Starting phenix.real_space_refine
on Mon Mar 11 05:21:35 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr2_16802/03_2024/8cr2_16802.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr2_16802/03_2024/8cr2_16802.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr2_16802/03_2024/8cr2_16802.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr2_16802/03_2024/8cr2_16802.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr2_16802/03_2024/8cr2_16802.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr2_16802/03_2024/8cr2_16802.pdb"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.028
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 306 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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      51      5.16       5
     C    4419      2.51       5
     N    1133      2.21       5
     O    1234      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  251": "OE1" <-> "OE2"
    Residue "B GLU  257": "OE1" <-> "OE2"
    Residue "B GLU  293": "OE1" <-> "OE2"
    Residue "B ASP  312": "OD1" <-> "OD2"
    Residue "B ASP  329": "OD1" <-> "OD2"
    Residue "C GLU 1052": "OE1" <-> "OE2"
    Residue "D TYR  230": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU 1046": "OE1" <-> "OE2"
    Residue "D PHE 1108": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 6838
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 2113
          Classifications: {'peptide': 268}
          Link IDs: {'PTRANS': 16, 'TRANS': 251}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2066
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 2066
          Classifications: {'peptide': 262}
          Link IDs: {'PTRANS': 16, 'TRANS': 245}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 1, 'TRANS': 95}
    Chain: "D"
      Number of atoms: 1856
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1856
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 4, 'TRANS': 223}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1658  SG  CYS A 289      37.717  41.793  15.466  1.00 88.42           S
  ATOM   1681  SG  CYS A 292      36.187  44.539  16.689  1.00 83.88           S
  ATOM   3724  SG  CYS B 289      39.158  45.820  14.919  1.00 94.34           S
  ATOM   3747  SG  CYS B 292      40.200  43.439  17.412  1.00 83.96           S

  Time building chain proxies: 4.03, per 1000 atoms: 0.59
  Number of scatterers: 6838
  At special positions: 0
  Unit cell: (74.37, 96.57, 135.42, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      51     16.00
     O    1234      8.00
     N    1133      7.00
     C    4419      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 208 " - pdb=" SG  CYS D 284 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.51
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 401 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS B 292 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS A 292 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS A 289 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS B 289 "
      Number of angles added : 6


