Starting phenix.real_space_refine
on Wed Sep 17 16:10:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bhm_44550/09_2025/9bhm_44550.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bhm_44550/09_2025/9bhm_44550.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bhm_44550/09_2025/9bhm_44550.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bhm_44550/09_2025/9bhm_44550.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bhm_44550/09_2025/9bhm_44550.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bhm_44550/09_2025/9bhm_44550.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.009 sd=   0.774
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3038 atoms to isotropic.
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      47      5.16       5
     C    4567      2.51       5
     N    1237      2.21       5
     O    1299      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7150
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 2297
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2297
          Classifications: {'peptide': 282}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273}
    Chain: "A"
      Number of atoms: 1763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1763
          Classifications: {'peptide': 210}
          Link IDs: {'PTRANS': 3, 'TRANS': 206}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2211
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2211
          Classifications: {'peptide': 289}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 284}
          Chain breaks: 2
    Chain: "N"
      Number of atoms: 844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 844
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 2, 'TRANS': 106}
          Chain breaks: 4
    Chain: "R"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'Y01': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.82, per 1000 atoms: 0.25
  Number of scatterers: 7150
  At special positions: 0
  Unit cell: (71.38, 87.98, 126.99, 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      47     16.00
     O    1299      8.00
     N    1237      7.00
     C    4567      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  13 " - pdb=" SG  CYS R 258 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  94 " - pdb=" SG  CYS R 172 " distance=2.03
    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=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.58
  Conformation dependent library (CDL) restraints added in 386.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1672

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 12 sheets defined
      40.7% alpha, 20.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'R' and resid 17 through 52
      removed outlier: 4.007A  pdb=" N   GLN R  21 " --> pdb=" O   HIS R  17 " (cutoff:3.500A)
      Proline residue:  R  25  - end of helix
      Proline residue:  R  37  - end of helix
    Processing helix  chain 'R' and resid 54 through 82
      removed outlier: 4.244A  pdb=" N   VAL R  58 " --> pdb=" O   ASN R  54 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   TYR R  59 " --> pdb=" O   GLU R  55 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   SER R  73 " --> pdb=" O   PHE R  69 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU R  74 " --> pdb=" O   TYR R  70 " (cutoff:3.500A)
      Proline residue:  R  75  - end of helix
    Processing helix  chain 'R' and resid 90 through 124
      removed outlier: 5.178A  pdb=" N   ILE R 105 " --> pdb=" O   LEU R 101 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   TYR R 106 " --> pdb=" O   TYR R 102 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 134 through 158
    Processing helix  chain 'R' and resid 159 through 161
      No H-bonds generated for 'chain 'R' and resid 159 through 161'
    Processing helix  chain 'R' and resid 179 through 215
      removed outlier: 3.686A  pdb=" N   TYR R 187 " --> pdb=" O   ARG R 183 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   TYR R 188 " --> pdb=" O   ALA R 184 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   PHE R 196 " --> pdb=" O   VAL R 192 " (cutoff:3.500A)
      Proline residue:  R 197  - end of helix
      removed outlier: 3.548A  pdb=" N   GLY R 207 " --> pdb=" O   ALA R 203 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 219 through 254
      Proline residue:  R 243  - end of helix
    Processing helix  chain 'R' and resid 257 through 288
      removed outlier: 4.774A  pdb=" N   ASN R 266 " --> pdb=" O   LYS R 262 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   ALA R 267 " --> pdb=" O   GLY R 263 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   CYS R 279 " --> pdb=" O   THR R 275 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   VAL R 280 " --> pdb=" O   SER R 276 " (cutoff:3.500A)
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'A' and resid 17 through 39
    Processing helix  chain 'A' and resid 52 through 58
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.657A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 279
      removed outlier: 3.714A  pdb=" N   GLN A 267 " --> pdb=" O   TYR A 253 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   GLU A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 285
      removed outlier: 3.748A  pdb=" N   THR A 284 " --> pdb=" O   TRP A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.531A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 317
    Processing helix  chain 'A' and resid 332 through 351
      removed outlier: 3.637A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'N' and resid 62 through 65
    Processing sheet with id=AA1, first strand: chain 'R' and resid 163 through 166
    Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 214
      removed outlier: 6.492A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.397A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 10.331A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.310A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.099A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 50
      removed outlier: 6.701A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.360A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.548A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   LEU B 139 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151
      removed outlier: 7.031A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.023A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.185A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.714A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.450A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.173A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.916A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ASN B 295 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.921A  pdb=" N   GLN N   3 " --> pdb=" O   SER N  25 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   SER N  25 " --> pdb=" O   GLN N   3 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU N  79 " --> pdb=" O   CYS N  22 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   THR N  69 " --> pdb=" O   GLN N  82 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11
      removed outlier: 7.832A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'N' and resid 59 through 60
      removed outlier: 3.829A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   VAL N  37 " --> pdb=" O   TYR N  95 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TYR N  95 " --> pdb=" O   VAL N  37 " (cutoff:3.500A)

    351 hydrogen bonds defined for protein.
