   1054
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.52 (0.26), residues: 948
  helix:  1.22 (0.25), residues: 372
  sheet: -0.50 (0.36), residues: 206
  loop : -1.89 (0.29), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  82 
 HIS   0.006   0.001   HIS B 183 
 PHE   0.025   0.001   PHE R 314 
 TYR   0.016   0.001   TYR R 263 
 ARG   0.006   0.001   ARG R 180 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 268
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 ASP cc_start: 0.8571 (t0) cc_final: 0.8293 (t0)
REVERT: A   24 LYS cc_start: 0.8125 (mttp) cc_final: 0.7696 (mttp)
REVERT: A   32 LYS cc_start: 0.9265 (ptpp) cc_final: 0.8989 (pttm)
REVERT: A   35 GLN cc_start: 0.8495 (pt0) cc_final: 0.7852 (pp30)
REVERT: A  233 LYS cc_start: 0.8533 (mtmt) cc_final: 0.8313 (mtmm)
REVERT: A  278 ASN cc_start: 0.9218 (m110) cc_final: 0.8747 (m-40)
REVERT: A  389 ARG cc_start: 0.8115 (ttm110) cc_final: 0.7839 (ttm110)
REVERT: B   15 LYS cc_start: 0.8541 (pptt) cc_final: 0.8126 (ptmt)
REVERT: B   75 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7548 (tm-30)
REVERT: B  127 LYS cc_start: 0.8360 (ptmm) cc_final: 0.8077 (ptmm)
REVERT: B  260 GLU cc_start: 0.7961 (mp0) cc_final: 0.7656 (mp0)
REVERT: G   22 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7895 (tm-30)
REVERT: R  179 GLN cc_start: 0.8481 (tp40) cc_final: 0.7504 (pm20)
REVERT: R  187 MET cc_start: 0.8050 (mmm) cc_final: 0.7460 (tpt)
REVERT: R  197 ILE cc_start: 0.8728 (tt) cc_final: 0.8408 (tt)
REVERT: R  204 GLU cc_start: 0.7557 (tt0) cc_final: 0.6558 (mm-30)
REVERT: R  223 HIS cc_start: 0.8080 (t70) cc_final: 0.7566 (t70)
REVERT: R  229 MET cc_start: 0.8823 (tpp) cc_final: 0.7770 (tpp)
REVERT: R  262 TYR cc_start: 0.8276 (m-80) cc_final: 0.7941 (m-80)
REVERT: R  340 LYS cc_start: 0.8197 (pttt) cc_final: 0.7799 (pptt)
  outliers start: 0
  outliers final: 0
  residues processed: 268
  average time/residue: 0.2097
  time to fit residues: 73.8823
Evaluate side-chains
  237 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 89 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 85 optimal weight:    0.2980
   chunk 74 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 90 optimal weight:    8.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
R 227 GLN
** R 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 383 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.125930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.102245 restraints weight = 14052.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.104929 restraints weight = 8221.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.106874 restraints weight = 5679.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.4847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7806  Z= 0.246
  Angle     :  0.714  11.805  10578  Z= 0.360
  Chirality :  0.045   0.186   1194
  Planarity :  0.004   0.047   1340
  Dihedral  :  4.640  17.799   1054
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.57 (0.26), residues: 948
  helix:  1.22 (0.25), residues: 368
  sheet: -0.58 (0.37), residues: 205
  loop : -1.90 (0.29), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  82 
 HIS   0.009   0.001   HIS B 183 
 PHE   0.021   0.001   PHE R 314 
 TYR   0.016   0.002   TYR A 358 
 ARG   0.006   0.001   ARG A 356 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 ASP cc_start: 0.8538 (t0) cc_final: 0.8281 (t0)
REVERT: A   32 LYS cc_start: 0.9107 (ptpp) cc_final: 0.8822 (ptpp)
REVERT: A   35 GLN cc_start: 0.8464 (pt0) cc_final: 0.7869 (pp30)
REVERT: A  389 ARG cc_start: 0.8125 (ttm110) cc_final: 0.7841 (ttm110)
REVERT: B   15 LYS cc_start: 0.8637 (pptt) cc_final: 0.8249 (ptpt)
REVERT: B   55 LEU cc_start: 0.9030 (mp) cc_final: 0.8820 (mt)
REVERT: B  127 LYS cc_start: 0.8360 (ptmm) cc_final: 0.8087 (ptmm)
REVERT: B  260 GLU cc_start: 0.7963 (mp0) cc_final: 0.7687 (mp0)
REVERT: G   14 LYS cc_start: 0.8797 (mptt) cc_final: 0.8467 (mmtt)
REVERT: G   22 GLU cc_start: 0.8266 (tm-30) cc_final: 0.8001 (tm-30)
REVERT: R  179 GLN cc_start: 0.8563 (tp40) cc_final: 0.7508 (pm20)
REVERT: R  187 MET cc_start: 0.8197 (mmm) cc_final: 0.7716 (tpt)
REVERT: R  197 ILE cc_start: 0.8726 (tt) cc_final: 0.8404 (tt)
REVERT: R  204 GLU cc_start: 0.7638 (tt0) cc_final: 0.6589 (mm-30)
REVERT: R  223 HIS cc_start: 0.8134 (t70) cc_final: 0.7237 (t-170)
REVERT: R  262 TYR cc_start: 0.8343 (m-80) cc_final: 0.7954 (m-80)
REVERT: R  279 ILE cc_start: 0.7741 (mt) cc_final: 0.7281 (pt)
REVERT: R  340 LYS cc_start: 0.8237 (pttt) cc_final: 0.7838 (pptt)
  outliers start: 0
  outliers final: 0
  residues processed: 262
  average time/residue: 0.2017