  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1642

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 4 sheets defined
      69.0% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 34
    Processing helix  chain 'A' and resid 49 through 65
      removed outlier: 3.949A  pdb=" N   LYS A  63 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   GLY A  64 " --> pdb=" O   GLN A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 84
      removed outlier: 3.922A  pdb=" N   ASP A  81 " --> pdb=" O   HIS A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 158
      removed outlier: 4.132A  pdb=" N   MET A 158 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 176
    Processing helix  chain 'A' and resid 177 through 192
    Processing helix  chain 'A' and resid 217 through 238
      Proline residue:  A 227  - end of helix
      removed outlier: 3.532A  pdb=" N   GLU A 234 " --> pdb=" O   ARG A 230 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   GLN A 235 " --> pdb=" O   SER A 231 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   PHE A 236 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 268
    Processing helix  chain 'A' and resid 290 through 310
      removed outlier: 3.562A  pdb=" N   HIS A 296 " --> pdb=" O   CYS A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 340
    Processing helix  chain 'B' and resid 28 through 33
    Processing helix  chain 'B' and resid 49 through 65
      removed outlier: 3.868A  pdb=" N   LYS B  63 " --> pdb=" O   VAL B  59 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   GLY B  64 " --> pdb=" O   GLN B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 84
      removed outlier: 3.775A  pdb=" N   ASP B  81 " --> pdb=" O   HIS B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 159
      removed outlier: 4.105A  pdb=" N   ALA B 145 " --> pdb=" O   GLY B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 178
      removed outlier: 4.092A  pdb=" N   LEU B 176 " --> pdb=" O   HIS B 172 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU B 177 " --> pdb=" O   THR B 173 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ASN B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 172 through 178'
    Processing helix  chain 'B' and resid 178 through 190
      removed outlier: 3.974A  pdb=" N   ILE B 182 " --> pdb=" O   ASN B 178 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU B 190 " --> pdb=" O   GLY B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 238
      Proline residue:  B 227  - end of helix
      removed outlier: 4.137A  pdb=" N   VAL B 232 " --> pdb=" O   VAL B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 268
    Processing helix  chain 'B' and resid 290 through 310
    Processing helix  chain 'B' and resid 327 through 337
      removed outlier: 3.681A  pdb=" N   LEU B 337 " --> pdb=" O   THR B 333 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1029 through 1039
    Processing helix  chain 'C' and resid 1039 through 1062
      removed outlier: 3.820A  pdb=" N   SER C1047 " --> pdb=" O   ALA C1043 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1068 through 1124
    Processing helix  chain 'D' and resid 190 through 207
    Processing helix  chain 'D' and resid 208 through 210
      No H-bonds generated for 'chain 'D' and resid 208 through 210'
    Processing helix  chain 'D' and resid 214 through 234
      removed outlier: 3.520A  pdb=" N   GLY D 226 " --> pdb=" O   LEU D 222 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   PHE D 231 " --> pdb=" O   LEU D 227 " (cutoff:3.500A)
      Proline residue:  D 232  - end of helix
    Processing helix  chain 'D' and resid 255 through 284
      removed outlier: 3.925A  pdb=" N   PHE D 281 " --> pdb=" O   TYR D 277 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE D 282 " --> pdb=" O   PHE D 278 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   PHE D 283 " --> pdb=" O   PHE D 279 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   CYS D 284 " --> pdb=" O   THR D 280 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 285 through 291
    Processing helix  chain 'D' and resid 1006 through 1035
      removed outlier: 3.969A  pdb=" N   VAL D1014 " --> pdb=" O   ALA D1010 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   LEU D1015 " --> pdb=" O   TRP D1011 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   SER D1016 " --> pdb=" O   LEU D1012 " (cutoff:3.500A)
      Proline residue:  D1029  - end of helix
    Processing helix  chain 'D' and resid 1035 through 1062
      removed outlier: 4.559A  pdb=" N   LYS D1041 " --> pdb=" O   ARG D1037 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   GLN D1045 " --> pdb=" O   LYS D1041 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   THR D1062 " --> pdb=" O   GLN D1058 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1068 through 1123
      removed outlier: 4.752A  pdb=" N   LYS D1099 " --> pdb=" O   ALA D1095 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1150 through 1161
    Processing helix  chain 'D' and resid 1162 through 1171
    Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 70
      removed outlier: 3.565A  pdb=" N   LEU A  69 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL A 164 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
      removed outlier: 10.597A  pdb=" N   THR A 242 " --> pdb=" O   THR A 272 " (cutoff:3.500A)
      removed outlier: 9.744A  pdb=" N   ASN A 274 " --> pdb=" O   THR A 242 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   PHE A 244 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   ILE A 276 " --> pdb=" O   PHE A 244 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   CYS A 246 " --> pdb=" O   ILE A 276 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   HIS A 273 " --> pdb=" O   HIS A 314 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   VAL A 316 " --> pdb=" O   HIS A 273 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ILE A 275 " --> pdb=" O   VAL A 316 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 93
    Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72
      removed outlier: 6.963A  pdb=" N   ILE B  40 " --> pdb=" O   PHE B 165 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   TRP B  39 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   ILE B 245 " --> pdb=" O   TRP B  39 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   PHE B  41 " --> pdb=" O   ILE B 245 " (cutoff:3.500A)
      removed outlier: 7.597A  pdb=" N   VAL B 247 " --> pdb=" O   PHE B  41 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   GLY B  43 " --> pdb=" O   VAL B 247 " (cutoff:3.500A)
      removed outlier: 8.521A  pdb=" N   ILE B 249 " --> pdb=" O   GLY B  43 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   THR B 272 " --> pdb=" O   THR B 242 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   PHE B 244 " --> pdb=" O   THR B 272 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ASN B 274 " --> pdb=" O   PHE B 244 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   HIS B 273 " --> pdb=" O   HIS B 314 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   VAL B 316 " --> pdb=" O   HIS B 273 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   ILE B 275 " --> pdb=" O   VAL B 316 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 69
      removed outlier: 6.008A  pdb=" N   VAL B  68 " --> pdb=" O   PHE B 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    429 hydrogen bonds defined for protein.
    1278 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: 1.89

  Time building geometry restraints manager: 2.75 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1313
        1.33 -     1.45: 1584
        1.45 -     1.57: 3997
        1.57 -     1.70: 0
        1.70 -     1.82: 81
  Bond restraints: 6975
  Sorted by residual:
  bond pdb=" CA  HIS A 323 "
       pdb=" C   HIS A 323 "
    ideal  model  delta    sigma   weight residual
    1.522  1.562 -0.041 1.72e-02 3.38e+03 5.62e+00
  bond pdb=" CG  GLN A 235 "
       pdb=" CD  GLN A 235 "
    ideal  model  delta    sigma   weight residual
    1.516  1.473  0.043 2.50e-02 1.60e+03 2.90e+00
  bond pdb=" CG  GLN D1112 "
       pdb=" CD  GLN D1112 "
    ideal  model  delta    sigma   weight residual
    1.516  1.474  0.042 2.50e-02 1.60e+03 2.88e+00
  bond pdb=" CG  GLU C1076 "
       pdb=" CD  GLU C1076 "
    ideal  model  delta    sigma   weight residual
    1.516  1.479  0.037 2.50e-02 1.60e+03 2.23e+00
  bond pdb=" CG1 ILE B 249 "
       pdb=" CD1 ILE B 249 "
    ideal  model  delta    sigma   weight residual
    1.513  1.456  0.057 3.90e-02 6.57e+02 2.12e+00
  ... (remaining 6970 not shown)