    990 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.15

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1138
        1.30 -     1.43: 2063
        1.43 -     1.56: 4034
        1.56 -     1.69: 14
        1.69 -     1.82: 60
  Bond restraints: 7309
  Sorted by residual:
  bond pdb=" CAI Y01 R1000 "
       pdb=" CAK Y01 R1000 "
    ideal  model  delta    sigma   weight residual
    1.492  1.235  0.257 2.00e-02 2.50e+03 1.65e+02
  bond pdb=" CAS Y01 R1000 "
       pdb=" CBF Y01 R1000 "
    ideal  model  delta    sigma   weight residual
    1.533  1.277  0.256 2.00e-02 2.50e+03 1.64e+02
  bond pdb=" CAZ Y01 R1000 "
       pdb=" CBH Y01 R1000 "
    ideal  model  delta    sigma   weight residual
    1.519  1.296  0.223 2.00e-02 2.50e+03 1.24e+02
  bond pdb=" CAU Y01 R1000 "
       pdb=" CBI Y01 R1000 "
    ideal  model  delta    sigma   weight residual
    1.530  1.733 -0.203 2.00e-02 2.50e+03 1.03e+02
  bond pdb=" CAI Y01 R1000 "
       pdb=" CAZ Y01 R1000 "
    ideal  model  delta    sigma   weight residual
    1.332  1.167  0.165 2.00e-02 2.50e+03 6.80e+01
  ... (remaining 7304 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 9703
        1.83 -     3.65: 156
        3.65 -     5.48: 28
        5.48 -     7.30: 12
        7.30 -     9.13: 4
  Bond angle restraints: 9903
  Sorted by residual:
  angle pdb=" CA  PRO B  94 "
        pdb=" N   PRO B  94 "
        pdb=" CD  PRO B  94 "
      ideal   model   delta    sigma   weight residual
     112.00  105.09    6.91 1.40e+00 5.10e-01 2.43e+01
  angle pdb=" CAM Y01 R1000 "
        pdb=" CAY Y01 R1000 "
        pdb=" OAW Y01 R1000 "
      ideal   model   delta    sigma   weight residual
     111.19  120.32   -9.13 3.00e+00 1.11e-01 9.26e+00
  angle pdb=" CA  MET N  83 "
        pdb=" CB  MET N  83 "
        pdb=" CG  MET N  83 "
      ideal   model   delta    sigma   weight residual
     114.10  119.69   -5.59 2.00e+00 2.50e-01 7.82e+00
  angle pdb=" CAS Y01 R1000 "
        pdb=" CAU Y01 R1000 "
        pdb=" CBI Y01 R1000 "
      ideal   model   delta    sigma   weight residual
     111.64  103.30    8.34 3.00e+00 1.11e-01 7.72e+00
  angle pdb=" N   GLU A  27 "
        pdb=" CA  GLU A  27 "
        pdb=" CB  GLU A  27 "
      ideal   model   delta    sigma   weight residual
     110.39  114.93   -4.54 1.66e+00 3.63e-01 7.48e+00
  ... (remaining 9898 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.25: 4088
       25.25 -    50.49: 205
       50.49 -    75.74: 25
       75.74 -   100.99: 7
      100.99 -   126.24: 1
  Dihedral angle restraints: 4326
    sinusoidal: 1737
      harmonic: 2589
  Sorted by residual:
  dihedral pdb=" CA  LEU A 291 "
           pdb=" C   LEU A 291 "
           pdb=" N   ASN A 292 "
           pdb=" CA  ASN A 292 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.45  -22.55     0      5.00e+00 4.00e-02 2.03e+01
  dihedral pdb=" CBC Y01 R1000 "
           pdb=" CAR Y01 R1000 "
           pdb=" CAT Y01 R1000 "
           pdb=" CBH Y01 R1000 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.13   69.11 -126.24     1      3.00e+01 1.11e-03 1.70e+01
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.73  -20.27     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 4323 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 904
       0.054 -    0.108: 172
       0.108 -    0.162: 27
       0.162 -    0.216: 2
       0.216 -    0.270: 3
  Chirality restraints: 1108
  Sorted by residual:
  chirality pdb=" CBF Y01 R1000 "
            pdb=" CAS Y01 R1000 "
            pdb=" CBD Y01 R1000 "
            pdb=" CBH Y01 R1000 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.72    0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" CBG Y01 R1000 "
            pdb=" CAQ Y01 R1000 "
            pdb=" CBD Y01 R1000 "
            pdb=" CBI Y01 R1000 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.58    0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" CBB Y01 R1000 "
            pdb=" CAC Y01 R1000 "
            pdb=" CAO Y01 R1000 "
            pdb=" CBE Y01 R1000 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.58    2.80   -0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 1105 not shown)

  Planarity restraints: 1245
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 111 "    0.025 2.00e-02 2.50e+03   2.61e-02 1.19e+01
        pdb=" CG  PHE R 111 "   -0.059 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 111 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 111 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 111 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 111 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 111 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B  93 "   -0.044 5.00e-02 4.00e+02   6.38e-02 6.51e+00
        pdb=" N   PRO B  94 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO B  94 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B  94 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN R 278 "   -0.007 2.00e-02 2.50e+03   1.50e-02 2.24e+00
        pdb=" CG  ASN R 278 "    0.026 2.00e-02 2.50e+03
        pdb=" OD1 ASN R 278 "   -0.010 2.00e-02 2.50e+03
        pdb=" ND2 ASN R 278 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1242 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 259
        2.71 -     3.26: 7531
        3.26 -     3.81: 12015
        3.81 -     4.35: 14953
        4.35 -     4.90: 25217
  Nonbonded interactions: 59975
  Sorted by model distance:
  nonbonded pdb=" O   LEU R 273 "
            pdb=" OG  SER R 276 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" OG  SER A 275 "
            pdb=" O   CYS N 107 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" OG  SER B 160 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   ARG A 356 "