  time to fit residues: 70.1951
Evaluate side-chains
  227 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 84 optimal weight:    0.0980
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:    0.4980
   chunk 81 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 377 ASN
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
G  24 ASN
N  31 ASN
R 223 HIS
** R 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 383 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.127879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.104539 restraints weight = 13966.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.107377 restraints weight = 7969.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.109159 restraints weight = 5406.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.4967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7806  Z= 0.197
  Angle     :  0.709  12.903  10578  Z= 0.353
  Chirality :  0.044   0.185   1194
  Planarity :  0.004   0.048   1340
  Dihedral  :  4.537  18.329   1054
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.62 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.56 (0.26), residues: 948
  helix:  1.19 (0.25), residues: 373
  sheet: -0.58 (0.38), residues: 195
  loop : -1.85 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.011   0.001   HIS R 223 
 PHE   0.027   0.001   PHE R 314 
 TYR   0.014   0.001   TYR R 263 
 ARG   0.005   0.001   ARG A 356 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 265
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 ASP cc_start: 0.8510 (t0) cc_final: 0.8266 (t0)
REVERT: A   29 GLN cc_start: 0.8628 (tp40) cc_final: 0.8235 (tp40)
REVERT: A   32 LYS cc_start: 0.9177 (ptpp) cc_final: 0.8893 (pttm)
REVERT: A   35 GLN cc_start: 0.8389 (pt0) cc_final: 0.7841 (pp30)
REVERT: A  389 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7842 (ttm110)
REVERT: B   15 LYS cc_start: 0.8558 (pptt) cc_final: 0.8179 (ptpt)
REVERT: B   55 LEU cc_start: 0.9044 (mp) cc_final: 0.8791 (mt)
REVERT: B   75 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7570 (tm-30)
REVERT: B  127 LYS cc_start: 0.8370 (ptmm) cc_final: 0.8091 (ptmm)
REVERT: B  260 GLU cc_start: 0.7873 (mp0) cc_final: 0.7604 (mp0)
REVERT: B  289 TYR cc_start: 0.9480 (m-80) cc_final: 0.9268 (m-80)
REVERT: G   22 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7845 (tm-30)
REVERT: N   70 ILE cc_start: 0.8879 (pt) cc_final: 0.8628 (pt)
REVERT: R  179 GLN cc_start: 0.8521 (tp40) cc_final: 0.7471 (pm20)
REVERT: R  187 MET cc_start: 0.8249 (mmm) cc_final: 0.7721 (tpt)
REVERT: R  204 GLU cc_start: 0.7563 (tt0) cc_final: 0.6547 (mm-30)
REVERT: R  227 GLN cc_start: 0.8614 (mp-120) cc_final: 0.8142 (mp10)
REVERT: R  262 TYR cc_start: 0.8319 (m-80) cc_final: 0.8022 (m-80)
REVERT: R  279 ILE cc_start: 0.7730 (mt) cc_final: 0.7284 (pt)
REVERT: R  406 TRP cc_start: 0.7651 (t60) cc_final: 0.7390 (t60)
  outliers start: 1
  outliers final: 0
  residues processed: 266
  average time/residue: 0.2060
  time to fit residues: 72.1391
Evaluate side-chains
  229 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 60 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 64 optimal weight:    0.1980
   chunk 14 optimal weight:    8.9990
   chunk 36 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0050
   chunk 90 optimal weight:    0.5980
   chunk 54 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 377 ASN
** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
G  24 ASN
N  13 GLN
** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.129953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.107217 restraints weight = 13634.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.109936 restraints weight = 8181.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.111806 restraints weight = 5673.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.5113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7806  Z= 0.180
  Angle     :  0.697  13.747  10578  Z= 0.347
  Chirality :  0.043   0.194   1194
  Planarity :  0.004   0.045   1340
  Dihedral  :  4.443  19.173   1054
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.75 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.47 (0.26), residues: 948
  helix:  1.20 (0.25), residues: 374
  sheet: -0.47 (0.38), residues: 193
  loop : -1.78 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 234 
 HIS   0.006   0.001   HIS R 381 
 PHE   0.026   0.001   PHE R 314 
 TYR   0.016   0.001   TYR R 263 
 ARG   0.014   0.001   ARG R 180 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2734.83 seconds
wall clock time: 48 minutes 6.06 seconds (2886.06 seconds total)