  Histogram of bond angle deviations from ideal:
       98.56 -   105.67: 172
      105.67 -   112.78: 3640
      112.78 -   119.89: 2538
      119.89 -   127.00: 2989
      127.00 -   134.11: 74
  Bond angle restraints: 9413
  Sorted by residual:
  angle pdb=" CA  HIS A 323 "
        pdb=" C   HIS A 323 "
        pdb=" N   GLU A 324 "
      ideal   model   delta    sigma   weight residual
     118.59  129.17  -10.58 1.63e+00 3.76e-01 4.21e+01
  angle pdb=" N   GLU C1076 "
        pdb=" CA  GLU C1076 "
        pdb=" CB  GLU C1076 "
      ideal   model   delta    sigma   weight residual
     110.12  118.20   -8.08 1.47e+00 4.63e-01 3.02e+01
  angle pdb=" N   GLN D1112 "
        pdb=" CA  GLN D1112 "
        pdb=" CB  GLN D1112 "
      ideal   model   delta    sigma   weight residual
     110.30  118.33   -8.03 1.54e+00 4.22e-01 2.72e+01
  angle pdb=" CB  MET D1116 "
        pdb=" CG  MET D1116 "
        pdb=" SD  MET D1116 "
      ideal   model   delta    sigma   weight residual
     112.70  128.16  -15.46 3.00e+00 1.11e-01 2.66e+01
  angle pdb=" CA  GLU C1076 "
        pdb=" CB  GLU C1076 "
        pdb=" CG  GLU C1076 "
      ideal   model   delta    sigma   weight residual
     114.10  123.54   -9.44 2.00e+00 2.50e-01 2.23e+01
  ... (remaining 9408 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 3863
       17.96 -    35.93: 337
       35.93 -    53.89: 48
       53.89 -    71.85: 4
       71.85 -    89.82: 6
  Dihedral angle restraints: 4258
    sinusoidal: 1745
      harmonic: 2513
  Sorted by residual:
  dihedral pdb=" CB  CYS D 208 "
           pdb=" SG  CYS D 208 "
           pdb=" SG  CYS D 284 "
           pdb=" CB  CYS D 284 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -175.82   89.82     1      1.00e+01 1.00e-02 9.57e+01
  dihedral pdb=" N   GLU C1076 "
           pdb=" C   GLU C1076 "
           pdb=" CA  GLU C1076 "
           pdb=" CB  GLU C1076 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  132.72   -9.92     0      2.50e+00 1.60e-01 1.57e+01
  dihedral pdb=" CA  HIS A 273 "
           pdb=" C   HIS A 273 "
           pdb=" N   ASN A 274 "
           pdb=" CA  ASN A 274 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.34  -17.66     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 4255 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 788
       0.056 -    0.111: 220
       0.111 -    0.167: 60
       0.167 -    0.222: 10
       0.222 -    0.278: 3
  Chirality restraints: 1081
  Sorted by residual:
  chirality pdb=" CA  PRO B 169 "
            pdb=" N   PRO B 169 "
            pdb=" C   PRO B 169 "
            pdb=" CB  PRO B 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.44    0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" CA  GLU C1076 "
            pdb=" N   GLU C1076 "
            pdb=" C   GLU C1076 "
            pdb=" CB  GLU C1076 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" CA  GLN A 235 "
            pdb=" N   GLN A 235 "
            pdb=" C   GLN A 235 "
            pdb=" CB  GLN A 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.32e+00
  ... (remaining 1078 not shown)