            pdb=" NH2 ARG A 385 "
     model   vdw
     2.231 3.120
  ... (remaining 59970 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.510
  Find NCS groups from input model:        0.030
  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:             0.000
  Load rotamer database and sin/cos tables:6.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6565
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   0.257   7313  Z= 0.389
  Angle     :  0.647   9.130   9911  Z= 0.332
  Chirality :  0.045   0.270   1108
  Planarity :  0.004   0.064   1245
  Dihedral  : 14.738 126.235   2642
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.26 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.56 (0.28), residues: 864
  helix:  1.04 (0.29), residues: 317
  sheet: -1.23 (0.34), residues: 208
  loop : -1.06 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 314 
 TYR   0.020   0.001   TYR R 106 
 PHE   0.059   0.002   PHE R 111 
 TRP   0.019   0.001   TRP N  47 
 HIS   0.005   0.001   HIS R 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00795 ( 7309)
  covalent geometry    : angle       0.64653 ( 9903)
  SS BOND              : bond        0.00165 (    4)
  SS BOND              : angle       0.79802 (    8)
  hydrogen bonds       : bond        0.18449 (  351)
  hydrogen bonds       : angle       7.53212 (  990)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 199
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   47 TYR cc_start: 0.7877 (t80) cc_final: 0.7317 (t80)
REVERT: R   48 LEU cc_start: 0.8014 (mm) cc_final: 0.7793 (mp)
REVERT: R   61 CYS cc_start: 0.7924 (m) cc_final: 0.7562 (m)
REVERT: R  144 VAL cc_start: 0.8385 (t) cc_final: 0.8105 (m)
REVERT: R  225 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7238 (tt0)
REVERT: R  238 LEU cc_start: 0.8318 (mm) cc_final: 0.8068 (mm)
REVERT: A   34 LYS cc_start: 0.6770 (tttp) cc_final: 0.6367 (tttp)
REVERT: A   37 TYR cc_start: 0.7312 (t80) cc_final: 0.6788 (t80)
REVERT: A  283 ARG cc_start: 0.7309 (mtm110) cc_final: 0.6912 (mtm110)
REVERT: A  370 GLU cc_start: 0.7291 (pp20) cc_final: 0.6822 (pp20)
REVERT: B   46 ARG cc_start: 0.7156 (ptt-90) cc_final: 0.6799 (mpp80)
REVERT: B   52 ARG cc_start: 0.7970 (ptp-110) cc_final: 0.7638 (ttm110)
REVERT: B  114 CYS cc_start: 0.7683 (t) cc_final: 0.7137 (t)
REVERT: B  163 ASP cc_start: 0.6653 (t70) cc_final: 0.6343 (p0)
REVERT: B  209 LYS cc_start: 0.6752 (mttp) cc_final: 0.6447 (mttm)
REVERT: B  217 MET cc_start: 0.5765 (ppp) cc_final: 0.5401 (pmm)
REVERT: B  252 LEU cc_start: 0.7553 (tt) cc_final: 0.7339 (tt)
REVERT: B  275 SER cc_start: 0.8193 (t) cc_final: 0.7781 (p)
REVERT: B  286 LEU cc_start: 0.8128 (mp) cc_final: 0.7896 (mp)
REVERT: B  301 LYS cc_start: 0.6475 (mptt) cc_final: 0.6061 (mptt)
REVERT: B  318 LEU cc_start: 0.8012 (tt) cc_final: 0.7791 (tt)
REVERT: B  335 PHE cc_start: 0.7592 (m-80) cc_final: 0.7360 (m-80)
REVERT: B  337 LYS cc_start: 0.7698 (mttp) cc_final: 0.7219 (mttp)
REVERT: N   72 ARG cc_start: 0.5978 (tmm-80) cc_final: 0.5462 (ttt-90)
REVERT: N  103 PHE cc_start: 0.7094 (m-80) cc_final: 0.6579 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 200
  average time/residue: 0.4517
  time to fit residues: 96.3973
Evaluate side-chains
  145 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 144
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  225 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.3980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
R  83 GLN
** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 131 GLN
R 225 GLN
R 227 GLN
A 213 GLN
A 220 HIS
A 267 GLN
A 384 GLN
B 125 ASN
B 176 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.191434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.171662 restraints weight = 10715.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.4002 rms_B_bonded: 2.22
r_work: 0.3925 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7313  Z= 0.185
  Angle     :  0.641   7.812   9911  Z= 0.336
  Chirality :  0.045   0.171   1108
  Planarity :  0.004   0.042   1245
  Dihedral  :  6.436  59.206   1048
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 12.53 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.28), residues: 864
  helix:  1.00 (0.28), residues: 312
  sheet: -1.11 (0.34), residues: 211
  loop : -0.99 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 210 
 TYR   0.024   0.002   TYR R 106 
 PHE   0.017   0.002   PHE R  76 
 TRP   0.021   0.002   TRP B 169 
 HIS   0.009   0.002   HIS R 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 7309)
  covalent geometry    : angle       0.63976 ( 9903)
  SS BOND              : bond        0.00442 (    4)
  SS BOND              : angle       1.77931 (    8)
  hydrogen bonds       : bond        0.04954 (  351)
  hydrogen bonds       : angle       5.62446 (  990)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 160
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   47 TYR cc_start: 0.8193 (t80) cc_final: 0.7462 (t80)
REVERT: R   61 CYS cc_start: 0.8539 (m) cc_final: 0.8235 (m)
REVERT: R  238 LEU cc_start: 0.8671 (mm) cc_final: 0.8465 (mm)
REVERT: A   34 LYS cc_start: 0.7578 (tttp) cc_final: 0.7098 (tttp)
REVERT: A   37 TYR cc_start: 0.7708 (t80) cc_final: 0.7306 (t80)
REVERT: A  213 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.7210 (pm20)
REVERT: A  370 GLU cc_start: 0.7739 (pp20) cc_final: 0.7502 (pm20)
REVERT: B   46 ARG cc_start: 0.7537 (ptt-90) cc_final: 0.7195 (mpp80)
REVERT: B   52 ARG cc_start: 0.8010 (ptp-110) cc_final: 0.7733 (ttm110)
REVERT: B  114 CYS cc_start: 0.7887 (t) cc_final: 0.7677 (t)
REVERT: B  301 LYS cc_start: 0.7101 (mptt) cc_final: 0.6771 (mptt)