  Planarity restraints: 1172
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D1158 "   -0.030 2.00e-02 2.50e+03   3.06e-02 2.34e+01
        pdb=" CG  TRP D1158 "    0.083 2.00e-02 2.50e+03
        pdb=" CD1 TRP D1158 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD2 TRP D1158 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP D1158 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP D1158 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP D1158 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D1158 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D1158 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP D1158 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D1011 "   -0.027 2.00e-02 2.50e+03   2.84e-02 2.01e+01
        pdb=" CG  TRP D1011 "    0.077 2.00e-02 2.50e+03
        pdb=" CD1 TRP D1011 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD2 TRP D1011 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP D1011 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP D1011 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP D1011 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D1011 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D1011 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP D1011 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 220 "   -0.022 2.00e-02 2.50e+03   4.43e-02 1.96e+01
        pdb=" C   LEU D 220 "    0.077 2.00e-02 2.50e+03
        pdb=" O   LEU D 220 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   GLN D 221 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 1169 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 43
        2.51 -     3.11: 5613
        3.11 -     3.71: 10443
        3.71 -     4.30: 14029
        4.30 -     4.90: 21621
  Nonbonded interactions: 51749
  Sorted by model distance:
  nonbonded pdb=" O   PHE B  83 "
            pdb=" OD1 ASP B  84 "
     model   vdw
     1.914 3.040
  nonbonded pdb=" O   LYS D1101 "
            pdb=" OG  SER D1105 "
     model   vdw
     2.198 2.440
  nonbonded pdb=" O   GLN A 235 "
            pdb=" OG1 THR A 242 "
     model   vdw
     2.223 2.440
  nonbonded pdb=" O   TYR D 277 "
            pdb=" OG1 THR D 280 "
     model   vdw
     2.231 2.440
  nonbonded pdb=" OE1 GLN A 263 "
            pdb=" NH2 ARG D1077 "
     model   vdw
     2.241 2.520
  ... (remaining 51744 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 23 through 190 or resid 220 through 344))
  selection = (chain 'B' and resid 23 through 344)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          3.960
  Check model and map are aligned:         0.100
  Set scattering table:                    0.060
  Process input model:                     23.010
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3059
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6975  Z= 0.281
  Angle     :  1.068  15.462   9413  Z= 0.593
  Chirality :  0.057   0.278   1081
  Planarity :  0.007   0.058   1172
  Dihedral  : 13.243  87.522   2613
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 20.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.18 (0.27), residues: 833
  helix: -1.65 (0.19), residues: 535
  sheet: -3.24 (0.52), residues: 81
  loop : -2.24 (0.44), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.083   0.005   TRP D1158 
 HIS   0.020   0.002   HIS B 172 
 PHE   0.036   0.002   PHE D1019 
 TYR   0.052   0.002   TYR D 224 
 ARG   0.013   0.001   ARG D1093 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 MET cc_start: -0.2862 (mmm) cc_final: -0.4250 (ptm)
REVERT: A  291 MET cc_start: 0.6140 (ptp) cc_final: 0.5606 (ptp)
REVERT: B  158 MET cc_start: 0.6750 (mpp) cc_final: 0.6458 (mpp)
REVERT: B  326 ARG cc_start: 0.3648 (tpt90) cc_final: 0.1145 (mmp80)
REVERT: C 1116 MET cc_start: 0.4065 (ttt) cc_final: 0.3604 (ttt)
REVERT: D  222 LEU cc_start: 0.7355 (pp) cc_final: 0.7115 (tp)
REVERT: D  259 ARG cc_start: 0.3986 (mtt180) cc_final: 0.2349 (mpt-90)
REVERT: D  261 MET cc_start: 0.2969 (ptt) cc_final: 0.1806 (tmm)
REVERT: D  270 VAL cc_start: 0.6126 (m) cc_final: 0.4950 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 218
  average time/residue: 0.2520
  time to fit residues: 67.6064
Evaluate side-chains
  122 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 62 optimal weight:   10.0000
   chunk 34 optimal weight:    0.0010
   chunk 21 optimal weight:    7.9990
   chunk 42 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0370
   chunk 25 optimal weight:    0.3980
   chunk 39 optimal weight:   20.0000
   chunk 48 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   overall best weight:    0.4666