REVERT: N   31 ASN cc_start: 0.6854 (m-40) cc_final: 0.6540 (m-40)
REVERT: N   72 ARG cc_start: 0.5783 (tmm-80) cc_final: 0.5561 (ttt-90)
  outliers start: 31
  outliers final: 16
  residues processed: 172
  average time/residue: 0.4736
  time to fit residues: 86.8245
Evaluate side-chains
  150 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 VAL
Chi-restraints excluded: chain R residue  234 VAL
Chi-restraints excluded: chain R residue  250 VAL
Chi-restraints excluded: chain R residue  276 SER
Chi-restraints excluded: chain R residue  280 VAL
Chi-restraints excluded: chain R residue  284 VAL
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain N residue  111 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 85 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 84 optimal weight:    0.2980
   chunk 58 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9980
   chunk 68 optimal weight:    0.2980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
B 176 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.195644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.175807 restraints weight = 10630.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.4066 rms_B_bonded: 2.26
r_work: 0.3988 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7202
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7313  Z= 0.127
  Angle     :  0.568   7.141   9911  Z= 0.298
  Chirality :  0.043   0.143   1108
  Planarity :  0.004   0.041   1245
  Dihedral  :  6.025  59.209   1045
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 16.02 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.27), residues: 864
  helix:  1.20 (0.28), residues: 314
  sheet: -1.19 (0.33), residues: 210
  loop : -1.05 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 283 
 TYR   0.019   0.001   TYR R 106 
 PHE   0.013   0.001   PHE R 111 
 TRP   0.018   0.002   TRP B 169 
 HIS   0.006   0.001   HIS R 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7309)
  covalent geometry    : angle       0.56722 ( 9903)
  SS BOND              : bond        0.00182 (    4)
  SS BOND              : angle       1.24083 (    8)
  hydrogen bonds       : bond        0.04076 (  351)
  hydrogen bonds       : angle       5.20336 (  990)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 150
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: R   47 TYR cc_start: 0.8211 (t80) cc_final: 0.7373 (t80)
REVERT: R   61 CYS cc_start: 0.8559 (m) cc_final: 0.8250 (m)
REVERT: A   27 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7422 (mp0)
REVERT: A   34 LYS cc_start: 0.7549 (tttp) cc_final: 0.7143 (tttp)
REVERT: A   37 TYR cc_start: 0.7661 (t80) cc_final: 0.7222 (t80)
REVERT: A  213 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7292 (pm20)
REVERT: A  362 HIS cc_start: 0.7760 (m-70) cc_final: 0.7546 (m90)
REVERT: B   46 ARG cc_start: 0.7548 (ptt-90) cc_final: 0.7236 (mpp80)
REVERT: B   52 ARG cc_start: 0.7988 (ptp-110) cc_final: 0.7738 (ttm110)
REVERT: B  110 ASN cc_start: 0.6678 (p0) cc_final: 0.6475 (m-40)
REVERT: B  196 THR cc_start: 0.7149 (p) cc_final: 0.6930 (t)
REVERT: B  274 THR cc_start: 0.7745 (t) cc_final: 0.7486 (p)
REVERT: B  289 TYR cc_start: 0.8332 (m-80) cc_final: 0.7929 (m-80)
REVERT: B  301 LYS cc_start: 0.7104 (mptt) cc_final: 0.6803 (mptt)
REVERT: N   12 VAL cc_start: 0.5715 (p) cc_final: 0.5362 (m)
REVERT: N   31 ASN cc_start: 0.6871 (m-40) cc_final: 0.6528 (m-40)
REVERT: N   38 ARG cc_start: 0.6367 (mtp85) cc_final: 0.6111 (ptp-110)
  outliers start: 31
  outliers final: 14
  residues processed: 163
  average time/residue: 0.3998
  time to fit residues: 70.0092
Evaluate side-chains
  155 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 VAL
Chi-restraints excluded: chain R residue  250 VAL
Chi-restraints excluded: chain R residue  276 SER
Chi-restraints excluded: chain R residue  280 VAL
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain N residue  111 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 227 GLN
A 213 GLN
B 176 GLN
** N  53 GLN ** 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 = 0.4198 r_free = 0.4198 target = 0.190655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.170149 restraints weight = 10715.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3999 rms_B_bonded: 2.31
r_work: 0.3917 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7313  Z= 0.180
  Angle     :  0.623   8.188   9911  Z= 0.328
  Chirality :  0.044   0.169   1108
  Planarity :  0.004   0.041   1245
  Dihedral  :  6.227  56.143   1045
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 18.48 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.28), residues: 864
  helix:  1.04 (0.28), residues: 312
  sheet: -1.15 (0.34), residues: 210
  loop : -1.03 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R 210 
 TYR   0.024   0.002   TYR R 106 
 PHE   0.019   0.002   PHE R 111 
 TRP   0.017   0.002   TRP B 169 
 HIS   0.009   0.001   HIS R 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 7309)
  covalent geometry    : angle       0.62236 ( 9903)
  SS BOND              : bond        0.00212 (    4)
  SS BOND              : angle       1.28588 (    8)
  hydrogen bonds       : bond        0.04564 (  351)
  hydrogen bonds       : angle       5.28167 (  990)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 152
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   47 TYR cc_start: 0.8262 (t80) cc_final: 0.7508 (t80)
REVERT: A   27 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7521 (mp0)
REVERT: A   34 LYS cc_start: 0.7647 (tttp) cc_final: 0.7240 (tttp)
REVERT: A   37 TYR cc_start: 0.7762 (t80) cc_final: 0.7320 (t80)
REVERT: A  213 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7187 (pm20)