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
A 241 GLN
B 274 ASN
** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1045 GLN
** D1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1054 GLN
D1096 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4290
moved from start:          0.4613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6975  Z= 0.245
  Angle     :  0.781  11.619   9413  Z= 0.403
  Chirality :  0.048   0.176   1081
  Planarity :  0.006   0.054   1172
  Dihedral  :  4.540  18.109    908
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 15.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  7.21 %
    Favored  : 92.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.28), residues: 833
  helix:  0.26 (0.21), residues: 545
  sheet: -2.46 (0.51), residues: 85
  loop : -1.15 (0.47), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.004   TRP D1158 
 HIS   0.006   0.002   HIS D1008 
 PHE   0.028   0.002   PHE D1108 
 TYR   0.024   0.002   TYR D 230 
 ARG   0.009   0.001   ARG B 295 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 175
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 GLU cc_start: 0.5147 (pt0) cc_final: 0.4246 (tt0)
REVERT: B  326 ARG cc_start: 0.4209 (tpt90) cc_final: 0.2114 (tpp-160)
REVERT: C 1116 MET cc_start: 0.3679 (ttt) cc_final: 0.3445 (ttp)
REVERT: D  217 PHE cc_start: 0.6143 (m-80) cc_final: 0.5791 (m-80)
REVERT: D  222 LEU cc_start: 0.7523 (pp) cc_final: 0.7285 (pp)
REVERT: D  258 ASN cc_start: 0.7683 (t0) cc_final: 0.7429 (t0)
REVERT: D  259 ARG cc_start: 0.3991 (mtt180) cc_final: 0.3278 (ttm170)
REVERT: D  261 MET cc_start: 0.4649 (ptt) cc_final: 0.3498 (tmm)
REVERT: D  270 VAL cc_start: 0.5277 (m) cc_final: 0.4938 (p)
REVERT: D 1022 ASN cc_start: 0.8220 (m110) cc_final: 0.7986 (m-40)
REVERT: D 1082 MET cc_start: 0.6900 (mmt) cc_final: 0.6646 (mmm)
  outliers start: 5
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1924
  time to fit residues: 44.6082
Evaluate side-chains
  123 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 41 optimal weight:    0.0970
   chunk 23 optimal weight:    0.4980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 81 optimal weight:    7.9990
   chunk 67 optimal weight:    5.9990
   chunk 74 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
** A  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 241 GLN
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 159 ASN
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 305 GLN
D1022 ASN
D1048 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5440
moved from start:          0.7028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6975  Z= 0.262
  Angle     :  0.767   8.477   9413  Z= 0.402
  Chirality :  0.047   0.185   1081
  Planarity :  0.005   0.049   1172
  Dihedral  :  4.613  18.640    908
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  4.85 %
    Favored  : 95.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.29), residues: 833
  helix:  0.68 (0.21), residues: 536
  sheet: -2.41 (0.50), residues: 88
  loop : -1.11 (0.45), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.004   TRP D1011 
 HIS   0.010   0.002   HIS A 323 
 PHE   0.025   0.002   PHE D1108 
 TYR   0.028   0.001   TYR D 230 
 ARG   0.007   0.001   ARG B 153 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 VAL cc_start: 0.7678 (m) cc_final: 0.7108 (t)
REVERT: A  247 VAL cc_start: 0.6398 (t) cc_final: 0.6193 (p)
REVERT: B  240 GLU cc_start: 0.8187 (mp0) cc_final: 0.7546 (tp30)
REVERT: B  326 ARG cc_start: 0.4583 (tpt90) cc_final: 0.2171 (tpp-160)
REVERT: B  332 ASN cc_start: 0.7028 (m110) cc_final: 0.6817 (m110)
REVERT: C 1116 MET cc_start: 0.3900 (ttt) cc_final: 0.3615 (ttp)
REVERT: D  224 TYR cc_start: 0.5175 (t80) cc_final: 0.4620 (t80)
REVERT: D  259 ARG cc_start: 0.4211 (mtt180) cc_final: 0.3686 (ttm170)
REVERT: D  261 MET cc_start: 0.4599 (ptt) cc_final: 0.3545 (tmm)
REVERT: D 1079 ILE cc_start: 0.8426 (pt) cc_final: 0.7868 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 169
  average time/residue: 0.2016
  time to fit residues: 44.4280
Evaluate side-chains
  121 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0370
   chunk 8 optimal weight:    0.0970
   chunk 36 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 75 optimal weight:    0.0060
   chunk 80 optimal weight:    6.9990
   chunk 71 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 66 optimal weight:   20.0000
   overall best weight:    0.3872

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
** A  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 172 HIS
A 241 GLN
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 273 HIS
B 274 ASN
B 305 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5601
moved from start:          0.7928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6975  Z= 0.190
  Angle     :  0.689   8.273   9413  Z= 0.359
  Chirality :  0.044   0.152   1081
  Planarity :  0.005   0.052   1172
  Dihedral  :  4.309  17.686    908
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  4.72 %
    Favored  : 95.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.29), residues: 833
  helix:  0.94 (0.22), residues: 543
  sheet: -1.89 (0.54), residues: 83
  loop : -0.87 (0.47), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.003   TRP D1011 
 HIS   0.006   0.001   HIS B 323 
 PHE   0.033   0.002   PHE A  87 
 TYR   0.023   0.002   TYR D 230 
 ARG   0.007   0.001   ARG B 295 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 142
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  306 MET cc_start: 0.6557 (ttp) cc_final: 0.6222 (tpp)
REVERT: B  326 ARG cc_start: 0.4396 (tpt90) cc_final: 0.2103 (tpp-160)
REVERT: C 1116 MET cc_start: 0.4697 (ttt) cc_final: 0.4203 (ttp)
REVERT: D  222 LEU cc_start: 0.7713 (pp) cc_final: 0.7438 (mp)
REVERT: D  259 ARG cc_start: 0.4163 (mtt180) cc_final: 0.2146 (mtm180)
REVERT: D  261 MET cc_start: 0.4648 (ptt) cc_final: 0.3846 (tmm)
REVERT: D 1066 MET cc_start: 0.6876 (mmm) cc_final: 0.6578 (mmm)
REVERT: D 1079 ILE cc_start: 0.8651 (pt) cc_final: 0.8157 (pt)
  outliers start: 2
  outliers final: 0
  residues processed: 144
  average time/residue: 0.1885
  time to fit residues: 35.8531
Evaluate side-chains
  114 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 45 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0470
   chunk 68 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 72 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.6680