REVERT: A  384 GLN cc_start: 0.7872 (mt0) cc_final: 0.7543 (tp40)
REVERT: A  390 GLN cc_start: 0.8704 (tt0) cc_final: 0.8393 (pt0)
REVERT: B   46 ARG cc_start: 0.7616 (ptt-90) cc_final: 0.7298 (mpp80)
REVERT: B   52 ARG cc_start: 0.8000 (ptp-110) cc_final: 0.7715 (ttm110)
REVERT: B   57 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8170 (pttp)
REVERT: B   61 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7868 (ppp)
REVERT: B  110 ASN cc_start: 0.6904 (p0) cc_final: 0.6415 (m-40)
REVERT: B  111 TYR cc_start: 0.7252 (m-80) cc_final: 0.6944 (m-80)
REVERT: B  117 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7861 (mt)
REVERT: B  274 THR cc_start: 0.7860 (t) cc_final: 0.7503 (p)
REVERT: B  289 TYR cc_start: 0.8462 (m-80) cc_final: 0.7993 (m-80)
REVERT: B  290 ASP cc_start: 0.7605 (m-30) cc_final: 0.7276 (m-30)
REVERT: B  301 LYS cc_start: 0.7042 (mptt) cc_final: 0.6792 (mptt)
REVERT: B  318 LEU cc_start: 0.8743 (tt) cc_final: 0.8460 (tt)
REVERT: N   12 VAL cc_start: 0.5791 (p) cc_final: 0.5487 (m)
REVERT: N   31 ASN cc_start: 0.6942 (m-40) cc_final: 0.6644 (m-40)
REVERT: N   72 ARG cc_start: 0.6135 (ttt-90) cc_final: 0.5772 (ttt-90)
  outliers start: 35
  outliers final: 19
  residues processed: 170
  average time/residue: 0.3932
  time to fit residues: 72.0021
Evaluate side-chains
  155 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 VAL
Chi-restraints excluded: chain R residue  250 VAL
Chi-restraints excluded: chain R residue  276 SER
Chi-restraints excluded: chain R residue  280 VAL
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  113 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 70 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 69 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
R  54 ASN
** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 213 GLN
A 362 HIS
B  62 HIS
B 176 GLN
N  53 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.193243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.173080 restraints weight = 10713.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.4021 rms_B_bonded: 2.26
r_work: 0.3943 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.3121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7313  Z= 0.142
  Angle     :  0.587   7.861   9911  Z= 0.309
  Chirality :  0.043   0.155   1108
  Planarity :  0.004   0.042   1245
  Dihedral  :  6.078  57.858   1045
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 19.90 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.28), residues: 864
  helix:  1.14 (0.28), residues: 313
  sheet: -1.09 (0.35), residues: 207
  loop : -1.03 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG R 210 
 TYR   0.031   0.002   TYR N 115 
 PHE   0.018   0.001   PHE R 111 
 TRP   0.016   0.002   TRP B 169 
 HIS   0.006   0.001   HIS R 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 7309)
  covalent geometry    : angle       0.58658 ( 9903)
  SS BOND              : bond        0.00176 (    4)
  SS BOND              : angle       1.07620 (    8)
  hydrogen bonds       : bond        0.04094 (  351)
  hydrogen bonds       : angle       5.09929 (  990)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 144
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   47 TYR cc_start: 0.8285 (t80) cc_final: 0.7534 (t80)
REVERT: R  174 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7908 (mm-30)
REVERT: A   34 LYS cc_start: 0.7645 (tttp) cc_final: 0.7204 (tttp)
REVERT: A   37 TYR cc_start: 0.7740 (t80) cc_final: 0.7356 (t80)
REVERT: A  213 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7345 (pm20)
REVERT: A  362 HIS cc_start: 0.7733 (m-70) cc_final: 0.7525 (m90)
REVERT: B   46 ARG cc_start: 0.7557 (ptt-90) cc_final: 0.7244 (mpp80)
REVERT: B   52 ARG cc_start: 0.8007 (ptp-110) cc_final: 0.7740 (ttm110)
REVERT: B   61 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7849 (ppp)
REVERT: B  110 ASN cc_start: 0.6809 (p0) cc_final: 0.6403 (m-40)
REVERT: B  111 TYR cc_start: 0.7246 (m-80) cc_final: 0.7017 (m-80)
REVERT: B  274 THR cc_start: 0.7844 (t) cc_final: 0.7495 (p)
REVERT: B  289 TYR cc_start: 0.8356 (m-80) cc_final: 0.8019 (m-80)
REVERT: B  301 LYS cc_start: 0.7072 (mptt) cc_final: 0.6819 (mptt)
REVERT: N   12 VAL cc_start: 0.5768 (p) cc_final: 0.5431 (m)
REVERT: N   31 ASN cc_start: 0.6905 (m-40) cc_final: 0.6601 (m-40)
REVERT: N   38 ARG cc_start: 0.6348 (mtp85) cc_final: 0.6091 (ptp-110)
REVERT: N   72 ARG cc_start: 0.6086 (ttt-90) cc_final: 0.5754 (ttt-90)
  outliers start: 41
  outliers final: 19
  residues processed: 166
  average time/residue: 0.4346
  time to fit residues: 77.2202
Evaluate side-chains
  156 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 VAL
Chi-restraints excluded: chain R residue  234 VAL
Chi-restraints excluded: chain R residue  276 SER
Chi-restraints excluded: chain R residue  280 VAL
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  113 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   chunk 56 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 48 optimal weight:    0.0970
   chunk 61 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 227 GLN
A 213 GLN
A 390 GLN
B 176 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.192776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.172678 restraints weight = 10660.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.4030 rms_B_bonded: 2.26
r_work: 0.3951 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.3293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7313  Z= 0.153
  Angle     :  0.611   8.079   9911  Z= 0.318
  Chirality :  0.044   0.155   1108
  Planarity :  0.004   0.046   1245
  Dihedral  :  6.082  57.499   1045
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 22.09 %
    Favored  : 73.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.28), residues: 864
  helix:  1.18 (0.28), residues: 311
  sheet: -1.07 (0.35), residues: 207
  loop : -1.00 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG R 210 
 TYR   0.020   0.002   TYR R 106 
 PHE   0.018   0.002   PHE R 111 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.007   0.001   HIS R 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 7309)
  covalent geometry    : angle       0.61035 ( 9903)
  SS BOND              : bond        0.00166 (    4)
  SS BOND              : angle       1.07568 (    8)
  hydrogen bonds       : bond        0.04155 (  351)
  hydrogen bonds       : angle       5.10255 (  990)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 140
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   47 TYR cc_start: 0.8286 (t80) cc_final: 0.7522 (t80)
REVERT: R  174 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7895 (mm-30)
REVERT: R  222 ARG cc_start: 0.7175 (mmt90) cc_final: 0.6841 (mmm160)
REVERT: A   34 LYS cc_start: 0.7668 (tttp) cc_final: 0.7224 (tttp)
REVERT: A   37 TYR cc_start: 0.7748 (t80) cc_final: 0.7357 (t80)
REVERT: A  239 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8602 (p0)
REVERT: A  356 ARG cc_start: 0.6356 (mpp-170) cc_final: 0.6068 (mpp-170)
REVERT: A  362 HIS cc_start: 0.7742 (m-70) cc_final: 0.7519 (m90)
REVERT: A  384 GLN cc_start: 0.7795 (mt0) cc_final: 0.7439 (tp40)
REVERT: B   46 ARG cc_start: 0.7549 (ptt-90) cc_final: 0.7240 (mpp80)
REVERT: B   52 ARG cc_start: 0.7947 (ptp-110) cc_final: 0.7670 (ttm110)
REVERT: B   61 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7784 (ppp)
REVERT: B  110 ASN cc_start: 0.6894 (p0) cc_final: 0.6473 (m-40)
REVERT: B  111 TYR cc_start: 0.7258 (m-80) cc_final: 0.7043 (m-80)
REVERT: B  274 THR cc_start: 0.7950 (t) cc_final: 0.7589 (p)
REVERT: B  289 TYR cc_start: 0.8355 (m-80) cc_final: 0.8001 (m-80)
REVERT: B  301 LYS cc_start: 0.7086 (mptt) cc_final: 0.6846 (mptt)
REVERT: B  317 CYS cc_start: 0.7990 (t) cc_final: 0.7721 (p)
REVERT: N   12 VAL cc_start: 0.5757 (p) cc_final: 0.5410 (m)
REVERT: N   31 ASN cc_start: 0.6953 (m-40) cc_final: 0.6629 (m-40)
REVERT: N   38 ARG cc_start: 0.6360 (mtp85) cc_final: 0.6093 (ptp-110)
REVERT: N   72 ARG cc_start: 0.6072 (ttt-90) cc_final: 0.5713 (ttt-90)
  outliers start: 34
  outliers final: 21
  residues processed: 157
  average time/residue: 0.4110
  time to fit residues: 69.2492
Evaluate side-chains
  155 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 VAL
Chi-restraints excluded: chain R residue  220 LYS
Chi-restraints excluded: chain R residue  250 VAL
Chi-restraints excluded: chain R residue  276 SER
Chi-restraints excluded: chain R residue  280 VAL
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  113 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0010
   chunk 79 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 32 optimal weight:    7.9990
   chunk 19 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6588

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

Flipped N/Q/H residues before XYZ refinement:
** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.194990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.175156 restraints weight = 10760.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.4056 rms_B_bonded: 2.28
r_work: 0.3979 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
moved from start:          0.3307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7313  Z= 0.130
  Angle     :  0.592   7.744   9911  Z= 0.307
  Chirality :  0.043   0.171   1108
  Planarity :  0.004   0.051   1245
  Dihedral  :  5.911  56.615   1045
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 23.39 %
    Favored  : 72.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.34 (0.28), residues: 864
  helix:  1.26 (0.28), residues: 312
  sheet: -1.07 (0.36), residues: 207
  loop : -0.97 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG R 210 
 TYR   0.020   0.001   TYR R 106 
 PHE   0.016   0.001   PHE R 111 
 TRP   0.014   0.002   TRP B 169 
 HIS   0.006   0.001   HIS R 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7309)
  covalent geometry    : angle       0.59115 ( 9903)
  SS BOND              : bond        0.00139 (    4)
  SS BOND              : angle       0.99033 (    8)
  hydrogen bonds       : bond        0.03877 (  351)
  hydrogen bonds       : angle       4.99165 (  990)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   47 TYR cc_start: 0.8284 (t80) cc_final: 0.7499 (t80)
REVERT: R  144 VAL cc_start: 0.8531 (t) cc_final: 0.8329 (m)
REVERT: R  222 ARG cc_start: 0.7108 (mmt90) cc_final: 0.6823 (mmm160)
REVERT: R  238 LEU cc_start: 0.8617 (mm) cc_final: 0.8386 (mm)
REVERT: A   37 TYR cc_start: 0.7707 (t80) cc_final: 0.7355 (t80)
REVERT: A  239 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8638 (p0)
REVERT: A  384 GLN cc_start: 0.7803 (mt0) cc_final: 0.7390 (tp40)
REVERT: B   46 ARG cc_start: 0.7598 (ptt-90) cc_final: 0.7279 (mpp80)
REVERT: B  110 ASN cc_start: 0.6779 (p0) cc_final: 0.6424 (m-40)
REVERT: B  289 TYR cc_start: 0.8280 (m-80) cc_final: 0.8047 (m-80)
REVERT: B  301 LYS cc_start: 0.7096 (mptt) cc_final: 0.6812 (mptt)
REVERT: B  317 CYS cc_start: 0.7936 (t) cc_final: 0.7692 (p)
REVERT: N   31 ASN cc_start: 0.6929 (m-40) cc_final: 0.6609 (m-40)
REVERT: N   38 ARG cc_start: 0.6291 (mtp85) cc_final: 0.6021 (ptp-110)
REVERT: N   72 ARG cc_start: 0.5933 (ttt-90) cc_final: 0.5556 (ttt180)
  outliers start: 33
  outliers final: 20
  residues processed: 152
  average time/residue: 0.3991
  time to fit residues: 65.2872
Evaluate side-chains
  142 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  250 VAL
Chi-restraints excluded: chain R residue  276 SER