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

Flipped N/Q/H residues before XYZ refinement:
** A  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  85 GLN
A 172 HIS
A 241 GLN
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 323 HIS
B 305 GLN
D1022 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6053
moved from start:          0.9259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6975  Z= 0.219
  Angle     :  0.707  10.430   9413  Z= 0.364
  Chirality :  0.045   0.193   1081
  Planarity :  0.005   0.052   1172
  Dihedral  :  4.276  15.707    908
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  3.01 %
    Favored  : 96.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.29), residues: 833
  helix:  0.93 (0.22), residues: 540
  sheet: -1.93 (0.52), residues: 92
  loop : -1.06 (0.47), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.003   TRP D1011 
 HIS   0.005   0.001   HIS B 323 
 PHE   0.019   0.002   PHE D1108 
 TYR   0.021   0.001   TYR D 224 
 ARG   0.004   0.000   ARG B 295 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 140
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 MET cc_start: 0.7625 (tpt) cc_final: 0.6825 (tpp)
REVERT: A  174 LEU cc_start: 0.6797 (tt) cc_final: 0.6194 (tt)
REVERT: A  272 THR cc_start: 0.7882 (t) cc_final: 0.7572 (m)
REVERT: B   55 CYS cc_start: 0.8340 (m) cc_final: 0.7010 (p)
REVERT: B  230 ARG cc_start: 0.8018 (tpp80) cc_final: 0.7733 (tpm170)
REVERT: B  291 MET cc_start: 0.8072 (ppp) cc_final: 0.7140 (ppp)
REVERT: B  338 LEU cc_start: 0.3530 (mt) cc_final: 0.3094 (mp)
REVERT: C 1116 MET cc_start: 0.4813 (ttt) cc_final: 0.4356 (ttt)
REVERT: D  217 PHE cc_start: 0.5934 (m-80) cc_final: 0.5673 (m-10)
REVERT: D  259 ARG cc_start: 0.4042 (mtt180) cc_final: 0.2045 (mtt180)
REVERT: D  261 MET cc_start: 0.4478 (ptt) cc_final: 0.3916 (tmm)
REVERT: D 1022 ASN cc_start: 0.8337 (m-40) cc_final: 0.8135 (m110)
REVERT: D 1079 ILE cc_start: 0.8685 (pt) cc_final: 0.8451 (pt)
REVERT: D 1082 MET cc_start: 0.7199 (mmm) cc_final: 0.6771 (mmt)
REVERT: D 1096 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6321 (tp-100)
  outliers start: 4
  outliers final: 0
  residues processed: 143
  average time/residue: 0.2015
  time to fit residues: 37.7678
Evaluate side-chains
  116 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 19 optimal weight:    0.3980
   chunk 80 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   chunk 77 optimal weight:    4.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 299 GLN
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 323 HIS
** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 305 GLN
B 323 HIS
C1045 GLN
D1008 HIS
** D1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6471
moved from start:          1.1139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   6975  Z= 0.267
  Angle     :  0.779  10.785   9413  Z= 0.406
  Chirality :  0.048   0.244   1081
  Planarity :  0.005   0.061   1172
  Dihedral  :  4.482  19.878    908
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.88 %
    Favored  : 96.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.29), residues: 833
  helix:  0.90 (0.22), residues: 533
  sheet: -2.12 (0.50), residues: 93
  loop : -1.22 (0.44), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.003   TRP D1011 
 HIS   0.006   0.001   HIS B 273 
 PHE   0.025   0.002   PHE A 313 
 TYR   0.027   0.002   TYR D 224 
 ARG   0.011   0.001   ARG D1050 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 LYS cc_start: 0.8656 (mttp) cc_final: 0.8438 (mtpp)
REVERT: A  103 MET cc_start: 0.7756 (tpt) cc_final: 0.7499 (tpp)
REVERT: A  240 GLU cc_start: 0.6188 (pp20) cc_final: 0.5141 (pt0)
REVERT: B   37 LEU cc_start: 0.7990 (mm) cc_final: 0.7714 (mm)
REVERT: B  305 GLN cc_start: 0.6286 (OUTLIER) cc_final: 0.5903 (tp40)
REVERT: B  332 ASN cc_start: 0.7300 (m110) cc_final: 0.7091 (m110)
REVERT: C 1059 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7368 (mt-10)
REVERT: C 1065 MET cc_start: 0.8261 (mmp) cc_final: 0.7651 (mmp)
REVERT: C 1116 MET cc_start: 0.4975 (ttt) cc_final: 0.4666 (ttt)
REVERT: D  261 MET cc_start: 0.5104 (ptt) cc_final: 0.3871 (tmm)
REVERT: D  280 THR cc_start: 0.3060 (p) cc_final: 0.2630 (m)
REVERT: D 1022 ASN cc_start: 0.8371 (m-40) cc_final: 0.8170 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1943
  time to fit residues: 39.2170
Evaluate side-chains
  125 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 45 optimal weight:    0.3980
   chunk 58 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 49 optimal weight:    0.3980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 241 GLN
A 299 GLN
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 323 HIS
B 235 GLN
** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 273 HIS
** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1045 GLN
** D1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6462
moved from start:          1.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6975  Z= 0.200
  Angle     :  0.687   8.191   9413  Z= 0.356
  Chirality :  0.044   0.171   1081
  Planarity :  0.004   0.051   1172
  Dihedral  :  4.207  15.989    908
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.29), residues: 833
  helix:  0.97 (0.22), residues: 537
  sheet: -1.88 (0.52), residues: 94
  loop : -1.16 (0.45), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.076   0.004   TRP D1158 
 HIS   0.006   0.001   HIS B 314 
 PHE   0.019   0.001   PHE D1019 
 TYR   0.015   0.001   TYR B 310 
 ARG   0.006   0.001   ARG D1050 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 MET cc_start: 0.7853 (tpt) cc_final: 0.7478 (tpp)
REVERT: A  174 LEU cc_start: 0.6779 (tp) cc_final: 0.6411 (tp)
REVERT: A  240 GLU cc_start: 0.5984 (pp20) cc_final: 0.5152 (pt0)
REVERT: B   37 LEU cc_start: 0.8152 (mm) cc_final: 0.7823 (mm)
REVERT: B  291 MET cc_start: 0.8319 (ppp) cc_final: 0.8028 (ppp)
REVERT: C 1116 MET cc_start: 0.5184 (ttt) cc_final: 0.4818 (ttt)
REVERT: D  261 MET cc_start: 0.5317 (ptt) cc_final: 0.3992 (tmm)
REVERT: D  280 THR cc_start: 0.2899 (p) cc_final: 0.2549 (m)
REVERT: D 1060 LEU cc_start: 0.7127 (tt) cc_final: 0.6798 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.2015
  time to fit residues: 40.6535
Evaluate side-chains
  121 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0870
   chunk 54 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 72 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   chunk 69 optimal weight:    3.9990
   overall best weight:    1.1760