Chi-restraints excluded: chain R residue  280 VAL
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  113 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 50 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0670
   chunk 59 optimal weight:    0.0470
   chunk 72 optimal weight:    0.0980
   chunk 7 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.3416

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

Flipped N/Q/H residues before XYZ refinement:
R  54 ASN
R 104 ASN
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS
B 176 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.198935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.178987 restraints weight = 10936.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.4095 rms_B_bonded: 2.40
r_work: 0.4016 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.4016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7313  Z= 0.118
  Angle     :  0.588   7.514   9911  Z= 0.305
  Chirality :  0.042   0.133   1108
  Planarity :  0.004   0.045   1245
  Dihedral  :  5.670  56.919   1045
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 23.64 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.28), residues: 864
  helix:  1.44 (0.28), residues: 312
  sheet: -1.06 (0.35), residues: 203
  loop : -0.96 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG R 251 
 TYR   0.020   0.001   TYR B 111 
 PHE   0.022   0.001   PHE N  68 
 TRP   0.019   0.002   TRP B  82 
 HIS   0.005   0.001   HIS R 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 7309)
  covalent geometry    : angle       0.58733 ( 9903)
  SS BOND              : bond        0.00461 (    4)
  SS BOND              : angle       0.88273 (    8)
  hydrogen bonds       : bond        0.03655 (  351)
  hydrogen bonds       : angle       4.88372 (  990)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 140
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   47 TYR cc_start: 0.8229 (t80) cc_final: 0.7334 (t80)
REVERT: R   72 CYS cc_start: 0.8443 (m) cc_final: 0.8164 (p)
REVERT: R  238 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8217 (mm)
REVERT: A   30 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6173 (mt)
REVERT: A   34 LYS cc_start: 0.7629 (tttp) cc_final: 0.7205 (tttp)
REVERT: A   37 TYR cc_start: 0.7654 (t80) cc_final: 0.7222 (t80)
REVERT: A  239 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8645 (p0)
REVERT: B   46 ARG cc_start: 0.7576 (ptt-90) cc_final: 0.7240 (mpp80)
REVERT: B  110 ASN cc_start: 0.6641 (p0) cc_final: 0.6164 (m-40)
REVERT: B  301 LYS cc_start: 0.7028 (mptt) cc_final: 0.6708 (mptt)
REVERT: B  317 CYS cc_start: 0.7780 (t) cc_final: 0.7538 (p)
REVERT: N   31 ASN cc_start: 0.6874 (m-40) cc_final: 0.6536 (m-40)
REVERT: N   38 ARG cc_start: 0.6102 (mtp85) cc_final: 0.5828 (ptp-110)
  outliers start: 32
  outliers final: 19
  residues processed: 161
  average time/residue: 0.4128
  time to fit residues: 71.3868
Evaluate side-chains
  151 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue   65 VAL
Chi-restraints excluded: chain R residue  104 ASN
Chi-restraints excluded: chain R residue  238 LEU
Chi-restraints excluded: chain R residue  250 VAL
Chi-restraints excluded: chain R residue  276 SER
Chi-restraints excluded: chain R residue  280 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  113 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 82 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 63 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9980
   chunk 57 optimal weight:    8.9990
   chunk 22 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
R 104 ASN
R 227 GLN
A 362 HIS
B 176 GLN
B 220 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.195075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.174844 restraints weight = 10712.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.4047 rms_B_bonded: 2.35
r_work: 0.3967 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7313  Z= 0.149
  Angle     :  0.621   8.393   9911  Z= 0.323
  Chirality :  0.044   0.148   1108
  Planarity :  0.004   0.045   1245
  Dihedral  :  5.835  55.148   1045
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 25.71 %
    Favored  : 70.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.28), residues: 864
  helix:  1.28 (0.28), residues: 313
  sheet: -1.05 (0.35), residues: 213
  loop : -0.90 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG R 251 
 TYR   0.028   0.002   TYR R 106 
 PHE   0.014   0.001   PHE R  76 
 TRP   0.013   0.002   TRP B 169 
 HIS   0.008   0.001   HIS R 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 7309)
  covalent geometry    : angle       0.62036 ( 9903)
  SS BOND              : bond        0.00145 (    4)
  SS BOND              : angle       1.06953 (    8)
  hydrogen bonds       : bond        0.04041 (  351)
  hydrogen bonds       : angle       5.00435 (  990)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: R   47 TYR cc_start: 0.8227 (t80) cc_final: 0.7343 (t80)
REVERT: R   72 CYS cc_start: 0.8537 (m) cc_final: 0.8229 (p)
REVERT: R  111 PHE cc_start: 0.7207 (m-80) cc_final: 0.6998 (m-80)
REVERT: R  238 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8315 (mm)
REVERT: A   34 LYS cc_start: 0.7648 (tttp) cc_final: 0.7318 (tttp)
REVERT: A  239 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8644 (p0)
REVERT: A  362 HIS cc_start: 0.7665 (m-70) cc_final: 0.7455 (m90)
REVERT: A  384 GLN cc_start: 0.7793 (mt0) cc_final: 0.7339 (tp40)
REVERT: B   46 ARG cc_start: 0.7611 (ptt-90) cc_final: 0.7278 (mpp80)
REVERT: B   61 MET cc_start: 0.8064 (ppp) cc_final: 0.7862 (ppp)
REVERT: B  110 ASN cc_start: 0.6637 (p0) cc_final: 0.6251 (m-40)