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

Flipped N/Q/H residues before XYZ refinement:
** A  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 323 HIS
** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6695
moved from start:          1.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6975  Z= 0.280
  Angle     :  0.794  10.709   9413  Z= 0.416
  Chirality :  0.048   0.222   1081
  Planarity :  0.005   0.051   1172
  Dihedral  :  4.495  18.430    908
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 15.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.29), residues: 833
  helix:  0.92 (0.22), residues: 544
  sheet: -2.14 (0.51), residues: 97
  loop : -1.19 (0.44), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.004   TRP D1158 
 HIS   0.005   0.001   HIS B 314 
 PHE   0.022   0.002   PHE D1019 
 TYR   0.028   0.002   TYR D 210 
 ARG   0.008   0.001   ARG A  65 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.6972 (tp) cc_final: 0.6473 (tp)
REVERT: A  240 GLU cc_start: 0.6071 (pp20) cc_final: 0.5332 (pt0)
REVERT: B   37 LEU cc_start: 0.8336 (mm) cc_final: 0.8105 (mm)
REVERT: B  299 GLN cc_start: 0.7446 (tt0) cc_final: 0.7230 (tt0)
REVERT: C 1065 MET cc_start: 0.8651 (mmp) cc_final: 0.8150 (mmp)
REVERT: C 1116 MET cc_start: 0.5204 (ttt) cc_final: 0.4902 (ttt)
REVERT: D  261 MET cc_start: 0.5634 (ptt) cc_final: 0.4424 (tmm)
REVERT: D  267 MET cc_start: 0.3250 (mmt) cc_final: 0.2979 (mmm)
REVERT: D  280 THR cc_start: 0.2802 (p) cc_final: 0.2453 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1823
  time to fit residues: 35.6260
Evaluate side-chains
  114 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0060
   chunk 58 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
A 273 HIS
A 305 GLN
** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6672
moved from start:          1.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6975  Z= 0.225
  Angle     :  0.776  11.188   9413  Z= 0.408
  Chirality :  0.046   0.195   1081
  Planarity :  0.005   0.051   1172
  Dihedral  :  4.360  21.341    908
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.30), residues: 833
  helix:  1.11 (0.22), residues: 539
  sheet: -1.90 (0.53), residues: 97
  loop : -1.17 (0.44), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.063   0.003   TRP D1011 
 HIS   0.008   0.001   HIS A 273 
 PHE   0.025   0.001   PHE D1019 
 TYR   0.019   0.002   TYR A 148 
 ARG   0.009   0.001   ARG A  65 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.7457 (tp) cc_final: 0.7074 (tp)
REVERT: A  240 GLU cc_start: 0.5955 (pp20) cc_final: 0.5552 (pt0)
REVERT: B  332 ASN cc_start: 0.7950 (m110) cc_final: 0.7670 (m110)
REVERT: C 1045 GLN cc_start: 0.8696 (mm110) cc_final: 0.8413 (mm110)
REVERT: C 1116 MET cc_start: 0.5159 (ttt) cc_final: 0.4877 (ttt)
REVERT: D  261 MET cc_start: 0.5638 (ptt) cc_final: 0.4609 (tmm)
REVERT: D  267 MET cc_start: 0.3438 (mmt) cc_final: 0.3236 (mmm)
REVERT: D 1082 MET cc_start: 0.7697 (mmm) cc_final: 0.7276 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.2219
  time to fit residues: 42.4926
Evaluate side-chains
  115 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 65 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   chunk 50 optimal weight:    7.9990
   chunk 40 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 235 GLN
** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 323 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6781
moved from start:          1.3754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6975  Z= 0.262
  Angle     :  0.823  11.032   9413  Z= 0.433
  Chirality :  0.048   0.234   1081
  Planarity :  0.005   0.051   1172
  Dihedral  :  4.539  29.478    908
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 16.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.29), residues: 833
  helix:  0.92 (0.22), residues: 545
  sheet: -2.09 (0.51), residues: 97
  loop : -1.03 (0.44), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.076   0.003   TRP D1158 
 HIS   0.004   0.001   HIS A  77 
 PHE   0.020   0.002   PHE D1019 
 TYR   0.026   0.002   TYR D 230 
 ARG   0.009   0.001   ARG A  65 

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

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

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1666 Ramachandran restraints generated.
    833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 1.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.7690 (tp) cc_final: 0.7393 (tp)
REVERT: A  230 ARG cc_start: 0.8847 (ptm160) cc_final: 0.8563 (ptm-80)
REVERT: A  240 GLU cc_start: 0.6084 (pp20) cc_final: 0.5694 (tp30)
REVERT: A  279 GLN cc_start: 0.8322 (mp10) cc_final: 0.8001 (mp10)
REVERT: A  332 ASN cc_start: 0.8084 (p0) cc_final: 0.7706 (m-40)
REVERT: B  150 GLU cc_start: 0.7669 (tp30) cc_final: 0.7453 (tp30)
REVERT: B  158 MET cc_start: 0.7253 (mpp) cc_final: 0.6989 (mtp)
REVERT: B  306 MET cc_start: 0.7753 (ttp) cc_final: 0.7457 (ttp)
REVERT: B  332 ASN cc_start: 0.8170 (m110) cc_final: 0.7766 (m110)
REVERT: C 1066 MET cc_start: 0.7247 (tmm) cc_final: 0.6802 (tmm)
REVERT: C 1072 TYR cc_start: 0.8040 (t80) cc_final: 0.7654 (t80)
REVERT: C 1080 ASN cc_start: 0.8454 (m-40) cc_final: 0.8237 (m110)
REVERT: C 1116 MET cc_start: 0.5173 (ttt) cc_final: 0.4947 (ttt)
REVERT: D  261 MET cc_start: 0.5629 (ptt) cc_final: 0.4591 (tmm)
REVERT: D 1007 ASP cc_start: 0.6494 (p0) cc_final: 0.5481 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1693
  time to fit residues: 31.9748
Evaluate side-chains
  114 residues out of total 763 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 65 optimal weight:   10.0000
   chunk 27 optimal weight:    0.7980
   chunk 67 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 57 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1022 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4470 r_free = 0.4470 target = 0.201981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.172294 restraints weight = 9340.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.168191 restraints weight = 12653.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.164281 restraints weight = 12156.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.4118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6709
moved from start:          1.4140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6975  Z= 0.236
  Angle     :  0.794  11.586   9413  Z= 0.417
  Chirality :  0.047   0.199   1081
  Planarity :  0.005   0.051   1172
  Dihedral  :  4.419  26.526    908
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 16.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.30), residues: 833
  helix:  1.02 (0.22), residues: 545
  sheet: -2.08 (0.52), residues: 97
  loop : -0.87 (0.46), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.083   0.005   TRP D1011 
 HIS   0.007   0.001   HIS D1008 
 PHE   0.027   0.002   PHE D1019 
 TYR   0.015   0.001   TYR B 310 
 ARG   0.008   0.001   ARG A  65 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1653.29 seconds
wall clock time: 30 minutes 45.57 seconds (1845.57 seconds total)