REVERT: B  111 TYR cc_start: 0.7288 (m-80) cc_final: 0.7044 (m-80)
REVERT: B  301 LYS cc_start: 0.7101 (mptt) cc_final: 0.6815 (mptt)
REVERT: B  317 CYS cc_start: 0.8006 (t) cc_final: 0.7725 (p)
REVERT: N   31 ASN cc_start: 0.6952 (m-40) cc_final: 0.6621 (m-40)
REVERT: N   38 ARG cc_start: 0.6175 (mtp85) cc_final: 0.5928 (ptp-110)
  outliers start: 27
  outliers final: 20
  residues processed: 151
  average time/residue: 0.3707
  time to fit residues: 60.5833
Evaluate side-chains
  150 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue   61 CYS
Chi-restraints excluded: chain R residue   65 VAL
Chi-restraints excluded: chain R residue  104 ASN
Chi-restraints excluded: chain R residue  238 LEU
Chi-restraints excluded: chain R residue  250 VAL
Chi-restraints excluded: chain R residue  276 SER
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  113 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 62 optimal weight:    9.9990
   chunk 2 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 46 optimal weight:    6.9990
   chunk 28 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
R 104 ASN
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
B 220 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.194615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.174729 restraints weight = 10794.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.4048 rms_B_bonded: 2.29
r_work: 0.3969 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
moved from start:          0.3610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7313  Z= 0.150
  Angle     :  0.639   9.660   9911  Z= 0.331
  Chirality :  0.044   0.189   1108
  Planarity :  0.004   0.062   1245
  Dihedral  :  5.864  53.597   1045
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 26.10 %
    Favored  : 70.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.28), residues: 864
  helix:  1.27 (0.28), residues: 312
  sheet: -1.03 (0.34), residues: 217
  loop : -0.96 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG R 210 
 TYR   0.029   0.002   TYR R 106 
 PHE   0.018   0.001   PHE N  68 
 TRP   0.013   0.002   TRP B 169 
 HIS   0.008   0.001   HIS R 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 7309)
  covalent geometry    : angle       0.63812 ( 9903)
  SS BOND              : bond        0.00135 (    4)
  SS BOND              : angle       1.07627 (    8)
  hydrogen bonds       : bond        0.04055 (  351)
  hydrogen bonds       : angle       5.02880 (  990)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
REVERT: R   47 TYR cc_start: 0.8238 (t80) cc_final: 0.7388 (t80)
REVERT: R   72 CYS cc_start: 0.8504 (m) cc_final: 0.8242 (p)
REVERT: R  111 PHE cc_start: 0.7329 (m-80) cc_final: 0.6965 (m-80)
REVERT: A   34 LYS cc_start: 0.7692 (tttp) cc_final: 0.7299 (tttp)
REVERT: A  239 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8659 (p0)
REVERT: A  384 GLN cc_start: 0.7799 (mt0) cc_final: 0.7436 (tp40)
REVERT: B   46 ARG cc_start: 0.7645 (ptt-90) cc_final: 0.7320 (mpp80)
REVERT: B  110 ASN cc_start: 0.6716 (p0) cc_final: 0.6332 (m-40)
REVERT: B  111 TYR cc_start: 0.7280 (m-80) cc_final: 0.7029 (m-80)
REVERT: B  175 GLN cc_start: 0.5739 (mm110) cc_final: 0.5530 (mm-40)
REVERT: B  289 TYR cc_start: 0.8084 (m-80) cc_final: 0.7803 (m-80)
REVERT: B  301 LYS cc_start: 0.7095 (mptt) cc_final: 0.6808 (mptt)
REVERT: N   31 ASN cc_start: 0.6942 (m-40) cc_final: 0.6647 (m-40)
REVERT: N   38 ARG cc_start: 0.6205 (mtp85) cc_final: 0.5934 (ptp-110)
  outliers start: 26
  outliers final: 20
  residues processed: 147
  average time/residue: 0.3650
  time to fit residues: 58.1844
Evaluate side-chains
  148 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue   61 CYS
Chi-restraints excluded: chain R residue   65 VAL
Chi-restraints excluded: chain R residue  104 ASN
Chi-restraints excluded: chain R residue  201 LEU
Chi-restraints excluded: chain R residue  250 VAL
Chi-restraints excluded: chain R residue  276 SER
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  113 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 84 optimal weight:    0.2980
   chunk 30 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9980
   chunk 70 optimal weight:    7.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
R 104 ASN
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS
B 176 GLN
B 220 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.195181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.175173 restraints weight = 10789.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.4053 rms_B_bonded: 2.36
r_work: 0.3973 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.3619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7313  Z= 0.144
  Angle     :  0.639   8.813   9911  Z= 0.329
  Chirality :  0.043   0.146   1108
  Planarity :  0.004   0.060   1245
  Dihedral  :  5.863  53.679   1045
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 26.23 %
    Favored  : 70.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.28), residues: 864
  helix:  1.29 (0.28), residues: 312
  sheet: -0.99 (0.35), residues: 210
  loop : -0.99 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG R 210 
 TYR   0.025   0.002   TYR R 106 
 PHE   0.012   0.001   PHE R  76 
 TRP   0.014   0.002   TRP B 169 
 HIS   0.007   0.001   HIS R 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 7309)
  covalent geometry    : angle       0.63839 ( 9903)
  SS BOND              : bond        0.00142 (    4)
  SS BOND              : angle       1.08024 (    8)
  hydrogen bonds       : bond        0.03974 (  351)
  hydrogen bonds       : angle       5.02326 (  990)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2285.23 seconds
wall clock time: 39 minutes 48.58 seconds (2388.58 seconds total)